2oxi - Revision history

OCA at 09:06, 21 February 2024

OCA — Wed, 21 Feb 2024 09:06:48 GMT

←Older revision		Revision as of 09:06, 21 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXI 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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.1Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [https://pdbe.org/2oxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [https://www.ebi.ac.uk/pdbsum/2oxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxi 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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [https://pdbe.org/2oxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [https://www.ebi.ac.uk/pdbsum/2oxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ADH1E_HORSE ADH1E_HORSE]
	== 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=2oxi 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=2oxi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Liver alcohol dehydrogenase (LADH) is a Zn(II)-dependent dimeric enzyme. LADH with the active-site Zn(II) substituted by Cu(II) resembles blue (type I) copper proteins by its spectroscopic characteristics. In this work we present the X-ray structure of the active site Cu(II)-substituted LADH complex with NADH and dimethyl sulfoxide (DMSO). The structure was solved by molecular replacement. The space group is P2(1) with cell dimensions a = 44.4, b = 180.6, c = 50.8 A and beta = 108 degrees. There is one dimer of the enzyme in the asymmetric unit. The refinement was carried out to a crystallographic R-factor of 16.1% for 41 119 unique reflections in the resolution range 12.0 to 2.1 A. The coordination geometry of Cu(II) in LADH is compared with the active-site metal coordination in the Zn-LADH-NADH-DMSO complex and blue-copper proteins. The distances from the metal to the protein ligands (Cys46, His67 and Cys174) are similar for the Zn(II) and Cu(II) ions. The distances of the O atom of the inhibitor DMSO to the Cu(II) ion in the two subunits of the dimer are 3.19 and 3.45 A. These are considerably longer than the corresponding distances for the Zn(II) enzyme, 2.19 and 2.15 A. The Cu(II) ion is positioned nearly in the plane of the three protein ligands (NS(2)) with a geometry similar to the trigonal arrangement of the three strongly bound ligands (N(2)S) in blue-copper proteins. This coordination probably accounts for the similarity of the spectral characteristics of Cu(II)-LADH and type I copper proteins.
-
-	Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 A resolution.,Al-Karadaghi S, Cedergren-Zeppezauer ES, Dauter Z, Wilson KS Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):805-13. PMID:15299812<ref>PMID:15299812</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2oxi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]		*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Al-Karadaghi, S]]	+	[[Category: Al-Karadaghi S]]
-	[[Category: Cedergren-Zeppezauer~~, E S~~]]	+	[[Category: Cedergren-Zeppezauer ES]]

OCA at 20:51, 20 October 2021

OCA — Wed, 20 Oct 2021 20:51:19 GMT

←Older revision		Revision as of 20:51, 20 October 2021
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	<StructureSection load='2oxi' size='340' side='right'caption='[[2oxi]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2oxi' size='340' side='right'caption='[[2oxi]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXI 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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [~~http~~://pdbe.org/2oxi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2oxi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxi 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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [https://pdbe.org/2oxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [https://www.ebi.ac.uk/pdbsum/2oxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxi ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 14:03, 18 December 2019

OCA — Wed, 18 Dec 2019 14:03:56 GMT

←Older revision		Revision as of 14:03, 18 December 2019
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	==REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION==		==REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION==
-	<StructureSection load='2oxi' size='340' side='right' caption='[[2oxi]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2oxi' size='340' side='right'caption='[[2oxi]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OXI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OXI FirstGlance]. <br>
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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/ox/2oxi_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ox/2oxi_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 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 2oxi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2oxi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Alcohol dehydrogenase]]		[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
		+	[[Category: Large Structures]]
	[[Category: Al-Karadaghi, S]]		[[Category: Al-Karadaghi, S]]
	[[Category: Cedergren-Zeppezauer, E S]]		[[Category: Cedergren-Zeppezauer, E S]]

OCA at 07:09, 29 November 2017

OCA — Wed, 29 Nov 2017 07:09:41 GMT

←Older revision		Revision as of 07:09, 29 November 2017
Line 1:		Line 1:
		+
	==REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION==		==REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION==
	<StructureSection load='2oxi' size='340' side='right' caption='[[2oxi]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2oxi' size='340' side='right' caption='[[2oxi]], [[Resolution\|resolution]] 2.10Å' scene=''>
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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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [http://pdbe.org/2oxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [http://www.ebi.ac.uk/pdbsum/2oxi 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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [http://pdbe.org/2oxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [http://www.ebi.ac.uk/pdbsum/2oxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxi ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 16:
	<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=2oxi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 2oxi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2oxi" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:20, 12 September 2015

OCA — Sat, 12 Sep 2015 02:20:59 GMT

←Older revision		Revision as of 02:20, 12 September 2015
Line 5:		Line 5:
	</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [http://www.ebi.ac.uk/pdbsum/2oxi 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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [http://pdbe.org/2oxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [http://www.ebi.ac.uk/pdbsum/2oxi PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 2oxi" style="background-color:#fffaf0;"></div>

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

OCA at 17:57, 19 January 2015

OCA — Mon, 19 Jan 2015 17:57:23 GMT

←Older revision		Revision as of 17:57, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OXI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OXI 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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [http://www.ebi.ac.uk/pdbsum/2oxi 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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [http://www.ebi.ac.uk/pdbsum/2oxi 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: Alcohol dehydrogenase]]		[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
-	[[Category: Al-Karadaghi, S.]]	+	[[Category: Al-Karadaghi, S]]
-	[[Category: Cedergren-Zeppezauer, E S.]]	+	[[Category: Cedergren-Zeppezauer, E S]]

OCA at 10:00, 29 September 2014

OCA — Mon, 29 Sep 2014 10:00:06 GMT

←Older revision		Revision as of 10:00, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2oxi.~~png\|left~~\|200px]]	+	==REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION==
		+	<StructureSection load='2oxi' size='340' side='right' caption='[[2oxi]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2oxi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OXI 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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </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=2oxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oxi RCSB], [http://www.ebi.ac.uk/pdbsum/2oxi 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/ox/2oxi_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 ==
		+	Liver alcohol dehydrogenase (LADH) is a Zn(II)-dependent dimeric enzyme. LADH with the active-site Zn(II) substituted by Cu(II) resembles blue (type I) copper proteins by its spectroscopic characteristics. In this work we present the X-ray structure of the active site Cu(II)-substituted LADH complex with NADH and dimethyl sulfoxide (DMSO). The structure was solved by molecular replacement. The space group is P2(1) with cell dimensions a = 44.4, b = 180.6, c = 50.8 A and beta = 108 degrees. There is one dimer of the enzyme in the asymmetric unit. The refinement was carried out to a crystallographic R-factor of 16.1% for 41 119 unique reflections in the resolution range 12.0 to 2.1 A. The coordination geometry of Cu(II) in LADH is compared with the active-site metal coordination in the Zn-LADH-NADH-DMSO complex and blue-copper proteins. The distances from the metal to the protein ligands (Cys46, His67 and Cys174) are similar for the Zn(II) and Cu(II) ions. The distances of the O atom of the inhibitor DMSO to the Cu(II) ion in the two subunits of the dimer are 3.19 and 3.45 A. These are considerably longer than the corresponding distances for the Zn(II) enzyme, 2.19 and 2.15 A. The Cu(II) ion is positioned nearly in the plane of the three protein ligands (NS(2)) with a geometry similar to the trigonal arrangement of the three strongly bound ligands (N(2)S) in blue-copper proteins. This coordination probably accounts for the similarity of the spectral characteristics of Cu(II)-LADH and type I copper proteins.

-	~~{{STRUCTURE_2oxi\| PDB=2oxi \| SCENE= }}~~	+	Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 A resolution.,Al-Karadaghi S, Cedergren-Zeppezauer ES, Dauter Z, Wilson KS Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):805-13. PMID:15299812<ref>PMID:15299812</ref>

-	~~===REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15299812}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2oxi]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Equus_caballus Equus caballus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA].~~	+

	==See Also==		==See Also==
	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]		*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015299812<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Alcohol dehydrogenase]]		[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
	[[Category: Al-Karadaghi, S.]]		[[Category: Al-Karadaghi, S.]]
	[[Category: Cedergren-Zeppezauer, E S.]]		[[Category: Cedergren-Zeppezauer, E S.]]

OCA at 22:28, 20 October 2012

OCA — Sat, 20 Oct 2012 22:28:26 GMT

←Older revision		Revision as of 22:28, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2oxi]] is a 2 chain structure ~~of [[Alcohol dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA].	+	[[2oxi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA].

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

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

OCA — Fri, 27 Jul 2012 16:25:00 GMT

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

←Older revision

Revision as of 16:25, 27 July 2012

OCA at 16:24, 27 July 2012

OCA — Fri, 27 Jul 2012 16:24:58 GMT

←Older revision		Revision as of 16:24, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2oxi.png\|left\|200px]]		[[Image:2oxi.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2oxi", creates the "Structure Box" on the page.
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	{{STRUCTURE_2oxi\| PDB=2oxi \| SCENE= }}		{{STRUCTURE_2oxi\| PDB=2oxi \| SCENE= }}

	===REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION===		===REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15299812}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15299812 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15299812}}		{{ABSTRACT_PUBMED_15299812}}

	==About this Structure==		==About this Structure==
-	~~2OXI~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA].	+	[[2oxi]] is a 2 chain structure of [[Alcohol dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXI OCA].
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15299812~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015299812</ref><references group="xtra"/>
	[[Category: Alcohol dehydrogenase]]		[[Category: Alcohol dehydrogenase]]
	[[Category: Equus caballus]]		[[Category: Equus caballus]]
	[[Category: Al-Karadaghi, S.]]		[[Category: Al-Karadaghi, S.]]
	[[Category: Cedergren-Zeppezauer, E S.]]		[[Category: Cedergren-Zeppezauer, E S.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:55:33 2009''