1b4l - Revision history

OCA at 23:19, 27 December 2023

OCA — Wed, 27 Dec 2023 23:19:43 GMT

←Older revision		Revision as of 23:19, 27 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B4L FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B4L 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]] 1.8Å</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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [https://pdbe.org/1b4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [https://www.ebi.ac.uk/pdbsum/1b4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4l 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [https://pdbe.org/1b4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [https://www.ebi.ac.uk/pdbsum/1b4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SODC_YEAST SODC_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[https://www.uniprot.org/uniprot/SODC_YEAST SODC_YEAST] 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==
		+	*[[Potassium channel 3D structures\|Potassium channel 3D structures]]
	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]		*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
	== References ==		== References ==
Line 38:		Line 39:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	~~[[Category: Superoxide dismutase]]~~	+	[[Category: Balbirnie MM]]
-	[[Category: Balbirnie~~, M M~~]]	+	[[Category: Eisenberg D]]
-	[[Category: Eisenberg, D]]	+	[[Category: Hart PJ]]
-	[[Category: Hart~~, P J~~]]	+	[[Category: Nersissian AM]]
-	[[Category: Nersissian~~, A M~~]]	+	[[Category: Ogihara NL]]
-	[[Category: Ogihara~~, N L~~]]	+	[[Category: Valentine JS]]
-	[[Category: Valentine~~, J S~~]]	+	[[Category: Weiss MS]]
-	[[Category: Weiss~~, M S]]~~	+
-	~~[[Category: Copper]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Superoxide acceptor]]~~	+
-	~~[[Category: Zinc~~]]	+

OCA at 15:04, 2 June 2021

OCA — Wed, 02 Jun 2021 15:04:20 GMT

←Older revision		Revision as of 15:04, 2 June 2021
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	<StructureSection load='1b4l' size='340' side='right'caption='[[1b4l]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1b4l' size='340' side='right'caption='[[1b4l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1B4L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B4L 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [~~http~~://pdbe.org/1b4l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1b4l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4l 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [https://pdbe.org/1b4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [https://www.ebi.ac.uk/pdbsum/1b4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SODC_YEAST SODC_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[[https://www.uniprot.org/uniprot/SODC_YEAST SODC_YEAST]] 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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	==See Also==		==See Also==
-	*[[Superoxide ~~Dismutase~~\|Superoxide ~~Dismutase~~]]	+	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:47, 28 August 2019

OCA — Wed, 28 Aug 2019 16:47:49 GMT

←Older revision		Revision as of 16:47, 28 August 2019
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	==15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE==		==15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE==
-	<StructureSection load='1b4l' size='340' side='right' caption='[[1b4l]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1b4l' size='340' side='right'caption='[[1b4l]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B4L FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B4L FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/1b4l_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/1b4l_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 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1b4l" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1b4l" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Superoxide Dismutase\|Superoxide Dismutase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]

OCA at 11:12, 22 November 2017

OCA — Wed, 22 Nov 2017 11:12:58 GMT

←Older revision		Revision as of 11:12, 22 November 2017
Line 1:		Line 1:
		+
	==15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE==		==15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE==
	<StructureSection load='1b4l' size='340' side='right' caption='[[1b4l]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1b4l' size='340' side='right' caption='[[1b4l]], [[Resolution\|resolution]] 1.80Å' 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://pdbe.org/1b4l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://pdbe.org/1b4l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1b4l" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1b4l" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Superoxide Dismutase\|Superoxide Dismutase]]
	== References ==		== References ==
	<references/>		<references/>
Line 44:		Line 42:
	[[Category: Valentine, J S]]		[[Category: Valentine, J S]]
	[[Category: Weiss, M S]]		[[Category: Weiss, M S]]
		+	[[Category: Copper]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Superoxide acceptor]]		[[Category: Superoxide acceptor]]
		+	[[Category: Zinc]]

OCA at 06:32, 8 February 2016

OCA — Mon, 08 Feb 2016 06:32:15 GMT

←Older revision		Revision as of 06:32, 8 February 2016
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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=1b4l ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:49, 10 September 2015

OCA — Thu, 10 Sep 2015 08:49:39 GMT

←Older revision		Revision as of 08:49, 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://pdbe.org/1b4l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 1b4l" style="background-color:#fffaf0;"></div>

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

OCA at 21:19, 24 December 2014

OCA — Wed, 24 Dec 2014 21:19:54 GMT

←Older revision		Revision as of 21:19, 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SODC_YEAST SODC_YEAST]] 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]]

OCA at 11:09, 22 December 2014

OCA — Mon, 22 Dec 2014 11:09:04 GMT

←Older revision		Revision as of 11:09, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B4L FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B4L 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l 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 34:		Line 34:
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
-	[[Category: Balbirnie, M M.]]	+	[[Category: Balbirnie, M M]]
-	[[Category: Eisenberg, D.]]	+	[[Category: Eisenberg, D]]
-	[[Category: Hart, P J.]]	+	[[Category: Hart, P J]]
-	[[Category: Nersissian, A M.]]	+	[[Category: Nersissian, A M]]
-	[[Category: Ogihara, N L.]]	+	[[Category: Ogihara, N L]]
-	[[Category: Valentine, J S.]]	+	[[Category: Valentine, J S]]
-	[[Category: Weiss, M S.]]	+	[[Category: Weiss, M S]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Superoxide acceptor]]		[[Category: Superoxide acceptor]]

OCA at 03:16, 7 August 2014

OCA — Thu, 07 Aug 2014 03:16:30 GMT

←Older revision		Revision as of 03:16, 7 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1b4l.~~png\|left~~\|200px]]	+	==15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE==
		+	<StructureSection load='1b4l' size='340' side='right' caption='[[1b4l]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1b4l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B4L 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=1b4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b4l RCSB], [http://www.ebi.ac.uk/pdbsum/1b4l 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/b4/1b4l_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 ==
		+	A reaction cycle is proposed for the mechanism of copper-zinc superoxide dismutase (CuZnSOD) that involves inner sphere electron transfer from superoxide to Cu(II) in one portion of the cycle and outer sphere electron transfer from Cu(I) to superoxide in the other portion of the cycle. This mechanism is based on three yeast CuZnSOD structures determined by X-ray crystallography together with many other observations. The new structures reported here are (1) wild type under 15 atm of oxygen pressure, (2) wild type in the presence of azide, and (3) the His48Cys mutant. Final R-values for the three structures are respectively 20.0%, 17.3%, and 20.9%. Comparison of these three new structures to the wild-type yeast Cu(I)ZnSOD model, which has a broken imidazolate bridge, reveals the following: (i) The protein backbones (the "SOD rack") remain essentially unchanged. (ii) A pressure of 15 atm of oxygen causes a displacement of the copper ion 0.37 A from its Cu(I) position in the trigonal plane formed by His46, His48, and His120. The displacement is perpendicular to this plane and toward the NE2 atom of His63 and is accompanied by elongated copper electron density in the direction of the displacement suggestive of two copper positions in the crystal. The copper geometry remains three coordinate, but the His48-Cu bond distance increases by 0.18 A. (iii) Azide binding also causes a displacement of the copper toward His63 such that it moves 1.28 A from the wild-type Cu(I) position, but unlike the effect of 15 atm of oxygen, there is no two-state character. The geometry becomes five-coordinate square pyramidal, and the His63 imidazolate bridge re-forms. The His48-Cu distance increases by 0.70 A, suggesting that His48 becomes an axial ligand. (iv) The His63 imidazole ring tilts upon 15 atm of oxygen treatment and azide binding. Its NE2 atom moves toward the trigonal plane by 0.28 and 0.66 A, respectively, in these structures. (v) The replacement of His48 by Cys, which does not bind copper, results in a five-coordinate square pyramidal, bridge-intact copper geometry with a novel chloride ligand. Combining results from these and other CuZnSOD crystal structures, we offer the outlines of a structure-based cyclic mechanism.

-	~~{{STRUCTURE_1b4l\| PDB=1b4l \| SCENE= }}~~	+	A structure-based mechanism for copper-zinc superoxide dismutase.,Hart PJ, Balbirnie MM, Ogihara NL, Nersissian AM, Weiss MS, Valentine JS, Eisenberg D Biochemistry. 1999 Feb 16;38(7):2167-78. PMID:10026301<ref>PMID:10026301</ref>

-	~~===15 ATMOSPHERE OXYGEN YEAST CU~~/~~ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10026301}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1b4l]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA].~~	+

	==See Also==		==See Also==
	*[[Superoxide Dismutase\|Superoxide Dismutase]]		*[[Superoxide Dismutase\|Superoxide Dismutase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010026301<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]

OCA at 09:15, 20 October 2012

OCA — Sat, 20 Oct 2012 09:15:03 GMT

←Older revision		Revision as of 09:15, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1b4l]] is a 1 chain structure ~~of [[Superoxide Dismutase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA].	+	[[1b4l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4L OCA].

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