DSSR-PyMOL cartoon-block schematics: PDB entry 1ply

PDB-id

1ply; DSSR-derived features in text and JSON formats

Class

DNA

Method

fiber diffraction

Summary

Sodium ions and water molecules in the structure of poly d(a)(dot)poly d(t)

Reference

Chandrasekaran R, Radha A, Park HS (1995): "Sodium ions and water molecules in the structure of poly(dA).poly(dT)." Acta Crystallogr.,Sect.D, 51, 1025-1035. doi: 10.1107/S0907444995001880.

Abstract

Analysis of X-ray diffraction data from a polycrystalline and well oriented fiber of the sodium salt of poly(dA).poly(dT) shows that this B'-DNA corresponds to a right-handed antiparallel tenfold double-helix of pitch 32.4 A, with C2'-endo furanose rings in both strands. The helix contrasts itself from B-DNA in terms of a very narrow minor groove. Difference electron-density maps have revealed that a continuous spine of water molecules, two per base pair, propagates along this groove with the same symmetry as the DNA and establishes new links between the two strands. In addition to this hydrated DNA helix, the monoclinic unit cell (space group P2(1)) accommodates about 20 sodium ions and 12 water molecules in the vicinity of phosphate groups. These structured guest molecules provide an intricate network of bridges, ranging in size from a single sodium ion to a multiple sodium-water-water-sodium unit, connecting phosphate groups belonging to adjacent DNA helices. The crystallographic R value for this structure is 0.23 for a total of 102 reflections extending out to 3.2 A resolution.