DSSR-PyMOL cartoon-block schematics: PDB entry 115d

PDB-id

115d; SNAP-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.7 Å)

Summary

Ordered water structure in an a-DNA octamer at 1.7 angstroms resolution

Reference

Kennard O, Cruse WB, Nachman J, Prange T, Shakked Z, Rabinovich D (1986): "Ordered water structure in an A-DNA octamer at 1.7 A resolution." J.Biomol.Struct.Dyn., 3, 623-647.

Abstract

The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Although the final results are identical the comparison of the two approaches highlights potential problems in the refinement of oligonucleotides when only limited data are available. As part of the analysis the positions of 84 solvent molecules in the asymmetric unit were established. The DNA molecule is highly solvated, particularly the phosphate-sugar back-bone and the functional groups of the bases. The major groove contains, in the central BrU-A-BrU-A region, a ribbon of water molecules forming closed pentagons with shared edges. These water molecules are linked to the base O and N atoms and to the solvent chains connecting the O-1 phosphate oxygen atoms on each strand. The minor groove is also extensively hydrated with a continuous network in the central region and other networks at each end. The pattern of hydration is briefly compared with that observed in the structure of a B-dodecamer.