The structure of horse methaemoglobin at 2.0 Å resolution

R. C. Ladner, Elizabeth J. Heidner, M. F. Perutz

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Abstract

The structure of horse methaemoglobin has been redetermined by phase extension and refinement. This has improved our knowledge of the haem geometry and the stereochemistry of the interfaces between the subunits, and confirmed the disorder of the C-terminal residues. Using new four-circle diffractometer data between the limiting spheres of radius 10 and 2.0 Å-1, the co-ordinates determined by Perutz et al. (1968a,b) were subjected to successive cycles of real-space refinement into electron density maps calculated with observed |F| values and phases derived from the latest refined model, until the reliability index had dropped from an initial value of 0.45 to 0.23. The positions of the iron atoms relative to the planes of the porphyrin rings were refined separately, and checked by Fourier syntheses based on anomalous scattering and by difference Fourier syntheses calculated with coefficients from which the iron contributions had been removed. The general root-mean-squared error in atomic positions is 0.32 Å; the probable error in the displacement of the iron atoms from the porphyrin planes is 0.06 Å. The difference Fourier synthesis, obtained after refinement of the protein was complete, showed 41 bound water molecules per asymmetric unit and also revealed five errors in amino acid sequence, one of which was confirmed chemically. The secondary structures of the subunits are stabilized by hydrogen bonds formed by main-chain NH and CO groups either with each other or with nearby polar side-chains. There are few internal hydrogen bonds linking the various chain segments; many of the external polar side-chains help to stabilize the tertiary structure by forming hydrogen bonds with each other or through bound water molecules. Several of the helical segments are irregular and the terminal residues are disordered. The contacts between the subunits are more polar than the earlier 2.8 Å map had led us to believe, because it had failed to show up the 15 bound water molecules at the α1β1 and the four at the α1β2 contact. Their inclusion has raised the number of hydrogen bonds between neighbouring subunits at α1β1 from five to 17 or possibly 19, and at α1β2 from two to six or possibly seven. The remaining 22 water molecules are distributed over the internal cavity and the molecular surface; most of them make hydrogen bonds with at least two polar groups of the protein. Despite several amino acid differences, the structure of the α1β1 contact, including the bound water, is the same as in human deoxyhaemoglobin (Fermi, 1975).

Original languageEnglish (US)
Pages (from-to)385-413
Number of pages29
JournalJournal of Molecular Biology
Volume114
Issue number3
DOIs
Publication statusPublished - Aug 15 1977

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ASJC Scopus subject areas

  • Virology

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