5f8a - Revision history

OCA at 06:41, 19 July 2023

2023-07-19T06:41:54Z

← Older revision		Revision as of 06:41, 19 July 2023
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	<StructureSection load='5f8a' size='340' side='right'caption='[[5f8a]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='5f8a' size='340' side='right'caption='[[5f8a]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5f8a]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[5f8a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F8A FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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]] 1.76Å</td></tr>
	~~<tr~~ id~~='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class~~="~~sblockDat~~">~~[[4orj\|4orj]]~~, [[~~5hlk~~\|~~5hlk~~]]</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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"~~>ecoRVR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~<~~/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=5f8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f8a OCA], [https://pdbe.org/5f8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f8a RCSB], [https://www.ebi.ac.uk/pdbsum/5f8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f8a ProSAT]</span></td></tr>
	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </~~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=5f8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f8a OCA], [~~http~~://pdbe.org/5f8a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f8a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f8a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f8a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.		[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Type II site-specific deoxyribonuclease~~]]		[[Category: Synthetic construct]]
	[[Category: Jen-Jacobson, L]]		[[Category: Jen-Jacobson L]]
	[[Category: Kehr~~, A D~~]]		[[Category: Kehr AD]]
	[[Category: Rule~~, G S~~]]		[[Category: Rule GS]]
	[[Category: Sangani~~, S S~~]]		[[Category: Sangani SS]]
	[[Category: Sinha, K]]		[[Category: Sinha K]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Hydrolase-dna complex]]~~
	~~[[Category: Lutetium]]~~
	~~[[Category: Protein-dna complex~~]]

OCA at 11:37, 25 December 2019

2019-12-25T11:37:26Z

← Older revision		Revision as of 11:37, 25 December 2019
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	==Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.==		==Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.==
	<StructureSection load='5f8a' size='340' side='right' caption='[[5f8a]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='5f8a' size='340' side='right'caption='[[5f8a]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5f8a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[5f8a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F8A FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5f8a" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f8a" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Jen-Jacobson, L]]		[[Category: Jen-Jacobson, L]]

OCA at 12:41, 6 November 2017

2017-11-06T12:41:39Z

← Older revision		Revision as of 12:41, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5f8a' size='340' side='right' caption='[[5f8a]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='5f8a' size='340' side='right' caption='[[5f8a]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5f8a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[5f8a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F8A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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">[[4orj\|4orj]], [[5hlk\|5hlk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4orj\|4orj]], [[5hlk\|5hlk]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ecoRVR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=5f8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f8a OCA], [http://pdbe.org/5f8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f8a RCSB], [http://www.ebi.ac.uk/pdbsum/5f8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f8a 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=5f8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f8a OCA], [http://pdbe.org/5f8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f8a RCSB], [http://www.ebi.ac.uk/pdbsum/5f8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f8a ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacillus coli migula 1895]]
	[[Category: Type II site-specific deoxyribonuclease]]		[[Category: Type II site-specific deoxyribonuclease]]
	[[Category: Jen-Jacobson, L]]		[[Category: Jen-Jacobson, L]]

OCA at 19:46, 9 December 2016

2016-12-09T19:46:19Z

← Older revision		Revision as of 19:46, 9 December 2016
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5f8a is ~~ON HOLD until Paper~~ Publication		==Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.==
			<StructureSection load='5f8a' size='340' side='right' caption='[[5f8a]], [[Resolution\|resolution]] 1.76Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[5f8a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F8A FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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">[[4orj\|4orj]], [[5hlk\|5hlk]]</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </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=5f8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f8a OCA], [http://pdbe.org/5f8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f8a RCSB], [http://www.ebi.ac.uk/pdbsum/5f8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f8a ProSAT]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX]] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Metal ion cofactors can alter the energetics and specificity of sequence specific protein-DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein-DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H-15N amide resonances, for 1H-13C Ile-delta-CH3 resonances, and for stereospecifically assigned Leu-delta-CH3 and Val-gamma-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 A from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a beta-sheet and an alpha-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex.

	~~Authors: Sangani, S.S~~., ~~Kehr~~, ~~A.D.~~, ~~Sinha, K.~~, Rule~~, G.S.~~, Jen-Jacobson, L.		Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.,Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L Biochemistry. 2016 Oct 27. PMID:27786446<ref>PMID:27786446</ref>

	~~Description: Crystal structure~~ of the ~~ternary EcoRV~~-~~DNA~~-~~Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV~~-~~DNA complex inhibits cleavage.~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
			<div class="pdbe-citations 5f8a" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Type II site-specific deoxyribonuclease]]
			[[Category: Jen-Jacobson, L]]
			[[Category: Kehr, A D]]
			[[Category: Rule, G S]]
			[[Category: Sangani, S S]]
	[[Category: Sinha, K]]		[[Category: Sinha, K]]
	[[Category: ~~Sangani, S.S~~]]		[[Category: Hydrolase]]
	[[Category: ~~Kehr, A.D~~]]		[[Category: Hydrolase-dna complex]]
	[[Category: ~~Rule, G.S~~]]		[[Category: Lutetium]]
	[[Category: ~~Jen~~-~~Jacobson, L~~]]		[[Category: Protein-dna complex]]

OCA at 17:58, 13 January 2016

2016-01-13T17:58:33Z

← Older revision		Revision as of 17:58, 13 January 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5f8a is ON HOLD		The entry 5f8a is ON HOLD until Paper Publication

	Authors: Sangani, S.S., Kehr, A.D., Sinha, K., Rule, G.S., Jen-Jacobson, L.		Authors: Sangani, S.S., Kehr, A.D., Sinha, K., Rule, G.S., Jen-Jacobson, L.

	Description: ~~Lanthanide binding to EcoRV-DNA complex inhibits cleavage. Structure~~ of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate.		Description: Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Sinha, K]]		[[Category: Sinha, K]]

OCA at 17:38, 30 December 2015

2015-12-30T17:38:10Z

← Older revision		Revision as of 17:38, 30 December 2015
Line 3:		Line 3:
	The entry 5f8a is ON HOLD		The entry 5f8a is ON HOLD

	Authors: ~~Sinha, K., Kurpiewski, M.R.,~~ Sangani, S.S., Kehr, A.D., Rule, G.S., Jen-Jacobson, L.		Authors: Sangani, S.S., Kehr, A.D., Sinha, K., Rule, G.S., Jen-Jacobson, L.

	Description: ~~Metal Ion Binding at~~ the ~~Catalytic Site Induces Widespread Changes in a Sequence~~-~~specific Protein~~-DNA ~~Complex~~		Description: Lanthanide binding to EcoRV-DNA complex inhibits cleavage. Structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Sinha, K]]		[[Category: Sinha, K]]
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	[[Category: Kehr, A.D]]		[[Category: Kehr, A.D]]
	[[Category: Rule, G.S]]		[[Category: Rule, G.S]]
	~~[[Category: Kurpiewski, M.R]]~~
	[[Category: Jen-Jacobson, L]]		[[Category: Jen-Jacobson, L]]

OCA: Protected "5f8a" [edit=sysop:move=sysop]

2015-12-16T12:42:36Z

Protected "5f8a" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:42, 16 December 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5f8a is ON HOLD Authors: Sinha, K., Kurpiewski, M.R., Sangani, S.S., Kehr, A.D., Rule, G.S., Jen-Jacobson, L. Description: Metal Ion Binding at the...

2015-12-16T12:42:35Z

New page: '''Unreleased structure''' The entry 5f8a is ON HOLD Authors: Sinha, K., Kurpiewski, M.R., Sangani, S.S., Kehr, A.D., Rule, G.S., Jen-Jacobson, L. Description: Metal Ion Binding at the...

New page

'''Unreleased structure'''

The entry 5f8a is ON HOLD

Authors: Sinha, K., Kurpiewski, M.R., Sangani, S.S., Kehr, A.D., Rule, G.S., Jen-Jacobson, L.

Description: Metal Ion Binding at the Catalytic Site Induces Widespread Changes in a Sequence-specific Protein-DNA Complex
[[Category: Unreleased Structures]]
[[Category: Sinha, K]]
[[Category: Sangani, S.S]]
[[Category: Kehr, A.D]]
[[Category: Rule, G.S]]
[[Category: Kurpiewski, M.R]]
[[Category: Jen-Jacobson, L]]