5n6y - Revision history

OCA at 12:30, 15 November 2023

2023-11-15T12:30:36Z

←Older revision		Revision as of 12:30, 15 November 2023
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	==Azotobacter vinelandii vanadium nitrogenase==		==Azotobacter vinelandii vanadium nitrogenase==
-	<StructureSection load='5n6y' size='340' side='right' caption='[[5n6y]], [[Resolution\|resolution]] 1.35Å' scene=''>	+	<StructureSection load='5n6y' size='340' side='right'caption='[[5n6y]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n6y]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_478 Atcc 478~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n6y]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N6Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8P8:C+Fe7+S8+V'>8P8</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.35Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vnfD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478]), vnfK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478]), vnfG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8P8:C+Fe7+S8+V'>8P8</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=5n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6y OCA], [https://pdbe.org/5n6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n6y RCSB], [https://www.ebi.ac.uk/pdbsum/5n6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6y 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=5n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6y OCA], [~~http~~://pdbe.org/5n6y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n6y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n6y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6y ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VNFD_AZOVI VNFD_AZOVI]] This vanadium-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [[http://www.uniprot.org/uniprot/VNFG_AZOVI VNFG_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein. [[http://www.uniprot.org/uniprot/VNFK_AZOVI VNFK_AZOVI]] This vanadium-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.	+	[https://www.uniprot.org/uniprot/VNFD_AZOVI VNFD_AZOVI] This vanadium-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
	<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 5n6y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5n6y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 478~~]]	+	[[Category: Azotobacter vinelandii]]
-	[[Category: ~~Nitrogenase~~]]	+	[[Category: Large Structures]]
-	[[Category: Einsle, O]]	+	[[Category: Einsle O]]
-	[[Category: Sippel, D]]	+	[[Category: Sippel D]]
-	~~[[Category: Nitrogenase metalloenzyme biological nitrogen fixation]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 18:45, 15 November 2017

2017-11-15T18:45:13Z

←Older revision		Revision as of 18:45, 15 November 2017
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	<StructureSection load='5n6y' size='340' side='right' caption='[[5n6y]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='5n6y' size='340' side='right' caption='[[5n6y]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n6y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n6y]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_478 Atcc 478]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N6Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8P8:C+Fe7+S8+V'>8P8</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8P8:C+Fe7+S8+V'>8P8</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vnfD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478]), vnfK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478]), vnfG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=5n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6y OCA], [http://pdbe.org/5n6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6y RCSB], [http://www.ebi.ac.uk/pdbsum/5n6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6y 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=5n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6y OCA], [http://pdbe.org/5n6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6y RCSB], [http://www.ebi.ac.uk/pdbsum/5n6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6y ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5n6y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5n6y" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nitrogenase\|Nitrogenase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 478]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Einsle, O]]		[[Category: Einsle, O]]

OCA at 03:57, 30 August 2017

2017-08-30T03:57:26Z

←Older revision		Revision as of 03:57, 30 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5n6y is ~~ON HOLD~~	+	==Azotobacter vinelandii vanadium nitrogenase==
		+	<StructureSection load='5n6y' size='340' side='right' caption='[[5n6y]], [[Resolution\|resolution]] 1.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5n6y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N6Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8P8:C+Fe7+S8+V'>8P8</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=5n6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n6y OCA], [http://pdbe.org/5n6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n6y RCSB], [http://www.ebi.ac.uk/pdbsum/5n6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n6y ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VNFD_AZOVI VNFD_AZOVI]] This vanadium-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [[http://www.uniprot.org/uniprot/VNFG_AZOVI VNFG_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein. [[http://www.uniprot.org/uniprot/VNFK_AZOVI VNFK_AZOVI]] This vanadium-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nitrogenases catalyze the reduction of dinitrogen (N2) gas to ammonium at a complex heterometallic cofactor. This most commonly occurs at the FeMo cofactor (FeMoco), a [Mo-7Fe-9S-C] cluster whose exact reactivity and substrate-binding mode remain unknown. Alternative nitrogenases replace molybdenum with either vanadium or iron and differ in reactivity, most prominently in the ability of vanadium nitrogenase to reduce CO to hydrocarbons. Here we report the 1.35-A structure of vanadium nitrogenase from Azotobacter vinelandii. The 240-kDa protein contains an additional alpha-helical subunit that is not present in molybdenum nitrogenase. The FeV cofactor (FeVco) is a [V-7Fe-8S-C] cluster with a homocitrate ligand to vanadium. Unexpectedly, it lacks one sulfide ion compared to FeMoco, which is replaced by a bridging ligand, likely a mu-1,3-carbonate. The anion fits into a pocket within the protein that is obstructed in molybdenum nitrogenase, and its different chemical character helps to rationalize the altered chemical properties of this unique N2- and CO-fixing enzyme.

-	~~Authors~~:	+	The structure of vanadium nitrogenase reveals an unusual bridging ligand.,Sippel D, Einsle O Nat Chem Biol. 2017 Sep;13(9):956-960. doi: 10.1038/nchembio.2428. Epub 2017 Jul , 10. PMID:28692069<ref>PMID:28692069</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5n6y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrogenase\|Nitrogenase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Nitrogenase]]
		+	[[Category: Einsle, O]]
		+	[[Category: Sippel, D]]
		+	[[Category: Nitrogenase metalloenzyme biological nitrogen fixation]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5n6y" [edit=sysop:move=sysop]

2017-03-09T12:11:45Z

Protected "5n6y" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:11, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5n6y is ON HOLD Authors: Description: Category: Unreleased Structures

2017-03-09T12:11:44Z

New page: '''Unreleased structure''' The entry 5n6y is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5n6y is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]