Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate.
The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed  in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.
D000244:Adenosine Diphosphate; D003460:Crystallization; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D014325:Tromethamine; D014867:Water; D014961:X-Ray Diffraction
D014325:Tromethamine; D014867:Water; D000244:Adenosine Diphosphate