2c8v - Revision history

OCA at 17:19, 8 September 2026

2026-09-08T17:19:46Z

← Older revision		Revision as of 17:19, 8 September 2026
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/2c8v_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/2c8v_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 09:23, 9 May 2024

2024-05-09T09:23:09Z

← Older revision		Revision as of 09:23, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c8v]] is a 1 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=2C8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c8v]] is a 1 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=2C8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C8V FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ATP:ADENOSINE~~-5~~-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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]] 2.5Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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~~'>~~[https://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [https://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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [https://pdbe.org/2c8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [https://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8v ProSAT]</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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [https://pdbe.org/2c8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [https://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_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.[HAMAP-Rule:MF_00533]		[https://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_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.[HAMAP-Rule:MF_00533]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Nitrogenase]]~~		[[Category: Johnson MK]]
	[[Category: Johnson~~, M K~~]]		[[Category: Krishnakumar A]]
	[[Category: Krishnakumar, A]]		[[Category: McClead J]]
	[[Category: McClead, J]]		[[Category: Peters JW]]
	[[Category: Peters~~, J W~~]]		[[Category: Seefeldt LC]]
	[[Category: Seefeldt~~, L C~~]]		[[Category: Sen S]]
	[[Category: Sen, S]]		[[Category: Szilagyi RK]]
	[[Category: Szilagyi~~, R K]]~~
	~~[[Category: 4fe- 4]]~~
	~~[[Category: Atp-binding]]~~
	~~[[Category: Av2]]~~
	~~[[Category: Fe protein]]~~
	~~[[Category: Iron]]~~
	~~[[Category: Iron-sulfur]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Mgadp]]~~
	~~[[Category: Nitrogen fixation]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 06:50, 1 December 2021

2021-12-01T06:50:45Z

← Older revision		Revision as of 06:50, 1 December 2021
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	<StructureSection load='2c8v' size='340' side='right'caption='[[2c8v]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2c8v' size='340' side='right'caption='[[2c8v]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c8v]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2C8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c8v]] is a 1 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=2C8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C8V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</div></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'>[https://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [https://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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [~~http~~://pdbe.org/2c8v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8v ProSAT]</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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [https://pdbe.org/2c8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [https://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_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.[HAMAP-Rule:MF_00533]		[[https://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_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.[HAMAP-Rule:MF_00533]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:49, 26 February 2020

2020-02-26T10:49:14Z

← Older revision		Revision as of 10:49, 26 February 2020
Line 1:		Line 1:

	==Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP==		==Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP==
	<StructureSection load='2c8v' size='340' side='right' caption='[[2c8v]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2c8v' size='340' side='right'caption='[[2c8v]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c8v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c8v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C8V FirstGlance]. <br>
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	==See Also==		==See Also==
	*[[Nitrogenase\|Nitrogenase]]		*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
			[[Category: Large Structures]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Johnson, M K]]		[[Category: Johnson, M K]]

OCA at 08:05, 23 May 2018

2018-05-23T08:05:32Z

← Older revision		Revision as of 08:05, 23 May 2018
Line 1:		Line 1:

	==Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP==		==Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP==
	<StructureSection load='2c8v' size='340' side='right' caption='[[2c8v]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2c8v' size='340' side='right' caption='[[2c8v]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://pdbe.org/2c8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v 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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://pdbe.org/2c8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2c8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/2c8v_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/2c8v_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>

OCA at 08:24, 7 February 2016

2016-02-07T08:24:44Z

← Older revision		Revision as of 08:24, 7 February 2016
Line 18:		Line 18:
	<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=2c8v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:36, 9 September 2015

2015-09-09T23:36:39Z

← Older revision		Revision as of 23:36, 9 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v 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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://pdbe.org/2c8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_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.[HAMAP-Rule:MF_00533]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 28:
	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 2c8v" style="background-color:#fffaf0;"></div>

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

OCA at 17:34, 15 January 2015

2015-01-15T17:34:43Z

← Older revision		Revision as of 17:34, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2c8v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[2c8v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C8V FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</td></tr>
	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v 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=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Johnson, M K.]]		[[Category: Johnson, M K]]
	[[Category: Krishnakumar, A.]]		[[Category: Krishnakumar, A]]
	[[Category: McClead, J.]]		[[Category: McClead, J]]
	[[Category: Peters, J W.]]		[[Category: Peters, J W]]
	[[Category: Seefeldt, L C.]]		[[Category: Seefeldt, L C]]
	[[Category: Sen, S.]]		[[Category: Sen, S]]
	[[Category: Szilagyi, R K.]]		[[Category: Szilagyi, R K]]
	[[Category: 4fe- 4]]		[[Category: 4fe- 4]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
Line 51:		Line 51:
	[[Category: Mgadp]]		[[Category: Mgadp]]
	[[Category: Nitrogen fixation]]		[[Category: Nitrogen fixation]]
	~~[[Category: Nitrogenase]]~~
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 02:26, 30 September 2014

2014-09-30T02:26:38Z

← Older revision		Revision as of 02:26, 30 September 2014
Line 1:		Line 1:
	~~{{STRUCTURE_2c8v\| PDB=2c8v \| SCENE= }}~~		==Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP==
	===Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP===		<StructureSection load='2c8v' size='340' side='right' caption='[[2c8v]], [[Resolution\|resolution]] 2.50Å' scene=''>
	~~{{ABSTRACT_PUBMED_16616373}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2c8v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C8V FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1de0\|1de0]], [[1fp6\|1fp6]], [[1g1m\|1g1m]], [[1g20\|1g20]], [[1g21\|1g21]], [[1g5p\|1g5p]], [[1m1y\|1m1y]], [[1m34\|1m34]], [[1n2c\|1n2c]], [[1nip\|1nip]], [[1rw4\|1rw4]], [[1xcp\|1xcp]], [[1xd8\|1xd8]], [[1xd9\|1xd9]], [[1xdb\|1xdb]], [[2afh\|2afh]], [[2afi\|2afi]], [[2afk\|2afk]], [[2nip\|2nip]]</td></tr>
			<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c8v RCSB], [http://www.ebi.ac.uk/pdbsum/2c8v 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/c8/2c8v_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 ==
			In the present work, determination of the structure of the nitrogenase Leu 127 deletion variant Fe protein with MgATP bound is presented, along with density functional theory calculations, to provide insights into the roles of MgATP in the nitrogenase reaction mechanism. Comparison of the MgATP-bound structure of this Fe protein to the nucleotide-free form indicates that the binding of MgATP does not alter the overall structure of the variant significantly with only small differences in the conformation of amino acids in direct contact with the two bound MgATP molecules being seen. The earlier observation of splitting of the [4Fe-4S] cluster into two [2Fe-2S] clusters was observed to be unaltered upon binding MgATP. Density functional theory was used to probe the assignment of ligands to the two [2Fe-2S] rhombs. The Mg(2+) environment in the MgATP-bound structure of the Leu127 deletion Fe protein is similar to that observed for the Fe protein in the nitrogenase Fe protein: MoFe protein complex stabilized by MgADP and tetrafluoroaluminate suggesting that large scale conformational change implicated for the Fe protein may not be mediated by changes in the Mg(2+) coordination. The results presented here indicated that MgATP may enhance the stability of an open conformation and prohibit intersubunit interactions, which have been implicated in promoting nucleotide hydrolysis. This could be critical to the tight control of MgATP hydrolysis observed within the nitrogenase complex and may be important for maintaining unidirectional electron flow toward substrate reduction.

	~~==About this Structure==~~		Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP.,Sen S, Krishnakumar A, McClead J, Johnson MK, Seefeldt LC, Szilagyi RK, Peters JW J Inorg Biochem. 2006 May;100(5-6):1041-52. Epub 2006 Mar 3. PMID:16616373<ref>PMID:16616373</ref>
	~~[[2c8v]] is a 1 chain structure~~ with ~~sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=2C8V OCA].~~
			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	==See Also==		==See Also==
	*[[Nitrogenase\|Nitrogenase]]		*[[Nitrogenase\|Nitrogenase]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:016616373</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]

OCA at 07:48, 27 March 2013

2013-03-27T07:48:19Z

← Older revision		Revision as of 07:48, 27 March 2013
Line 1:		Line 1:
	~~[[Image:2c8v.png\|left\|200px]]~~

	{{STRUCTURE_2c8v\| PDB=2c8v \| SCENE= }}		{{STRUCTURE_2c8v\| PDB=2c8v \| SCENE= }}
			===Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP===
	===~~INSIGHTS INTO THE ROLE OF NUCLEOTIDE~~-~~DEPENDENT CONFORMATIONAL CHANGE IN NITROGENASE CATALYSIS~~: ~~STRUCTURAL CHARACTERIZATION OF THE NITROGENASE FE PROTEIN LEU127 DELETION VARIANT WITH BOUND MGATP~~===

	{{ABSTRACT_PUBMED_16616373}}		{{ABSTRACT_PUBMED_16616373}}

Line 14:		Line 10:

	==Reference==		==Reference==
	<ref group="xtra">PMID:016616373</ref><references group="xtra"/>		<ref group="xtra">PMID:016616373</ref><references group="xtra"/><references/>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Johnson, M K.]]		[[Category: Johnson, M K.]]
	[[Category: Krishnakumar, A.]]		[[Category: Krishnakumar, A.]]
	[[Category: ~~Mcclead~~, J.]]		[[Category: McClead, J.]]
	[[Category: Peters, J W.]]		[[Category: Peters, J W.]]
	[[Category: Seefeldt, L C.]]		[[Category: Seefeldt, L C.]]