Crystal structure of 2'-deoxycytidine hemidihydrogenphosphate reveals C+.C base pairs and tight, hydrogen-bonded (H2PO4-)infinity columns (1)

J Biomol Struct Dyn. 1994 Jun;11(6):1287-306. doi: 10.1080/07391102.1994.10508069.

Abstract

2'-Deoxycytidine hemidihydrogenphosphate has been crystallized in the hexagonal space group P6(2) with a = 25.839(3), c = 12.529(1) A. The structure has been solved using the Patterson search method. The asymmetric unit contains two protonated, base-paired 2'-deoxycytidine dimers and two H2PO4- anions. The C+.C base pairs are composed of a protonated and a neutral species each and are triple H-bonded, the central N(3) ... N(3) bonds being 2.850(7) and 2.884(5) A. The conformations of the four nucleosides fall in the same category (sugar puckers 2'-endo, glycosidic links anti) but in one of them the glycosidic torsion angle is quite low with consequences in other geometrical parameters. The H2PO4- anions are located on twofold axes and form two types of tight columns with P ... P separations about 4.18 A. The neighboring units along a column are linked via two very short O ... H ... O hydrogen bonds (O ... O about 2.49 A) leading to effective equalization of the P-O bonds. The base pairs of the two dC+.dC cations are coplanar and form layers perpendicular to the phosphate columns repeating every c/3. Within the layers, the dimers form a network through O(5') ... O(2) hydrogen bonds but their primary intermolecular interactions have the form of H-bond anchors [N(4)-H ... O-P and O(3')-H ... O-P] to the phosphate groups.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Cations
  • Crystallization
  • Crystallography, X-Ray
  • Deoxycytidine / analogs & derivatives*
  • Deoxycytidine / chemistry*
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Structure
  • Nucleic Acid Conformation*
  • Phosphates / chemistry*
  • Spectroscopy, Fourier Transform Infrared

Substances

  • Cations
  • Phosphates
  • Deoxycytidine