2r4z: Difference between revisions
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|PDB= 2r4z |SIZE=350|CAPTION= <scene name='initialview01'>2r4z</scene>, resolution 1.60Å | |PDB= 2r4z |SIZE=350|CAPTION= <scene name='initialview01'>2r4z</scene>, resolution 1.60Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <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> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 Scapharca inaequivalvis]) | |GENE= HBI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6561 Scapharca inaequivalvis]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[3sdh|3SDH]], [[4sdh|4SDH]], [[2grh|2GRH]], [[2z85|2Z85]], [[2z8a|2Z8A]], [[2r4w|2R4W]], [[2r4x|2R4X]], [[2r4y|2R4Y]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4z OCA], [http://www.ebi.ac.uk/pdbsum/2r4z PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2r4z RCSB]</span> | |||
}} | }} | ||
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[[Category: Nienhaus, K.]] | [[Category: Nienhaus, K.]] | ||
[[Category: Palladino, P.]] | [[Category: Palladino, P.]] | ||
[[Category: allostery]] | [[Category: allostery]] | ||
[[Category: cytoplasm]] | [[Category: cytoplasm]] | ||
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[[Category: oxygen transport]] | [[Category: oxygen transport]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:56:34 2008'' | ||
Revision as of 04:56, 31 March 2008
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| , resolution 1.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | HBI (Scapharca inaequivalvis) | ||||||
| Related: | 3SDH, 4SDH, 2GRH, 2Z85, 2Z8A, 2R4W, 2R4X, 2R4Y
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO
OverviewOverview
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.
About this StructureAbout this Structure
2R4Z is a Single protein structure of sequence from Scapharca inaequivalvis. Full crystallographic information is available from OCA.
ReferenceReference
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
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