7icf - Revision history

OCA at 11:07, 2 August 2023

2023-08-02T11:07:19Z

← Older revision		Revision as of 11:07, 2 August 2023
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	==DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)==		==DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)==
	<StructureSection load='7icf' size='340' side='right' caption='[[7icf]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='7icf' size='340' side='right'caption='[[7icf]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7icf]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=7ICF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7icf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ICF FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CD:CADMIUM+ION'>CD</scene~~>, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.1Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[7ice\|7ice]]~~, [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=7icf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7icf OCA], [~~http~~://pdbe.org/7icf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7icf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7icf PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7icf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7icf OCA], [https://pdbe.org/7icf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7icf RCSB], [https://www.ebi.ac.uk/pdbsum/7icf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7icf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>		[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/7icf_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/7icf_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: ~~Pelletier, H~~]]		[[Category: Large Structures]]
	[[Category: ~~Sawaya, M R~~]]		[[Category: Pelletier H]]
	[[Category: ~~Dna repair]]~~		[[Category: Sawaya MR]]
	~~[[Category: Dna replication]]~~
	~~[[Category: Dna-directed dna polymerase]]~~
	~~[[Category: Nucleotidyltransferase]]~~
	~~[[Category: Transferase-dna complex~~]]

OCA at 08:34, 7 February 2016

2016-02-07T08:34:57Z

← Older revision		Revision as of 08:34, 7 February 2016
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	<StructureSection load='7icf' size='340' side='right' caption='[[7icf]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='7icf' size='340' side='right' caption='[[7icf]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7icf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ICF FirstGlance]. <br>		<table><tr><td colspan='2'>[[7icf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ICF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7icf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7icf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7icf RCSB], [http://www.ebi.ac.uk/pdbsum/7icf PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7icf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7icf OCA], [http://pdbe.org/7icf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7icf RCSB], [http://www.ebi.ac.uk/pdbsum/7icf PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=7icf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 7icf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Pelletier, H]]		[[Category: Pelletier, H]]
	[[Category: Sawaya, M R]]		[[Category: Sawaya, M R]]

OCA at 16:56, 10 December 2014

2014-12-10T16:56:32Z

← Older revision		Revision as of 16:56, 10 December 2014
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	[[Image:~~7icf~~.~~png~~\|~~left~~\|~~200px~~]]		==DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)==
			<StructureSection load='7icf' size='340' side='right' caption='[[7icf]], [[Resolution\|resolution]] 3.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[7icf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ICF FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7ict\|7ict]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</td></tr>
			<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7icf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7icf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7icf RCSB], [http://www.ebi.ac.uk/pdbsum/7icf PDBsum]</span></td></tr>
			</table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/7icf_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.

	~~{{STRUCTURE_7icf\| PDB=7icf \| SCENE= }}~~		A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.,Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J Biochemistry. 1996 Oct 1;35(39):12762-77. PMID:8841119<ref>PMID:8841119</ref>

	~~===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA~~; ~~SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_8841119}}~~

	~~==About this Structure==~~
	~~[[7icf]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=7ICF OCA].~~

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:008841119<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
	[[Category: Dna replication]]		[[Category: Dna replication]]

OCA at 06:07, 20 October 2012

2012-10-20T06:07:33Z

← Older revision		Revision as of 06:07, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[7icf]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA].		[[7icf]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA].

	==See Also==		==See Also==

OCA: Protected "7icf" [edit=sysop:move=sysop]

2012-07-25T12:12:23Z

Protected "7icf" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:12, 25 July 2012
(No difference)

OCA at 12:12, 25 July 2012

2012-07-25T12:12:22Z

← Older revision		Revision as of 12:12, 25 July 2012
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	~~{{Seed}}~~
	[[Image:7icf.png\|left\|200px]]		[[Image:7icf.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_7icf", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_7icf\| PDB=7icf \| SCENE= }}		{{STRUCTURE_7icf\| PDB=7icf \| SCENE= }}

	===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)===		===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)===

			{{ABSTRACT_PUBMED_8841119}}

	~~<!--~~		==About this Structure==
	~~The line below~~ this ~~paragraph, {{ABSTRACT_PUBMED_8841120}}, adds the Publication Abstract to the page~~		[[7icf]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA].
	~~(as it appears on PubMed at~~ http://~~www~~.~~pubmed~~.~~gov), where 8841120~~ is ~~the PubMed ID number~~.
	-->
	~~{{ABSTRACT_PUBMED_8841120}}~~

	==~~About this Structure~~==		==See Also==
	~~7ICF is a 3 chains structure of sequences from~~ [~~http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA~~].		*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~8841120~~</ref><references group="xtra"/>		<ref group="xtra">PMID:008841119</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
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	[[Category: Dna-directed dna polymerase]]		[[Category: Dna-directed dna polymerase]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
			[[Category: Transferase-dna complex]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 12:36:49 2009''~~

OCA at 10:36, 16 February 2009

2009-02-16T10:36:50Z

← Older revision		Revision as of 10:36, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	7ICF is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA].		7ICF is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ICF OCA].

	==Reference==		==Reference==
	~~Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis., Pelletier H, Sawaya MR, Biochemistry. 1996 Oct 1;35(39):12778-87.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/8841120 8841120]~~		<ref group="xtra">PMID:8841120</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	~~[[Category: Single protein]]~~
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
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	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14~~:37:~~08 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:36:49 2009''

OCA at 11:37, 3 July 2008

2008-07-03T11:37:09Z

← Older revision		Revision as of 11:37, 3 July 2008
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	[[Image:7icf.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:7icf.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_7icf\| PDB=7icf \| SCENE= }}		{{STRUCTURE_7icf\| PDB=7icf \| SCENE= }}

	~~'''~~DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)~~'''~~		===DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)===


	~~==Overview==~~		<!--
	X-~~ray crystallographic studies have shown that DNA binding by human polymerase beta (pol beta) occurs primarily through two structurally and sequentially homologous helix~~-~~hairpin-helix (HhH) motifs~~, ~~one in the fingers subdomain and the other in the 8-kDa domain [Pelletier~~, ~~H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996a) Biochemistry 35, 12742-12761]. In that DNA binding by each HhH motif is facilitated by a metal ion, we set out to determine~~ the ~~identity of the metal ion that most likely binds~~ to the ~~HhH motif in vivo. Crystal soaking experiments were performed~~ on ~~human pol beta-DNA cocrystals with Mg2+, Ca2+, Na+, and K+, the four most prevalent metal ions in the cell, and in each case a data set was collected and the resulting structure was refined~~. Under the conditions tested, the HhH motifs of pol beta have an affinity for these biologically prevalent metal ions in the order Mg2+ < Ca2+ < Na+ < K+, with K+ displaying the strongest binding. Crystals soaked in the presence of Tl+, a commonly used spectroscopic probe for K+, were too X-ray-sensitive to establish the binding behavior of Tl+, but soaking experiments with Ba2+ and Cs+ resulted in relatively stable crystals that gave evidence of metal ion binding in both HhH motifs, confirming that larger monovalent and divalent metal ions are capable of binding to the HhH metal sites. Although Mn2+, which has been categorized as a potent polymerase mutagen, binds to the HhH motifs with a greater affinity than Mg2+, Mn2+ does not bind to the HhH motifs in the presence of equimolar concentrations of Na+. These results suggest that in vivo, where ~~Mn2+~~ is present only in trace amounts, Mn2+ probably does not have a large effect on DNA binding and may instead manifest a mutagenic effect on pol beta primarily by distorting nucleotide binding or by directly affecting the ~~catalytic step [Pelletier, H~~.~~, Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996b) Biochemistry 35, 12762~~-~~12777]. Crystal soaking experiments with 31~~-kDa apoenzyme crystals show that, in the absence of DNA, the HhH motif in the fingers subdomain binds metal ions with either much lower occupancy or not at all, indicating that metal ion binding is dependent on the presence of the DNA substrate.		The line below this paragraph, {{ABSTRACT_PUBMED_8841120}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 8841120 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_8841120}}

	==About this Structure==		==About this Structure==
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	[[Category: Dna-directed dna polymerase]]		[[Category: Dna-directed dna polymerase]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:45:27 2008''
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OCA at 19:45, 4 May 2008

2008-05-04T19:45:28Z

← Older revision		Revision as of 19:45, 4 May 2008
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	[[Image:7icf.gif\|left\|200px]]		[[Image:7icf.gif\|left\|200px]]

	{{Structure		<!--
	\|PDB~~= 7icf \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>7icf</scene>~~, ~~resolution 3~~.~~100Å~~		The line below this paragraph, containing "STRUCTURE_7icf", creates the "Structure Box" on the page.
	~~\|SITE=~~		You may change the PDB parameter (which sets the PDB file loaded into the applet)
	\|LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-~~5'~~-~~MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene~~>		or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
	\|~~ACTIVITY~~=		or leave the SCENE parameter empty for the default display.
	\|~~GENE~~=		-->
	~~\|DOMAIN=~~		{{STRUCTURE_7icf\| PDB=7icf \| SCENE= }}
	~~\|RELATEDENTRY=~~
	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7icf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7icf OCA], [http://www.ebi.ac.uk/pdbsum/7icf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7icf RCSB]</span>
	}}

	'''DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)'''		'''DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK)'''
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	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
	[[Category: ~~complex (nucleotidyltransferase/dna]]~~		[[Category: Dna repair]]
	~~[[Category: dna~~ repair]]		[[Category: Dna replication]]
	[[Category: ~~dna~~ replication]]		[[Category: Dna-directed dna polymerase]]
	[[Category: ~~dna~~-directed dna polymerase]]		[[Category: Nucleotidyltransferase]]
	[[Category: ~~nucleotidyltransferase~~]]		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:45:27 2008''

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:44:17 2008''

OCA at 02:44, 31 March 2008

2008-03-31T02:44:18Z

← Older revision		Revision as of 02:44, 31 March 2008
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	\|PDB= 7icf \|SIZE=350\|CAPTION= <scene name='initialview01'>7icf</scene>, resolution 3.100Å		\|PDB= 7icf \|SIZE=350\|CAPTION= <scene name='initialview01'>7icf</scene>, resolution 3.100Å
	\|SITE=		\|SITE=
	\|LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> ~~and~~ <scene name='pdbligand=NA:SODIUM ION'>NA</scene>		\|LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
			\|DOMAIN=
			\|RELATEDENTRY=
			\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7icf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7icf OCA], [http://www.ebi.ac.uk/pdbsum/7icf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7icf RCSB]</span>
	}}		}}

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	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
	~~[[Category: CD]]~~
	~~[[Category: NA]]~~
	[[Category: complex (nucleotidyltransferase/dna]]		[[Category: complex (nucleotidyltransferase/dna]]
	[[Category: dna repair]]		[[Category: dna repair]]
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	[[Category: nucleotidyltransferase]]		[[Category: nucleotidyltransferase]]

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