Ribosyl group

P2j Z = 2 D = 1.57 R = 0.048 for 931 intensities. The base exists in the thioxo form, with C-8=S and N-7 protonated. The 8-thio substituent causes the base to assume the syn (—102.6°) orientation. The o-ribosyl group is 2T3 (174.8 °, 44.1 °). The exocyclic, C-4 -C-5 bond orientation is trans (—173.2°). This does not favor intramolecular hydrogen-bonding of 0-5 to N-3 of the syn base. The C=S distance is 166.8 pm. The S atom is involved in a weak, acceptor hydrogen-bond to a water molecule, S H-O(w) = 361 pm. The bases are stacked head-to-tail, with overlap of the C=S bonds and the purine ring, in contrast to the known, related structure l-/ -D-ribofuranosyl-2-thioxo-3ff-benzimidazole,197 where similar head-to-tail stacking of the bases involves overlap of the base rings only. 

Ci0HuN5O10P2- C4H12N03+ 2 H20 Adenosine 5 -[tris(hydroxy-methyl)methylammonium diphosphate], dihydrate (HMADPH)203 P2i Z = 2 Dx = 1.65 R = 0.047 for 1,624 reflections. The disposition of the base is anti (75.5°). The D-ribosyl group is T (183.0°, 35.4°) and the orientation about the exocyclic, C-4 - C-5 bond is gauche + (53.7 °). These features are similar to those of the favored conformations adopted by the nucleotide monophosphates. The pyrophosphate chain displays... 

P212121 Z — 8 Dx= 1.57 R = 0.085 for 1,743 intensities. The two independent molecules have similar conformations. The glycosyl dispositions are anti (90.1°, 91.2°), and the D-ribosyl groups are 3T4 (24.0°, 34.1° 15.6°, 35.5°). The exocyclic, C-4 -C-5 bond orientations are gauche+ (63.1°, 53.8°). The orientation of the methyl groups in both molecules is such that it is directed away from the imidazole moiety of the base, that is, the 0-6-C-7 bond is trans to the C-5-C-6 bond this arrangement constitutes an obstacle to formation of Watson-Crick hydrogen-bonds to the complementary base cytosine. In molecule A, 0-6 and C-7 are displaced from the purine plane by 79 and 87 pm, and, in molecule B, by 49 and 16 pm. The bases are stacked. 

P2j Z = 2 DX = 1.43 R = 0.067 for 1269 intensities. The uracil residue is in the anti (63.4°) disposition. The conformation of the D-ribosyl group is 2T3 (176.8°, 37.5°). The orientation about the exocyclic, C-4 -C-5 bond is t (—174.2°). The phenyl and uracil ringsofthe same molecule lie in almost parallel planes, 120 pm apart. The phenyl group is disordered. The uracil ring is sandwiched by the phenyl rings, and vice versa. The 0-1 and N-a atoms of the peptide backbone are hydrogen-bonded to 0-4 and N-3 of atranslationally related uracil to form cyclic dimers. Such interactions serve as models for nucleic acid-protein interactions. [Coordinate errors H(02 ) x should be —1574, instead of —1474 H(Na)2 z should be —145 instead of— 645.]... 

P212121 Z = 4 D, = 1.362 R = 0.162 for 2112 intensities. The structure is very similar to that found308 for air-dried vitamin B12 crystals. Two water molecules move into phosphate oxygen-atom positions when the phosphate in the precursor is removed, and one acetamido group in contact with these water molecules in the vitamin is rotated out of the way in the phosphate. The disposition of the a-D-glycosyl bond between the D-ribosyl group and the 5,6-dimethylbenzimidazole is anti (—45°), and the conformation of the D-ribosyl group is 2T3 (P = 352.1 rm = 47.1). The orientation about the exocyclic, C-4 -C-5 bond is g+ (53°). 

P2J2A Z = 8 Dx = 1.931 R = 0.034 for 2,321 intensities. There are two molecules in the asymmetry unit, and both exhibit the syn disposition (—84.5°, + 76.1°) for the base. The conformation of the D-ribosyl group is 3T4 (28.5°, 39.4°) in molecule A and 3T2 (359.9°, 36.2°) in molecule B. The exocyclic, C-4 -C-5 bond torsion-angle is gauche+ for both molecules (55.2°, 59.7°). The purine bases of the crystallograph-ically independent molecules are paired by N-l-H 0-6 hydrogen bonds across a pseudo-two-fold axis. The bases are stacked such that the Br atoms are tucked under the pyrimidine moiety of the adjacent... 

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