1dxd | pdb_00001dxd

Photolyzed CO complex of Myoglobin Mb-YQR at 20K

spinqualitylabelsall models 1dxd, resolution 1.40Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1dxd is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CMO, HEM, SO4 Related: 1dxc Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-A resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe-CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 A from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F., Jr., Kuntz, I. D. & Petsko, G. A. (1984) Biochemistry 23, 2849-2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng et al. (1994) Nat. Struct. Biol. 1, 701-705] and room temperature [Srajer et al. (1996) Science 274, 1726-1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein. The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin.,Brunori M, Vallone B, Cutruzzola F, Travaglini-Allocatelli C, Berendzen J, Chu K, Sweet RM, Schlichting I Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2058-63. PMID:10681426 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Myoglobin 3D structures

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