The structure, chirality and zwitterionic character of potassium adenosine diphosphate dihydrate, KADP.2H₂O

Abstract

IntroductionPotassium adenosine diphosphate dihydrate, K +.C10 HNNSOIOP~-. 2H20 , crystallizes in the orthorhombic space group P2~2~2 with four molecules in a unit cell of dimensions a --28.491 (6), b --10.446 (3) and c = 6.316 (1) A. The structure was solved by direct methods and refined to an R index of 0.062 (R w = 0.076) on 1384 intensities. The mean e.s.d.'s in bond lengths and angles are 0.013 A and 0.7 ° respectively. The crystal structure has revealed that the adenosine diphosphate exists as a zwitterion with N(1) of the base protonated and the pyrophosphate group dinegatively charged (one negative charge on each phosphate) and has provided details of the molecular conformation and chirality of the chelate ring. The two water molecules in the asymmetric unit are distributed over three positions, two on the same diad axis and one in a general position. The molecule is folded into one of the preferred compact conformations, viz. sugar pucker 2E (P---163.3 °, r m = 38.3°), the exocyclic C(4')-C(5') bond torsion angle ~ gauche + (57.8 °) and the glycosyl torsion angle X anti (32.4°), with an anionic oxygen of the o-phosphate and the hydroxyl oxygen of the fl-phosphate ligated to the K + ion. A second anionic oxygen of the fl-phosphate forms a slightly weaker coordination to the metal; thus, the metal ion is engaged in an tt,fl, fl chelate complex. In addition, the metal ion is coordinated to the base N(3), the ribose 0(2'), the anionic phosphate oxygen O(13) of neighboring nucleotides, and to one of the water molecules on the diad axis. Thus, the K + ion is surrounded by seven possible ligands. The chirality of the chelate ring corresponds to the A diastereomer. The N(1) and N(6) sites and N(6) and N(7) sites of the adenine base form pairs of hydrogen bonds with the oxygens of the ~-phosphate groups of neighboring molecules. There are no basestacking interactions observed in the structure.

Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP.2H2O

“…Note: Following the submission of this paper we learned of a report on the same structure by Swaminathan & Sundaralingam (1980) (following paper). The two independently determined crystal structures of KADP.2H20 described here (I) and by Swaminathan & Sundaralingam (II) are, in a broad sense, indentical but differ in some details.…”

Quantitative analysis of cation binding to the adenosine nucleotides using the Variable Ionic Strength method: Validation of the Debye–Hückel–Onsager theory of electrophoresis in the absence of counterion binding

“…By contrast, the nitrogen atoms in singly and triply substituted ammonium ions, which are binding ligands, have at least one N-H bond. Since NH 4 1 is a binding ligand (Fig. 1A), the small size of the hydrogen atom apparently allows the positively charged nitrogen atoms to approach the negatively charged phosphate residues sufficiently closely to form a stable complex.…”

Models of metal–nucleoside polyphosphates: structures of unidentate [CoHP2O7(NH3)5].H2O [pentaamminepyrophosphatocobalt(III) monohydrate] and bidentate [CoHP2O7(NH3)4].2H2O [tetraamminepyrophosphatocobalt(III) dihydrate]

“…The crystal structures of the following biological polyphosphates have been reported to date: RbADP (Muller & DeLuke, 1971;Viswamitra, Hosur, Shakked & Kennard, 1976), KADP (Swaminathan & Sundaralingam, 1980), dipotassium uridine 5'-diphosphate (K2UDP) (Viswamitra, Post & Kennard, 1979), NazATP (Kennard et al, 1972), cytidine 5'-diphosphate (CDP) (Viswamitra, Seshadri, Post & Kennard, 1975), CDP- …”

“…6 incorporate a 2'-endo sugar pucker (P = 163 °, r,, = 37 °) and a glycosyl torsion angle in the anti range (X =-32"40) • These values are taken from the crystal structure of KADP recently determined in this laboratory (Swaminathan & Sundaralingam, 1980), and are representative of one class of favored conformations. Possible structures for CoADP were generated by equating atom O(11 l) of [CoHP2OT(NH3) 4] to 0(5') of KADP and adjusting the torsion angles ~0 and co (Fig.…”

“…These models have been generated by combining the metal-phosphate geometries observed in the present crystal structures [CoHP2OT(NH3) 41.2HzO and [CoHzP3OI0(NH3)41.HzO with the adenosine moiety (sugar + base only) from the crystal structure of KADP.2H20 (Swaminathan & Sundaralingam, 1980). Torsion-angle definitions are as follows: Swaminathan & Sundaralingam (1980) Muller & DeLuke (1971) Viswamitra et al (1976) Notes: The ring parameters Q, 0, ~ are as defined by Cremer & Pople (1975). containing the shorter metal-fl-phosphate coordination distance (lower ring in average of the two metal-phosphate oxygen distances in each ring.…”