115D

ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION

Summary for 115D

• Entry DOI: 10.2210/pdb115d/pdb
• Descriptor: DNA (5'-D(*GP*GP*(BRU)P*AP*(BRU)P*AP*CP*C)-3') (2 entities in total)
• Functional Keywords: a-dna, double helix, modified, dna
• Total number of polymer chains: 2
• Total formula weight: 5112.71

Authors

Kennard, O.,Cruse, W.B.T.,Nachman, J.,Prange, T.,Shakked, Z.,Rabinovich, D. (deposition date: 1993-02-12, release date: 1993-07-15, Last modification date: 2024-02-07)

Primary citation

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

PubMed 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.

PubMed: 3271041

Experimental method

X-RAY DIFFRACTION (1.7 Å)