2dws - Revision history

OCA at 08:31, 25 October 2023

2023-10-25T08:31:30Z

← Older revision		Revision as of 08:31, 25 October 2023
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	<StructureSection load='2dws' size='340' side='right'caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2dws' size='340' side='right'caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DWS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DWS FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>~~, ~~<scene name='pdbligand=NO2:NITRITE+ION'>NO2</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='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em~~;~~'>[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nirK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1063~~ "~~Rhodococcus capsulatus~~" ~~Molisch 1907])</td~~><~~/tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1]~~ </~~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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [https://pdbe.org/2dws PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [https://www.ebi.ac.uk/pdbsum/2dws PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dws 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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [https://pdbe.org/2dws PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [https://www.ebi.ac.uk/pdbsum/2dws PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dws ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/NIR_CERS5 NIR_CERS5]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Rhodococcus capsulatus molisch 1907~~]]		[[Category: Cereibacter sphaeroides]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Jacobson, F]]		[[Category: Jacobson F]]
	~~[[Category: Copper protein]]~~
	~~[[Category: Cupredoxin]]~~
	~~[[Category: Denitrification]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 11:39, 10 February 2021

2021-02-10T11:39:35Z

← Older revision		Revision as of 11:39, 10 February 2021
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	==Cu-containing nitrite reductase at pH 8.4 with bound nitrite==		==Cu-containing nitrite reductase at pH 8.4 with bound nitrite==
	<StructureSection load='2dws' size='340' side='right' caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2dws' size='340' side='right'caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DWS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DWS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [~~http~~://pdbe.org/2dws PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dws PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dws 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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [https://pdbe.org/2dws PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [https://www.ebi.ac.uk/pdbsum/2dws PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dws ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/2dws_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/2dws_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>
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	</div>		</div>
	<div class="pdbe-citations 2dws" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2dws" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Rhodococcus capsulatus molisch 1907]]		[[Category: Rhodococcus capsulatus molisch 1907]]
			[[Category: Large Structures]]
	[[Category: Jacobson, F]]		[[Category: Jacobson, F]]
	[[Category: Copper protein]]		[[Category: Copper protein]]

OCA at 10:31, 12 October 2017

2017-10-12T10:31:34Z

← Older revision		Revision as of 10:31, 12 October 2017
Line 1:		Line 1:

	==Cu-containing nitrite reductase at pH 8.4 with bound nitrite==		==Cu-containing nitrite reductase at pH 8.4 with bound nitrite==
	<StructureSection load='2dws' size='340' side='right' caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2dws' size='340' side='right' caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://pdbe.org/2dws PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [http://www.ebi.ac.uk/pdbsum/2dws 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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://pdbe.org/2dws PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [http://www.ebi.ac.uk/pdbsum/2dws PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dws ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=2dws ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 2dws" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2dws" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Nitric reductase\|Nitric reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:22, 11 September 2015

2015-09-11T14:22:54Z

← Older revision		Revision as of 14:22, 11 September 2015
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	<StructureSection load='2dws' size='340' side='right' caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2dws' size='340' side='right' caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodobacter_sphaeroides Rhodobacter sphaeroides~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DWS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DWS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 ~~Rhodobacter sphaeroides~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [http://www.ebi.ac.uk/pdbsum/2dws 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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://pdbe.org/2dws PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [http://www.ebi.ac.uk/pdbsum/2dws PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2dws" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Rhodobacter sphaeroides~~]]		[[Category: Rhodococcus capsulatus molisch 1907]]
	[[Category: Jacobson, F]]		[[Category: Jacobson, F]]
	[[Category: Copper protein]]		[[Category: Copper protein]]

OCA at 17:35, 15 January 2015

2015-01-15T17:35:31Z

← Older revision		Revision as of 17:35, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DWS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DWS FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 Rhodobacter sphaeroides])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 Rhodobacter sphaeroides])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [http://www.ebi.ac.uk/pdbsum/2dws 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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [http://www.ebi.ac.uk/pdbsum/2dws 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:
	</StructureSection>		</StructureSection>
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	[[Category: Jacobson, F.]]		[[Category: Jacobson, F]]
	[[Category: Copper protein]]		[[Category: Copper protein]]
	[[Category: Cupredoxin]]		[[Category: Cupredoxin]]
	[[Category: Denitrification]]		[[Category: Denitrification]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 05:02, 29 September 2014

2014-09-29T05:02:17Z

← Older revision		Revision as of 05:02, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2dws~~.~~png~~\|~~left~~\|~~200px~~]]		==Cu-containing nitrite reductase at pH 8.4 with bound nitrite==
			<StructureSection load='2dws' size='340' side='right' caption='[[2dws]], [[Resolution\|resolution]] 1.85Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DWS FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1zv2\|1zv2]], [[2dwt\|2dwt]], [[2dy2\|2dy2]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 Rhodobacter sphaeroides])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [http://www.ebi.ac.uk/pdbsum/2dws 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/dw/2dws_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 ==
			Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

	~~{{STRUCTURE_2dws\| PDB=2dws \| SCENE= }}~~		pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase.,Jacobson F, Pistorius A, Farkas D, De Grip W, Hansson O, Sjolin L, Neutze R J Biol Chem. 2007 Mar 2;282(9):6347-55. Epub 2006 Dec 5. PMID:17148448<ref>PMID:17148448</ref>

	~~===Cu-containing nitrite reductase at pH 8.4 with bound nitrite===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17148448}}~~

	~~==About this Structure==~~
	~~[[2dws]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA].~~

	==See Also==		==See Also==
	*[[Nitric reductase\|Nitric reductase]]		*[[Nitric reductase\|Nitric reductase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:017148448<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	[[Category: Jacobson, F.]]		[[Category: Jacobson, F.]]

OCA at 19:33, 20 October 2012

2012-10-20T19:33:35Z

← Older revision		Revision as of 19:33, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2dws]] is a 1 chain structure ~~of [[Nitric reductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA].		[[2dws]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA].

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

OCA: Protected "2dws" [edit=sysop:move=sysop]

2012-07-27T07:44:43Z

Protected "2dws" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:44, 27 July 2012
(No difference)

OCA at 07:44, 27 July 2012

2012-07-27T07:44:42Z

← Older revision		Revision as of 07:44, 27 July 2012
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	~~{{Seed}}~~
	[[Image:2dws.png\|left\|200px]]		[[Image:2dws.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dws", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2dws\| PDB=2dws \| SCENE= }}		{{STRUCTURE_2dws\| PDB=2dws \| SCENE= }}

	===Cu-containing nitrite reductase at pH 8.4 with bound nitrite===		===Cu-containing nitrite reductase at pH 8.4 with bound nitrite===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17148448}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17148448 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17148448}}		{{ABSTRACT_PUBMED_17148448}}

	==About this Structure==		==About this Structure==
	~~2DWS~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA].		[[2dws]] is a 1 chain structure of [[Nitric reductase]] with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA].

			==See Also==
			*[[Nitric reductase\|Nitric reductase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17148448~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017148448</ref><references group="xtra"/>
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	[[Category: Jacobson, F.]]		[[Category: Jacobson, F.]]
Line 29:		Line 20:
	[[Category: Cupredoxin]]		[[Category: Cupredoxin]]
	[[Category: Denitrification]]		[[Category: Denitrification]]
			[[Category: Oxidoreductase]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 00:28:15 2009''~~

OCA at 22:28, 17 February 2009

2009-02-17T22:28:16Z

← Older revision		Revision as of 22:28, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2DWS is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA].		2DWS is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA].

	==Reference==		==Reference==
	pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase., Jacobson F, Pistorius A, Farkas D, De Grip W, Hansson O, Sjolin L, Neutze R, J Biol Chem. 2007 Mar 2;282(9):6347-55. Epub 2006 Dec 5. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17148448 17148448]~~		<ref group="xtra">PMID:17148448</ref><references group="xtra"/>
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	~~[[Category: Single protein]]~~
	[[Category: Jacobson, F.]]		[[Category: Jacobson, F.]]
	[[Category: Copper protein]]		[[Category: Copper protein]]
Line 31:		Line 30:
	[[Category: Denitrification]]		[[Category: Denitrification]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:51:~~02 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:28:15 2009''