1as8: Difference between revisions

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-[[Image:1as8.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1as8", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1as8|  PDB=1as8  |  SCENE=  }}
-'''STRUCTURE OF NITRITE BOUND TO REDUCED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE'''
+==STRUCTURE OF NITRITE BOUND TO REDUCED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE==
+<StructureSection load='1as8' size='340' side='right'caption='[[1as8]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1as8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AS8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AS8 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</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=NO2:NITRITE+ION'>NO2</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=1as8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1as8 OCA], [https://pdbe.org/1as8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1as8 RCSB], [https://www.ebi.ac.uk/pdbsum/1as8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1as8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
+== 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/as/1as8_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/main_output.php?pdb_ID=1as8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.
-==Overview==
+Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.,Murphy ME, Turley S, Adman ET J Biol Chem. 1997 Nov 7;272(45):28455-60. PMID:9353305<ref>PMID:9353305</ref>
-The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-AS8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AS8 OCA].
+</div>
+<div class="pdbe-citations 1as8" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications., Murphy ME, Turley S, Adman ET, J Biol Chem. 1997 Nov 7;272(45):28455-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9353305 9353305]
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Alcaligenes faecalis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Adman, E T.]]
+[[Category: Adman ET]]
-[[Category: Murphy, M E.P.]]
+[[Category: Murphy MEP]]
-[[Category: Turley, S.]]
+[[Category: Turley S]]
-[[Category: Copper]]
-[[Category: Denitrification]]
-[[Category: Nitrite]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 10:38:25 2008''