3g4y

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[[Image:3g4y.png|left|200px]]
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==Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloromethyl benzene bound to the XE4 cavity==
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<StructureSection load='3g4y' size='340' side='right' caption='[[3g4y]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3g4y]] is a 2 chain structure with sequence 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=3G4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G4Y FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9CL:(CHLOROMETHYL)BENZENE'>9CL</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4sdh|4sdh]], [[3sdh|3sdh]], [[3g46|3g46]], [[3g4q|3g4q]], [[3g4r|3g4r]], [[3g4u|3g4u]], [[3g4v|3g4v]], [[3g4w|3g4w]], [[3g52|3g52]], [[3g53|3g53]]</td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 Scapharca inaequivalvis])</td></tr>
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<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=3g4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g4y RCSB], [http://www.ebi.ac.uk/pdbsum/3g4y PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g4/3g4y_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.
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{{STRUCTURE_3g4y| PDB=3g4y | SCENE= }}
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Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.,Knapp JE, Pahl R, Cohen J, Nichols JC, Schulten K, Gibson QH, Srajer V, Royer WE Jr Structure. 2009 Nov 11;17(11):1494-504. PMID:19913484<ref>PMID:19913484</ref>
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===Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloromethyl benzene bound to the XE4 cavity===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_19913484}}
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==About this Structure==
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[[3g4y]] is a 2 chain structure with sequence 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=3G4Y OCA].
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==See Also==
==See Also==
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*[[Hemoglobin|Hemoglobin]]
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*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:019913484</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Scapharca inaequivalvis]]
[[Category: Scapharca inaequivalvis]]
[[Category: Cohen, J.]]
[[Category: Cohen, J.]]

Revision as of 13:02, 29 September 2014

Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloromethyl benzene bound to the XE4 cavity

3g4y, resolution 1.70Å

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