Stereochemistry of nucleic acid constituents. III. Crystal and molecular structure of adenosine 3'-phosphate dihydrate (adenylic acidb)

The crystal structure of adenosine Y-phosphate dihydrate, H14C10NsO7P.2H20, has been solved with three-dimensional integrated Weissenberg intensities. The crystals have space group P2~ and the following lattice constants: a = 9939 + 0005, b = 6343 + 0.002, c = 11.896 + 0.005 /~ and B = 92 ° 13' + 3'. Approximate x and z coordinates were obtained from the results of Brown and co-workers. The y coordinates were determined from molecular models and successive structure factor and Fourier calculations. Refinement was by the method of full-matrix least squares. P, O, N and C atoms were refined anisotropically and the H atoms were refined isotropically. The final R index is 4.3 %. Average standard deviations in atomic positions are: P, 00009/~; O, 0.003 ,~; N, 0-004 A,; C, 0-005/~ and H, 006 A. One of the water molecules displays a planar, nearly trigonal hydrogen bonding pattern, while the the other is involved in a highly distorted tetrahedral hydrogen bonding scheme. H(O2') is simultaneously involved in two hydrogen bonds, one of which is an intramolecular hydrogen bond to the ester oxygen 0(3'). The structure also exhibits a C ( 8 ) H ' ' ' Ow hydrogen bond. The nucleotide exists as a zwitterion with N(1) of the purine protonated by a phosphate proton. The angle between the base and the ribose planes is 55 ° with the glycosidic torsion angle ~0cr~ = -39 °. C(Y) of the ribose is displaced by 0.562 A from the plane of the remaining ring atoms and on the same side as C(5'). The orientation of the C(5')-O(5') bond is unusual in that C(5')-O(5') is trans to C(Y)-C(4') and gauche to O(1')-C(4').