4ncq - Revision history

OCA at 16:53, 20 September 2023

OCA — Wed, 20 Sep 2023 16:53:26 GMT

←Older revision		Revision as of 16:53, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ncq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NCQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ncq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NCQ FirstGlance]. <br>
-	</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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [https://pdbe.org/4ncq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [https://www.ebi.ac.uk/pdbsum/4ncq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncq ProSAT]</span></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]] 2.08Å</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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [https://pdbe.org/4ncq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [https://www.ebi.ac.uk/pdbsum/4ncq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:22, 11 January 2023

OCA — Wed, 11 Jan 2023 08:22:16 GMT

←Older revision		Revision as of 08:22, 11 January 2023
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	==Crystal structure of NiSOD H1A mutant==		==Crystal structure of NiSOD H1A mutant==
-	<StructureSection load='4ncq' size='340' side='right' caption='[[4ncq]], [[Resolution\|resolution]] 2.08Å' scene=''>	+	<StructureSection load='4ncq' size='340' side='right'caption='[[4ncq]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ncq]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces~~ coelicolor~~" (muller 1908) lieske 1921~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ncq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NCQ FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6u\|1t6u]], [[3g4x\|3g4x]], [[3g4z\|3g4z]], [[3g50\|3g50]]</td></tr>~~	+	</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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [https://pdbe.org/4ncq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [https://www.ebi.ac.uk/pdbsum/4ncq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncq ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2SC7G11.16c, SCO5254, sod1, sodN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [~~http~~://pdbe.org/4ncq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ncq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SODN_STRCO SODN_STRCO]
	<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 4ncq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ncq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Superoxide dismutase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Garman, S C~~]]	+	[[Category: Streptomyces coelicolor]]
-	[[Category: ~~Guce, A I~~]]	+	[[Category: Garman SC]]
-	[[Category: ~~Antioxidant]]~~	+	[[Category: Guce AI]]
-	~~[[Category: Hexamer]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Ni]]~~	+
-	~~[[Category: Ni-binding]]~~	+
-	~~[[Category: Nisod]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Sod~~]]	+

OCA at 10:04, 15 November 2017

OCA — Wed, 15 Nov 2017 10:04:14 GMT

←Older revision		Revision as of 10:04, 15 November 2017
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	<StructureSection load='4ncq' size='340' side='right' caption='[[4ncq]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='4ncq' size='340' side='right' caption='[[4ncq]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ncq]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NCQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ncq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces coelicolor" (muller 1908) lieske 1921]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NCQ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6u\|1t6u]], [[3g4x\|3g4x]], [[3g4z\|3g4z]], [[3g50\|3g50]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6u\|1t6u]], [[3g4x\|3g4x]], [[3g4z\|3g4z]], [[3g50\|3g50]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">2SC7G11.16c, SCO5254, sod1, sodN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [http://pdbe.org/4ncq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [http://www.ebi.ac.uk/pdbsum/4ncq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncq 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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [http://pdbe.org/4ncq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [http://www.ebi.ac.uk/pdbsum/4ncq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncq ProSAT]</span></td></tr>
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4ncq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ncq" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Superoxide Dismutase\|Superoxide Dismutase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:25, 18 January 2017

OCA — Wed, 18 Jan 2017 17:25:30 GMT

←Older revision		Revision as of 17:25, 18 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of NiSOD H1A mutant==		==Crystal structure of NiSOD H1A mutant==
	<StructureSection load='4ncq' size='340' side='right' caption='[[4ncq]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='4ncq' size='340' side='right' caption='[[4ncq]], [[Resolution\|resolution]] 2.08Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6u\|1t6u]], [[3g4x\|3g4x]], [[3g4z\|3g4z]], [[3g50\|3g50]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6u\|1t6u]], [[3g4x\|3g4x]], [[3g4z\|3g4z]], [[3g50\|3g50]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [http://www.ebi.ac.uk/pdbsum/4ncq 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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [http://pdbe.org/4ncq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [http://www.ebi.ac.uk/pdbsum/4ncq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ncq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4ncq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Superoxide Dismutase\|Superoxide Dismutase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:46, 8 April 2015

OCA — Wed, 08 Apr 2015 05:46:02 GMT

←Older revision		Revision as of 05:46, 8 April 2015
Line 7:		Line 7:
	<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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [http://www.ebi.ac.uk/pdbsum/4ncq 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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [http://www.ebi.ac.uk/pdbsum/4ncq PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystal structures of nickel-dependent superoxide dismutases (NiSODs) reveal the presence of a H-bonding network formed between the NH group of the apical imidazole ligand from His1 and the Glu17 carboxylate from a neighboring subunit in the hexameric enzyme. This interaction is supported by another intrasubunit H-bond between Glu17 and Arg47. In this study, four mutant NiSOD proteins were produced to experimentally evaluate the roles of this H-bonding network and compare the results with prior predictions from density functional theory calculations. The X-ray crystal structure of H1A-NiSOD, which lacks the apical ligand entirely, reveals that in the absence of the Glu17-His1 H-bond, the active site is disordered. Characterization of this variant using X-ray absorption spectroscopy (XAS) shows that Ni(II) is bound in the expected N2S2 planar coordination site. Despite these structural perturbations, the H1A-NiSOD variant retains 4% of wild-type (WT) NiSOD activity. Three other mutations were designed to preserve the apical imidazole ligand but perturb the H-bonding network: R47A-NiSOD, which lacks the intramolecular H-bonding interaction; E17R/R47A-NiSOD, which retains the intramolecular H-bond but lacks the intermolecular Glu17-His1 H-bond; and E17A/R47A-NiSOD, which lacks both H-bonding interactions. These variants were characterized by a combination of techniques, including XAS to probe the nickel site structure, kinetic studies employing pulse-radiolytic production of superoxide, and electron paramagnetic resonance to assess the Ni redox activity. The results indicate that in addition to the roles in redox tuning suggested on the basis of previous computational studies, the Glu17-His1 H-bond plays an important structural role in the proper folding of the "Ni-hook" motif that is a critical feature of the active site.
		+
		+	Nickel superoxide dismutase: structural and functional roles of His1 and its H-bonding network.,Ryan KC, Guce AI, Johnson OE, Brunold TC, Cabelli DE, Garman SC, Maroney MJ Biochemistry. 2015 Feb 3;54(4):1016-27. doi: 10.1021/bi501258u. Epub 2015 Jan 21. PMID:25580509<ref>PMID:25580509</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:06, 24 December 2014

OCA — Wed, 24 Dec 2014 11:06:22 GMT

←Older revision		Revision as of 11:06, 24 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of NiSOD H1A mutant==
-		+	<StructureSection load='4ncq' size='340' side='right' caption='[[4ncq]], [[Resolution\|resolution]] 2.08Å' scene=''>
-	~~The entry~~ 4ncq is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ncq]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NCQ FirstGlance]. <br>
-	~~Authors~~: ~~Guce~~, A.I., Garman, S.C.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6u\|1t6u]], [[3g4x\|3g4x]], [[3g4z\|3g4z]], [[3g50\|3g50]]</td></tr>
-		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>
-	~~Description~~: ~~Crystal structure of NiSOD H1A mutant~~	+	<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=4ncq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ncq RCSB], [http://www.ebi.ac.uk/pdbsum/4ncq PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Superoxide dismutase]]
		+	[[Category: Garman, S C]]
		+	[[Category: Guce, A I]]
		+	[[Category: Antioxidant]]
		+	[[Category: Hexamer]]
		+	[[Category: Metal-binding]]
		+	[[Category: Ni]]
		+	[[Category: Ni-binding]]
		+	[[Category: Nisod]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Sod]]

OCA at 07:37, 15 January 2014

OCA — Wed, 15 Jan 2014 07:37:01 GMT

←Older revision		Revision as of 07:37, 15 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ncq is ON HOLD	+	The entry 4ncq is ON HOLD until Paper Publication

	Authors: Guce, A.I., Garman, S.C.		Authors: Guce, A.I., Garman, S.C.

	Description: Crystal structure of NiSOD H1A mutant		Description: Crystal structure of NiSOD H1A mutant

OCA: Protected "4ncq" [edit=sysop:move=sysop]

OCA — Wed, 06 Nov 2013 07:09:05 GMT

Protected "4ncq" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:09, 6 November 2013

OCA: New page: '''Unreleased structure''' The entry 4ncq is ON HOLD Authors: Guce, A.I., Garman, S.C. Description: Crystal structure of NiSOD H1A mutant

OCA — Wed, 06 Nov 2013 07:09:05 GMT

New page: '''Unreleased structure''' The entry 4ncq is ON HOLD Authors: Guce, A.I., Garman, S.C. Description: Crystal structure of NiSOD H1A mutant

New page

'''Unreleased structure'''

The entry 4ncq is ON HOLD

Authors: Guce, A.I., Garman, S.C.

Description: Crystal structure of NiSOD H1A mutant