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

ABSTRACT

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.