The structure of vitamin B 12 - VII. The X-ray analysis of the vitamin B 12 coenzyme

Abstract

The three-dimensional molecular structure of coenzyme B$_{12}$ (5'-deoxyadenosylcobalamin) has been determined by X-ray diffraction. The crystals, as grown from an acetone-water solution and photographed wet, are orthorhombic (space group P2$_1$2$_1$2$_1$) with a = 27.93, b = 21.73 and c = 15.34 $\overset{\circ}{\mathrm A}$. Four coenzyme molecules (C$_{72}$H$_{100}$O$_{17}$N$_{18}$PCo) and about 68 water molecules make up the unit cell. 3068 Bragg reflexions, extending to a spacing of 0.9 $\overset{\circ}{\mathrm A}$, were measured with the crystals in contact with their mother liquor. The intensities were estimated visually from Weissenberg films taken with Cu K$\alpha$ radiation. The cobalt atoms were easily located from the Patterson synthesis. The structure was solved in three steps, using first cobalt alone, then cobalt and 53 light atoms, and in the third approximation, 106 atoms, which meluded nearly the full asymmetric unit, except for water and hydrogen. Refinement of the atomic coordinates was accomplished initially by calculation of difference syntheses and finally by differential synthesis. The atomic positions have standard deviations of about 0.04 $\mathrm{\circ}{\mathrm A}$. The conformation of the molecule is very similar to cyanocobalamin. The principal differences are in the orientation of the acetamide and propionamide side chains. Factors which influence the conformation of the corrin nucleus are analysed by comparing several corrinoids of known structure. Features of the molecule which have been examined in detail include the pucker in the pyrroline rings, the bend in the corrin macrocycle, the conformation of the nucleotide and nucleoside moieties and the orientation of the deoxyadenosine moiety with respect to the corrin nucleus. The packing of the molecules and the hydrogen bonding is discussed and compared with that found in the wet and dry vitamin B$_{12}$ crystals. Each coenzyme molecule participates in 18 direct intermolecular hydrogen bonds.