Three-dimensional fourier synthesis of human deoxyhaemoglobin at 2-5 A resolution: refinement of the atomic model.

The structure of human deoxyhaemoglobin has been refined by fitting atomic co-ordinates to a multiple-isomorphous replacement electron-density map of 2·5 A resolution (Ten Eyck & Arnone, 1975) ; an R -factor of 28·8% was obtained. A subsequent single cycle of Fourier refinement reduced the R -factor to 27·6%. The root-mean-square error in atomic positions, estimated by two independent methods, is 0·40 A for all atoms. The estimated positional error for all alpha carbons is 0·30 A, for alpha carbons of internal segments it is 0·23 A, and for the iron it is 0·10 A. The distance of the iron atom from the porphyrin plane is 0·60 A in the α haem and 0·63 A in the β haem; the distance of the N (ɛ) of the iron-linked histidine from the porphyrin plane is 2·6 A in the α haem and 2·8 A in the β haem. These distances assume a planar porphyrin; the resolution is insufficient to distinguish between a planar conformation and a domed one, with a lesser displacement of the iron from the plane of the porphyrin nitrogens. The distance of C ( γ ) of ValE11 from the ligand site is 3·4 A in the α haem and 1·8 A in the β haem, so that the ligand site in the β haem is blocked. A probable salt bridge between Arg FG4(92) α 1 and Glu CD2(43) β 2 is found in the present structure; as this salt bridge cannot be formed in haemoglobin Chesapeake (Arg FG4α→Leu) it may account for the higher oxygen affinity of the mutant (Gibson & Nagel, 1974) through its effect on the equilibrium between the oxy and deoxy quaternary structures. Comparison of the structures of human and horse deoxyhaemoglobin indicates that significant differences occur only in the region of the amino terminus and the A helix of the β chain: the positions of the centres of mass of the A helices differ by 1·3 A and those of the amino terminal valine residue by 4 to 5 A in the two structures, the separation between the A and E helices being greater in human than in horse deoxyhaemoglobin.