2r4z: Difference between revisions

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-{{Seed}}
-[[Image:2r4z.png|left|200px]]
-<!--
+==Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO==
-The line below this paragraph, containing "STRUCTURE_2r4z", creates the "Structure Box" on the page.
+<StructureSection load='2r4z' size='340' side='right'caption='[[2r4z]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2r4z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anadara_inaequivalvis Anadara inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R4Z FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2r4z|  PDB=2r4z  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4z OCA], [https://pdbe.org/2r4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r4z RCSB], [https://www.ebi.ac.uk/pdbsum/2r4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r4z ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLB1_ANAIN GLB1_ANAIN]
+== 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/r4/2r4z_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=2r4z ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.
-===Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO===
+Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis.,Nienhaus K, Knapp JE, Palladino P, Royer WE Jr, Nienhaus GU Biochemistry. 2007 Dec 11;46(49):14018-31. Epub 2007 Nov 15. PMID:18001141<ref>PMID:18001141</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2r4z" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18001141}}, adds the Publication Abstract to the page
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18001141 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18001141}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Anadara inaequivalvis]]
-R4Z is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4Z OCA].
+[[Category: Large Structures]]
+[[Category: Knapp JE]]
-==Reference==
+[[Category: Nienhaus GU]]
-<ref group="xtra">PMID:18001141</ref><references group="xtra"/>
+[[Category: Nienhaus K]]
-[[Category: Scapharca inaequivalvis]]
+[[Category: Palladino P]]
-[[Category: Jr., W E.Royer.]]
+[[Category: Royer Jr WE]]
-[[Category: Knapp, J E.]]
-[[Category: Nienhaus, G U.]]
-[[Category: Nienhaus, K.]]
-[[Category: Palladino, P.]]
-[[Category: Allostery]]
-[[Category: Cytoplasm]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Metal-binding]]
-[[Category: Oxygen affinity]]
-[[Category: Oxygen binding]]
-[[Category: Oxygen storage/transport]]
-[[Category: Oxygen transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:42:17 2009''