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PDBsum entry 2r4x
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Oxygen binding
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PDB id
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2r4x
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References listed in PDB file
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Key reference
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Title
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Ligand migration and binding in the dimeric hemoglobin of scapharca inaequivalvis.
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Authors
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K.Nienhaus,
J.E.Knapp,
P.Palladino,
W.E.Royer,
G.U.Nienhaus.
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Ref.
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Biochemistry, 2007,
46,
14018-14031.
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PubMed id
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Abstract
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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.
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