Crystal and molecular structure of L-histidyl-L-serine trihydrate: occurrence of C(alpha)-H...O=C hydrogen bond motif similar to the motif in collagen triple helix and beta-sheets.

L-Histidyl-L-serine (HSN) trihydrate, C9H14N4O4-H2O, crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 4.865(4), b = 15.604(4), c = 18.918(5) and Z = 4. The crystal structure was solved by direct methods and refined to R1 = 0.070 by a full-matrix least-squares method. The peptide exists in a zwitterionic form, with the N-terminus in a protonated form and the C-terminus in an ionized form. The imidazole ring of histidine in its neutral His(epsilon) tautomeric state has conformational angles chi(1)2 of -53.5(7) degrees and chi(21)1 of -55.4(8) degrees and the serine hydroxyl group has chi(1)2 of 68.2(7) degrees. The conformational angles deviate significantly from those of the dipeptide complexed with glycyl-L-glutamic acid in which the histidine is protonated. A noteworthy feature of the crystal packing is the occurrence of a C(alpha)-H O=C hydrogen bond motif similar to that observed in collagen triple helix and beta-sheets.

Preference for syn conformation: crystal structures of free acid and ammonium salt of adenosine 2'-monophosphate: an inhibitor of RNase T1.

This paper reports the crystal structures of free acid and ammonium salt of adenosine 2'-monophosphate (2'-AMP). 2'-AMP crystallizes in the hexagonal space group P6(5)22 with a = 9.530(3) A, c = 73.422(2) A, and Z= 12. 2'-AMP.NH4 crystallizes in the trigonal space group P3(1) with a = 9.003(2) A, c = 34.743(2) A and Z= 6. Both the structures were solved by direct methods and refined by full matrix least- squares method to final R factors of 0.080 and 0.038 for 2'-AMP and 2'-AMP.NH4 respectively. The adenine bases of both the structures are in syn conformation contrasting with the anti geometry in 3'-AMP, 5'-AMP and the enzyme bound state. Ribose moiety of 2'-AMP is in C2' -endo conformation. However, the ribose moieties of both the nucleotide molecules display C2'-endo-C3'-exo twist conformation in 2'- AMP.NH4 structure. Both structures demonstrate g+ conformation about C4' -C5' bond. 2'-AMP and one of the nucleotide molecules of 2'-AMP.NH4 are protonated at N1 and the ammonium ion is involved in a bifurcated hydrogen bond with O3' B and O3A atoms. A characteristic feature of both the structures is the intramolecular O5' -N3 hydrogen bond. Our crystallographic results on 2'-AMP corroborates the earlier conclusion that the enzyme-bound state is not the lowest energy state of this nucleotide. 2' -AMP displays base-ribose 04' stacking not seen in the 2'-AMP.NH4 structure. Theoretical and experimental studies on 2'-, 3'- and 5'-AMP structures have been discussed.

Metal-nucleotide interactions: crystal structures of alkali (Li+, Na+, K+) and alkaline earth (Ca2+, Mg2+) metal complexes of adenosine 2'-monophosphate.

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 P2(1) with a = 7.472(3)A, b = 26.853(6) A, c = 9.184(1)A, b = 113.36(1)A and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P3(1) and P3(1)21 with a = 8.762(1)A, c = 34.630(5)A, Z= 6 and a = 8.931(4), Ac = 34.852(9)A and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6(5)22 and P2(1) with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 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 O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (chiCN = -156.4(2)degrees) 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.K 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 1.99A. 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 OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42A forming an octahedron. A classic example of an exception to the existence of the O5'-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 2.11 A. 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. Manning, Am. Chem. 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.