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Preference for Syn conformation: Crystal structures of free acid and ammonium salt of adenosine 2 '-monophosphate: An inhibitor of RNase T-1

Padiyar, GS and Seshadri, TP (1998) Preference for Syn conformation: Crystal structures of free acid and ammonium salt of adenosine 2 '-monophosphate: An inhibitor of RNase T-1. In: Journal of Biomolecular Structure & Dynamics, 15 (4). pp. 793-802.

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Official URL: http://www.jbsdonline.com/Issue-October-2010-c4302...

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) Angstrom, c = 73.422(2) Angstrom, and Z = 12. 2'-AMP.NH4 crystallizes in the trigonal space group P3(1) with a = 9.003(2) Angstrom, c = 34.743(2) Angstrom 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 O4' stacking not seen in the 2'-AMP.NH4 structure. Theoretical and experimental studies on 2'-, 3'- and 5'-AMP structures have been discussed.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Adenine Press.
Department/Centre: Division of Physical & Mathematical Sciences > Physics
Date Deposited: 19 Jul 2010 09:31
Last Modified: 19 Jul 2010 09:31
URI: http://eprints.iisc.ernet.in/id/eprint/19085

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