The crystal and molecular structure of a dinucleoside phosphate: β-adenosine-2'-β-uridine-5'-phosphoric acid

Abstract

The dinucleoside phosphate A2'P5'U, C19H24N7012P, forms monoclinic crystals from aqueous solution, with a0=9-783, b0= 16.013, co= 8.718 A, fl=90"79 ° and two molecules in the unit cell, together with eight molecules of water. The space group is P2~. The phosphate group was located by a rigidbody search and least-squares fit to the sharpened Patterson distribution, and the remainder of the structure was then determined by Fourier methods, phasing first with the phosphate and then with successively increasing numbers of atoms. After least-squares refinement, all of the hydrogen atoms whose positions are fixed by the molecular framework were found in difference maps; some of the others were also indicated. The final R index was 0.060 for 1781 observed reflections. The molecular topography shows no unexpected features, and is compared with related molecules; a detailed summary of the conformations of phosphate diesters is included. Each A2'P5'U molecule is hydrogen-bonded to four adjacent nucleotide molecules and nine water molecules; no hydrogen bonds link base moeities directly, but the bases are stacked so that they overlap slightly, with an average interplanar separation of about 3.4/~. Close contacts of furanose-ring oxygen atoms with nearby bases are also present, as in some other structures of nucleic acid fragments.

The crystal structure of N,N'-bis-(4-ethoxyphenyl)acetamidinium bis-p-nitrophenylphosphate monohydrate

“…In the phenacaine complex the following values are observed: C (8) Klyne & Prelog (1960), these conformations are ap, sc in the complex with phenacaine and -sc, -sc in the procaine adduct. They are the most commonly observed conformations in phosphate diesters, according to • Shefter, Barlow, Sparks & Trueblood (1969). The dihedral angle between the two COP planes is 126.5 ° in the phenacaine and 101.1 o in the procaine complex which agree with the values expected for these specific Klyne-Prelog conformations, as pointed out by Shefter, Barlow, Sparks & Trueblood (1969).…”

“…These angles are 6.8 and 20.0 ° in phenacaine bis-p-nitrophenylphosphate monohydrate, whereas they are 4.0 and 6.9 ° in procaine bis-p-nitrophenylphosphate. Shefter, Barlow, Sparks & Trueblood (1969) have tabulated the internal rotation angles around the PO bonds and the dihedral angles between the POC planes for all of the phosphate diesters and triesters for which parameters had been reported in the literature at the time. Among the compounds listed by them, L-a-glycerophosphorylcholine (Abrahamson & Pascher, 1966), vitamin Bx2 (Brink-Shoemaker, Cruickshank, Hodgkin, Kamper & Pilling, 1964Hodgkin, Lindsey, Sparks, Trueblood & White, 1962;Lenhert, 1968), and the triphosphate salt NasP3010 (Corbridge, 1960;Davies & Corbridge, 1958) were the only ones Table 6.…”

“…They are the most commonly observed conformations in phosphate diesters, according to • Shefter, Barlow, Sparks & Trueblood (1969). The dihedral angle between the two COP planes is 126.5 ° in the phenacaine and 101.1 o in the procaine complex which agree with the values expected for these specific Klyne-Prelog conformations, as pointed out by Shefter, Barlow, Sparks & Trueblood (1969). The torsion angle around the C-N bond connecting the phenyl ring and its nitro substituent in the bis-p- nitrophenylphosphate ion also reflects the differences in the environment of this anion in the two crystal structures.…”

Conformational Analysis of the Nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U from Nuclear Magnetic Resonance and Circular Dichroism Studies

“…This is explained by assuming that the 2'-5'-linked compounds are more compact than their 3'-5' isomers, which assumption is in agreement with the concept of more extensive base-base overlap in 2'-5' nucleotides. The only crystal structure of a 2'-5' dimer known to date was reported by Shefter et al [12]. In the crystal of A2'-5'U the bases are stacked in a right-handed helix so that they overlap slightly with an average interplanar distance of 0.34 nm.…”

The crystal structure of magnesium diethyl phosphate, Mg[PO2(OC2H5)2]2

“…Single-crystal X-ray diffraction analysis of phosphoNesters has provided information on the possible conformations of the sugar-phosphate backbone in polynucleotides and nucleic acids (Shefter, Barlow, Sparks & Trueblood, 1969;Sundaralingam, 1969).…”