Metal-Nucleotide Interactions: Crystal Structures of Alkali (Li+, Na+, K+) and Alkaline Earth (Ca2+, Mg2+) Metal Complexes of Adenosine 2′ -Monophosphate

Abstract

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2′–monophosphate (2′–AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2′-AMP.Li belongs to the monoclinic space group P21 with a= 7.472(3)Å, b = 26.853(6) Å, c = 9.184(l)Å, b = 113.36(l)Å and Z= 4. 2′-AMP.Na and 2′-AMP.K crystallize in the trigonal space groups P31 and P3 121 with a= 8.762(l)Å, c = 34.630(5)Å, Z= 6 and a= 8.931(4), Åc = 34.852(9)Å and Z= 6 respectively while 2′-AMP.Ca and 2′-AMP.Mg belong to space groups P6522 and P21 with cell parameters a= 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 1 0.023(2), c = 16.506(2), β = 91.1 (0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2′-AMP.Li, 2′-AMP.Na, 2′-AMP.K, 2′AMP. Ca and 2′-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the 05′ -N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry(XCN = -156.4(2)°) in 2′-AMP.Mg. Ribose moieties adopt C2′-endo puckering in 2′-AMP.Li and 2′-AMP.Ca, C2′-endo-C3′-exo twist puckering in 2′-AMP.Na and 2′-AMP. and a C3′-endo-C2′-exo twist puckering in 2′-AMP.Mg structure. The conformation about the exocyclic C4′-C5′ bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g−) conformation observed in 2′ -AMP. Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99Å. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2′ -AMP. Na and 2′ -AMP.K structures is the involvement of ribose 04′ in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OWl, OW2 and 02 and their symmetry mates at distances 2.18 to 2.42Å forming an octahedron. A classic example of an exception to the existence of the 05′-N3 intramolecular hydorgen bond is the 2′-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11Å. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5′ compared to 2′ and 3′ nucleotides (J. Lawless, E. Edelson, and L. Manring, Am. Chern. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur. J. Biochem. 179,451–458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245–336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2′-AMP.Na and 2′-AMP.K structures resemble the 2′-AMP.NH4 structure reported in the previous article. 2′-AMP.Li, 2′-AMP.Ca and 2′-AMP.Mg structures display base-ribose 04′ stacking. An overview of interaction of monovalent and divalent cations with 2′ and 5′-nucleotides has been presented.