6ctr - Revision history

OCA at 15:11, 4 October 2023

2023-10-04T15:11:05Z

← Older revision		Revision as of 15:11, 4 October 2023
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	==Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue==		==Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue==
	<StructureSection load='6ctr' size='340' side='right' caption='[[6ctr]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6ctr' size='340' side='right'caption='[[6ctr]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ctr]] is a 4 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=6CTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ctr]] is a 4 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=6CTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</scene>, <scene name='pdbligand=FF4:2-deoxy-5-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>FF4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.85Å</td></tr>
	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</scene>, <scene name='pdbligand=FF4:2-deoxy-5-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>FF4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=6ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ctr OCA], [https://pdbe.org/6ctr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ctr RCSB], [https://www.ebi.ac.uk/pdbsum/6ctr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ctr ProSAT]</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=6ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ctr OCA], [~~http~~://pdbe.org/6ctr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ctr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ctr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ctr 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6ctr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ctr" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: ~~Batra, V K~~]]		[[Category: Large Structures]]
	[[Category: ~~Wilson, S H~~]]		[[Category: Batra VK]]
	[[Category: ~~Conformational change]]~~		[[Category: Wilson SH]]
	~~[[Category: Dna polymerase beta]]~~
	~~[[Category: Enzyme mechanism]]~~
	~~[[Category: Lfer]]~~
	~~[[Category: Transcription-dna complex~~]]

OCA at 06:14, 11 July 2018

2018-07-11T06:14:23Z

← Older revision		Revision as of 06:14, 11 July 2018
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	<StructureSection load='6ctr' size='340' side='right' caption='[[6ctr]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6ctr' size='340' side='right' caption='[[6ctr]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ctr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ctr]] is a 4 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=6CTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</scene>, <scene name='pdbligand=FF4:2-deoxy-5-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>FF4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3C:2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>F3C</scene>, <scene name='pdbligand=FF4:2-deoxy-5-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine'>FF4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ctr OCA], [http://pdbe.org/6ctr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ctr RCSB], [http://www.ebi.ac.uk/pdbsum/6ctr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ctr ProSAT]</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=6ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ctr OCA], [http://pdbe.org/6ctr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ctr RCSB], [http://www.ebi.ac.uk/pdbsum/6ctr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ctr ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Wilson, S H]]		[[Category: Wilson, S H]]

OCA at 05:51, 20 June 2018

2018-06-20T05:51:46Z

@@ Line 1: / Line 1: @@
-The entry 6ctr is ON HOLD  until Paper Publication
+==Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue==
-Authors: Batra, V.K., Wilson, S.H.
+Mapping functional substrate-enzyme interactions in the pol beta active site through chemical biology: Structural responses to acidity modification of incoming dNTPs.,Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH Biochemistry. 2018 Jun 6. doi: 10.1021/acs.biochem.8b00418. PMID:29874056<ref>PMID:29874056</ref>
-Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Wilson, S.H]]
+<div class="pdbe-citations 6ctr" style="background-color:#fffaf0;"></div>
-[[Category: Batra, V.K]]
+== References ==

OCA at 06:38, 2 May 2018

2018-05-02T06:38:38Z

← Older revision		Revision as of 06:38, 2 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6ctr is ON HOLD until ~~sometime in the future~~		The entry 6ctr is ON HOLD until Paper Publication

	Authors: Batra, V.K., Wilson, S.H.		Authors: Batra, V.K., Wilson, S.H.

OCA at 04:10, 18 April 2018

2018-04-18T04:10:42Z

← Older revision		Revision as of 04:10, 18 April 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6ctr is ON HOLD		The entry 6ctr is ON HOLD until sometime in the future

	Authors: Batra, V.K., Wilson, S.H.		Authors: Batra, V.K., Wilson, S.H.

OCA: Protected "6ctr" [edit=sysop:move=sysop]

2018-04-04T04:41:04Z

Protected "6ctr" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:41, 4 April 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6ctr is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated ...

2018-04-04T04:41:03Z

New page: '''Unreleased structure''' The entry 6ctr is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated ...

New page

'''Unreleased structure'''

The entry 6ctr is ON HOLD

Authors: Batra, V.K., Wilson, S.H.

Description: Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue
[[Category: Unreleased Structures]]
[[Category: Wilson, S.H]]
[[Category: Batra, V.K]]