3s3c: Difference between revisions

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 <StructureSection load='3s3c' size='340' side='right'caption='[[3s3c]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3s3c]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S3C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3s3c]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S3C 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=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</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]] 4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3s33|3s33]], [[3s38|3s38]], [[3s39|3s39]], [[3s3a|3s3a]], [[3s3b|3s3b]], [[3s3d|3s3d]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cbaA, TTHA1135 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbaB, cbac, ctaC, TTHA1134 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbaD, TTHA1133 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3s3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s3c OCA], [https://pdbe.org/3s3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s3c RCSB], [https://www.ebi.ac.uk/pdbsum/3s3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s3c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/COX2_THET8 COX2_THET8]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
+[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-We use a form of "freeze-trap, kinetic-crystallography" to explore the migration of Xe atoms away from the dinuclear heme-a3/CuB center in Thermus thermophilus cytochrome ba3 oxidase. This enzyme is a member of the heme-copper oxidase super-family, and is thus crucial for dioxygen dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O2 diffusion channel in cytochrome ba3 oxidase that is continuous, Y-shaped, 18-20 A in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a3-CuB center in the active site. To understand movement of gas molecules within the O2 channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 seconds while undergoing out-gassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 --&gt; Xe5 --&gt; Xe3 --&gt; Xe4 sites, suggesting that ingress of O2 is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.
-Mobility of Xe atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase.,Luna VM, Fee JA, Deniz AA, Stout CD Biochemistry. 2012 May 19. PMID:22607023<ref>PMID:22607023</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3s3c" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Cytochrome-c oxidase]]
 [[Category: Large Structures]]
-[[Category: Thet8]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Deniz, A A]]
+[[Category: Deniz AA]]
-[[Category: Fee, J A]]
+[[Category: Fee JA]]
-[[Category: Luna, V M]]
+[[Category: Luna VM]]
-[[Category: Stout, C D]]
+[[Category: Stout CD]]
-[[Category: Oxidoreductase]]
-[[Category: Xenon]]