Glycera dibranchiata hemoglobin. X-ray structure of carbonmonoxide hemoglobin at 1.5 A resolution

Abstract

The structure of carbonmonoxide Glycera hemoglobin has been determined to 1.5 A resolution by X-ray diffraction. The model, including ordered solvent, has been refined by the method of restrained least-squares to an R-value of 0.146. The positions of 1104 protein atoms and the oxygens of 155 water molecules have been determined with an estimated r.m.s. error of 0.10 to 0.13 A. The r.m.s. errors in protein geometry are 0.027 A for bond distances, 0.038 A for angle distances and 0.012 A for deviations of planar groups from their least-squares planes. The iron lies exactly in the plane of the heme nitrogens and the heme is very slightly domed toward the proximal side. The carbon-oxygen bond in the carbon monoxide ligand is bent 7.9 degrees away from the normal to the plane of the heme nitrogens. The ligand is in close contact with, and slightly removed from the heme normal by distal residues Leu 58(E7) and Val62(E11). Comparison of the CO structure with the 1.5 A deoxy structure shows that the majority of the rather small structural changes occurring upon ligation are mediated by movement of the heme due to shortening of the five iron to nitrogen bonds. There is very little empty space inside the molecule, and no direct channel from the solvent into the heme pocket; however, rotation of the side-chain of the distal leucine residue Leu 58(E6) could provide a ligand pathway.