1q0g: Difference between revisions

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 ==Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after full x-ray-induced reduction==
-<StructureSection load='1q0g' size='340' side='right' caption='[[1q0g]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='1q0g' size='340' side='right'caption='[[1q0g]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1q0g]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_seoulensis Streptomyces seoulensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q0G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1q0g]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_seoulensis Streptomyces seoulensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q0G FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1q0d|1q0d]], [[1q0f|1q0f]], [[1q0k|1q0k]], [[1q0m|1q0m]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0g OCA], [https://pdbe.org/1q0g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q0g RCSB], [https://www.ebi.ac.uk/pdbsum/1q0g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0g ProSAT]</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=1q0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0g OCA], [http://pdbe.org/1q0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q0g RCSB], [http://www.ebi.ac.uk/pdbsum/1q0g PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SODN_STRSO SODN_STRSO]
 == 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/q0/1q0g_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q0/1q0g_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].
+</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=1q0g ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.
-Crystal structure of nickel-containing superoxide dismutase reveals another type of active site.,Wuerges J, Lee JW, Yim YI, Yim HS, Kang SO, Djinovic Carugo K Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8569-74. Epub 2004 Jun 1. PMID:15173586<ref>PMID:15173586</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1q0g" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Superoxide Dismutase|Superoxide Dismutase]]
+*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces seoulensis]]
-[[Category: Superoxide dismutase]]
+[[Category: Djinovic Carugo K]]
-[[Category: Carugo, K Djinovic]]
+[[Category: Kang S-O]]
-[[Category: Kang, S O]]
+[[Category: Lee J-W]]
-[[Category: Lee, J W]]
+[[Category: Wuerges J]]
-[[Category: Wuerges, J]]
+[[Category: Yim H-S]]
-[[Category: Yim, H S]]
+[[Category: Yim Y-I]]
-[[Category: Yim, Y I]]
-[[Category: Homohexamer of four-helix bundle]]
-[[Category: Oxidoreductase]]