2dy2 - Revision history

OCA at 08:32, 25 October 2023

2023-10-25T08:32:02Z

←Older revision		Revision as of 08:32, 25 October 2023
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	<StructureSection load='2dy2' size='340' side='right'caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='2dy2' size='340' side='right'caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DY2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DY2 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></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]] 2.26Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[2dwt\|2dwt]]~~, [[~~2dws~~\|~~2dws]], [[1zv2\|1zv2~~]]~~</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></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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [https://pdbe.org/2dy2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [https://www.ebi.ac.uk/pdbsum/2dy2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy2 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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [https://pdbe.org/2dy2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [https://www.ebi.ac.uk/pdbsum/2dy2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy2 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]]
Line 36:		Line 36:
	__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 11:40, 10 February 2021

2021-02-10T11:40:52Z

←Older revision		Revision as of 11:40, 10 February 2021
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	==Nitrite reductase pH 6.0==		==Nitrite reductase pH 6.0==
-	<StructureSection load='2dy2' size='340' side='right' caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>	+	<StructureSection load='2dy2' size='340' side='right'caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DY2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DY2 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></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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dwt\|2dwt]], [[2dws\|2dws]], [[1zv2\|1zv2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dwt\|2dwt]], [[2dws\|2dws]], [[1zv2\|1zv2]]</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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [~~http~~://pdbe.org/2dy2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dy2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy2 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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [https://pdbe.org/2dy2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [https://www.ebi.ac.uk/pdbsum/2dy2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy2 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Nitrite reductase\|Nitrite reductase]]	+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</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 07:32, 23 May 2018

2018-05-23T07:32:15Z

←Older revision		Revision as of 07:32, 23 May 2018
Line 1:		Line 1:
		+
	==Nitrite reductase pH 6.0==		==Nitrite reductase pH 6.0==
	<StructureSection load='2dy2' size='340' side='right' caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='2dy2' size='340' side='right' caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>
Line 7:		Line 8:
	<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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [http://pdbe.org/2dy2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [http://www.ebi.ac.uk/pdbsum/2dy2 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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [http://pdbe.org/2dy2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [http://www.ebi.ac.uk/pdbsum/2dy2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy2 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/2dy2_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/2dy2_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>
Line 30:		Line 31:

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

OCA at 19:10, 9 February 2016

2016-02-09T19:10:44Z

←Older revision		Revision as of 19:10, 9 February 2016
Line 17:		Line 17:
	<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=2dy2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:13, 11 September 2015

2015-09-11T01:13:37Z

←Older revision		Revision as of 01:13, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2dy2' size='340' side='right' caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='2dy2' size='340' side='right' caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DY2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DY2 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dwt\|2dwt]], [[2dws\|2dws]], [[1zv2\|1zv2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dwt\|2dwt]], [[2dws\|2dws]], [[1zv2\|1zv2]]</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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [http://www.ebi.ac.uk/pdbsum/2dy2 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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [http://pdbe.org/2dy2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [http://www.ebi.ac.uk/pdbsum/2dy2 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2dy2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__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 18:17, 15 January 2015

2015-01-15T18:17:38Z

←Older revision		Revision as of 18:17, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DY2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DY2 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><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dwt\|2dwt]], [[2dws\|2dws]], [[1zv2\|1zv2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dwt\|2dwt]], [[2dws\|2dws]], [[1zv2\|1zv2]]</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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [http://www.ebi.ac.uk/pdbsum/2dy2 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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [http://www.ebi.ac.uk/pdbsum/2dy2 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 04:09, 29 September 2014

2014-09-29T04:09:07Z

←Older revision		Revision as of 04:09, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dy2.~~png~~\|~~left~~\|200px]]	+	==Nitrite reductase pH 6.0==
		+	<StructureSection load='2dy2' size='340' side='right' caption='[[2dy2]], [[Resolution\|resolution]] 2.26Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dy2]] 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=2DY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DY2 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><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dwt\|2dwt]], [[2dws\|2dws]], [[1zv2\|1zv2]]</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=2dy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dy2 RCSB], [http://www.ebi.ac.uk/pdbsum/2dy2 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/dy/2dy2_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_2dy2\| PDB=2dy2 \| 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>

-	~~===Nitrite reductase pH 6.0===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17148448}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2dy2]] 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=2DY2 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 14:50, 20 October 2012

2012-10-20T14:50:45Z

←Older revision		Revision as of 14:50, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2dy2]] 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=2DY2 OCA].	+	[[2dy2]] 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=2DY2 OCA].

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

OCA: Protected "2dy2" [edit=sysop:move=sysop]

2012-07-26T16:27:55Z

Protected "2dy2" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:27, 26 July 2012

OCA at 16:27, 26 July 2012

2012-07-26T16:27:54Z

←Older revision		Revision as of 16:27, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2dy2.png\|left\|200px]]		[[Image:2dy2.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dy2", 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_2dy2\| PDB=2dy2 \| SCENE= }}		{{STRUCTURE_2dy2\| PDB=2dy2 \| SCENE= }}

	===Nitrite reductase pH 6.0===		===Nitrite reductase pH 6.0===

-
-	<!--
-	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==
-	~~2DY2~~ 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=2DY2 OCA].	+	[[2dy2]] 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=2DY2 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 Tue Feb 17 12:06:02 2009''~~	+