1srd - Revision history

OCA at 08:34, 1 May 2024

2024-05-01T08:34:35Z

←Older revision		Revision as of 08:34, 1 May 2024
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	<StructureSection load='1srd' size='340' side='right'caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1srd' size='340' side='right'caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Spiol Spiol~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SRD 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=ZN:ZINC+ION'>ZN</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]] 2Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:/~~/~~en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1]~~ </~~span~~></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=ZN:ZINC+ION'>ZN</scene></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=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [https://pdbe.org/1srd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [https://www.ebi.ac.uk/pdbsum/1srd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1srd 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=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [https://pdbe.org/1srd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [https://www.ebi.ac.uk/pdbsum/1srd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1srd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SODCP_SPIOL SODCP_SPIOL]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[https://www.uniprot.org/uniprot/SODCP_SPIOL SODCP_SPIOL] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1srd 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=1srd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach leaves has been determined by X-ray crystal structure analysis. The atomic coordinates were refined at 2.0 A resolution using the Hendrickson and Konnert program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 24.9%, with a root mean square deviation of 0.03 A from the ideal bond length and an average atomic temperature factor of 9.6 A. A dimeric molecule of the enzyme is comprised of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit of 154 amino acid residues is composed primarily of eight anti-parallel beta-strands that form a flattened cylinder, plus three external loops. The main-chain hydrogen bonds primarily link the beta-strands. The overall structure of this enzyme is quite similar to that of the bovine dismutase except for some parts. The single disulfide bridge (Cys57-Cys146) and the salt bridge (Arg79-Asp101) may stabilize the loop regions of the structure. The Cu2+ and Zn2+ ions in the active site lie 6.1 A apart at the bottom of the long channel. The Cu2+ ligands (ND1 of His-46, and NE2 of His-48, -63, and -120) show an uneven tetrahedral distortion from a square plane. The Zn2+ ligands (ND1 of His-63, -71, and -80 and OD1 of Asp-83) show an almost tetrahedral geometry. The imidazole ring of His-63 forms a bridge between the Cu2+ and Zn2+ ions.(ABSTRACT TRUNCATED AT 250 WORDS)
-
-	Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution.,Kitagawa Y, Tanaka N, Hata Y, Kusunoki M, Lee GP, Katsube Y, Asada K, Aibara S, Morita Y J Biochem. 1991 Mar;109(3):477-85. PMID:1880134<ref>PMID:1880134</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1srd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]		*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Spiol]]~~	+	[[Category: Spinacia oleracea]]
-	~~[[Category: Superoxide dismutase~~]]	+	[[Category: Katsube Y]]
-	[[Category: Katsube, Y]]	+	[[Category: Kitagawa Y]]
-	[[Category: Kitagawa, Y]]	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Superoxide acceptor~~]]	+

OCA at 07:36, 22 September 2021

2021-09-22T07:36:14Z

←Older revision		Revision as of 07:36, 22 September 2021
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	<StructureSection load='1srd' size='340' side='right'caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1srd' size='340' side='right'caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SRD 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=ZN:ZINC+ION'>ZN</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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [~~http~~://pdbe.org/1srd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1srd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1srd 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=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [https://pdbe.org/1srd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [https://www.ebi.ac.uk/pdbsum/1srd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1srd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SODCP_SPIOL SODCP_SPIOL]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[[https://www.uniprot.org/uniprot/SODCP_SPIOL SODCP_SPIOL]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Superoxide ~~Dismutase~~\|Superoxide ~~Dismutase~~]]	+	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:36, 18 December 2019

2019-12-18T13:36:28Z

←Older revision		Revision as of 13:36, 18 December 2019
Line 1:		Line 1:

	==Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 Angstroms resolution==		==Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 Angstroms resolution==
-	<StructureSection load='1srd' size='340' side='right' caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1srd' size='340' side='right'caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRD FirstGlance]. <br>
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Spiol]]		[[Category: Spiol]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]

OCA at 07:25, 14 March 2018

2018-03-14T07:25:00Z

←Older revision		Revision as of 07:25, 14 March 2018
Line 1:		Line 1:
		+
	==Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 Angstroms resolution==		==Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 Angstroms resolution==
	<StructureSection load='1srd' size='340' side='right' caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1srd' size='340' side='right' caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 5:		Line 6:
	</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=ZN:ZINC+ION'>ZN</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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://pdbe.org/1srd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd 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=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://pdbe.org/1srd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1srd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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/sr/1srd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sr/1srd_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 10:35, 8 February 2016

2016-02-08T10:35:59Z

←Older revision		Revision as of 10:35, 8 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=1srd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:43, 10 September 2015

2015-09-10T10:43:08Z

←Older revision		Revision as of 10:43, 10 September 2015
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	</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=ZN:ZINC+ION'>ZN</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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd 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=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://pdbe.org/1srd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1srd" style="background-color:#fffaf0;"></div>

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

OCA at 22:43, 24 December 2014

2014-12-24T22:43:17Z

←Older revision		Revision as of 22:43, 24 December 2014
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd 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=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SODCP_SPIOL SODCP_SPIOL]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Spiol]]		[[Category: Spiol]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
-	[[Category: Katsube, Y.]]	+	[[Category: Katsube, Y]]
-	[[Category: Kitagawa, Y.]]	+	[[Category: Kitagawa, Y]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Superoxide acceptor]]		[[Category: Superoxide acceptor]]

OCA at 08:19, 22 October 2014

2014-10-22T08:19:15Z

←Older revision		Revision as of 08:19, 22 October 2014
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-	==~~THREE~~-~~DIMENSIONAL STRUCTURE OF~~ CU,ZN-~~SUPEROXIDE DISMUTASE FROM SPINACH AT~~ 2.0 ~~ANGSTROMS RESOLUTION~~==	+	==Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 Angstroms resolution==
	<StructureSection load='1srd' size='340' side='right' caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1srd' size='340' side='right' caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Spinacia_oleracea Spinacia oleracea~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRD 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=ZN:ZINC+ION'>ZN</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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd 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=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd 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 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Spinacia oleracea~~]]	+	[[Category: Spiol]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Katsube, Y.]]		[[Category: Katsube, Y.]]
	[[Category: Kitagawa, Y.]]		[[Category: Kitagawa, Y.]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Superoxide acceptor]]

OCA at 20:02, 28 September 2014

2014-09-28T20:02:44Z

←Older revision		Revision as of 20:02, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1srd.~~png\|left~~\|200px]]	+	==THREE-DIMENSIONAL STRUCTURE OF CU,ZN-SUPEROXIDE DISMUTASE FROM SPINACH AT 2.0 ANGSTROMS RESOLUTION==
		+	<StructureSection load='1srd' size='340' side='right' caption='[[1srd]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1srd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SRD 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=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1srd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1srd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1srd RCSB], [http://www.ebi.ac.uk/pdbsum/1srd 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/sr/1srd_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 ==
		+	The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach leaves has been determined by X-ray crystal structure analysis. The atomic coordinates were refined at 2.0 A resolution using the Hendrickson and Konnert program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 24.9%, with a root mean square deviation of 0.03 A from the ideal bond length and an average atomic temperature factor of 9.6 A. A dimeric molecule of the enzyme is comprised of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit of 154 amino acid residues is composed primarily of eight anti-parallel beta-strands that form a flattened cylinder, plus three external loops. The main-chain hydrogen bonds primarily link the beta-strands. The overall structure of this enzyme is quite similar to that of the bovine dismutase except for some parts. The single disulfide bridge (Cys57-Cys146) and the salt bridge (Arg79-Asp101) may stabilize the loop regions of the structure. The Cu2+ and Zn2+ ions in the active site lie 6.1 A apart at the bottom of the long channel. The Cu2+ ligands (ND1 of His-46, and NE2 of His-48, -63, and -120) show an uneven tetrahedral distortion from a square plane. The Zn2+ ligands (ND1 of His-63, -71, and -80 and OD1 of Asp-83) show an almost tetrahedral geometry. The imidazole ring of His-63 forms a bridge between the Cu2+ and Zn2+ ions.(ABSTRACT TRUNCATED AT 250 WORDS)

-	~~{{STRUCTURE_1srd\| PDB=1srd \| SCENE= }}~~	+	Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution.,Kitagawa Y, Tanaka N, Hata Y, Kusunoki M, Lee GP, Katsube Y, Asada K, Aibara S, Morita Y J Biochem. 1991 Mar;109(3):477-85. PMID:1880134<ref>PMID:1880134</ref>

-	~~===THREE-DIMENSIONAL STRUCTURE OF CU~~,~~ZN-SUPEROXIDE DISMUTASE FROM SPINACH AT 2.0 ANGSTROMS RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1880134}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1srd]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Spinacia_oleracea Spinacia oleracea]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA].~~	+

	==See Also==		==See Also==
	*[[Superoxide Dismutase\|Superoxide Dismutase]]		*[[Superoxide Dismutase\|Superoxide Dismutase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:001880134<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Katsube, Y.]]		[[Category: Katsube, Y.]]
	[[Category: Kitagawa, Y.]]		[[Category: Kitagawa, Y.]]

OCA at 09:52, 20 October 2012

2012-10-20T09:52:54Z

←Older revision		Revision as of 09:52, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1srd]] is a 4 chain structure ~~of [[Superoxide Dismutase]]~~ with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA].	+	[[1srd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SRD OCA].

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