Structure of myoglobin refined at 2·0 Å resolution: II. Structure of deoxymyoglobin from sperm whale

Abstract

Observed structure amplitudes, together with the calculated phase angles of metmyoglobin derived in the preceding paper, were used for a difference Fourier synthesis of deoxy-minus metmyoglobin. This was followed by refinement of atomic co-ordinates, using alternate cycles of real-space and fourier refinement as described in the preceding paper. The overall accuracy of atomic positions estimated from a plot of the correlation coefficients is 0·28 A, and the mean atomic shift between deoxy and metmyoglobin is 0·23 A. The detailed results show that the displacement of the iron atom from the plane of the porphyrin ring increases from 0·40 to 0·55 A on going from met to deoxy. The displacement is accompanied by a lateral movement of the proximal histidine and movements of helix F and the FG segment towards the EF-corner. One result of these concerted movements is that the important hydrogen bond between the carbonyl oxygen of ile 4FG and the hydroxyl of TYR 23H ‡ seems to be shortened. The amino-terminal part of helix E moves closer to the haem, but the side chain of the distal histidine moves away from the surface of the molecule and from the site where the haem-linked water had been attached to it in metmyoglobin. However, a water molecule remains attached to N(e) if HIS 7E; this water molecule is in contact with the porphyrin, but not with the iron. The changes in tertiary structure of myoglobin in going from the met to the deoxy form are similar to those of haemoglobin, only smaller in scale.