1WQY

X-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal grown in D2O solution

Summary for 1WQY

• Entry DOI: 10.2210/pdb1wqy/pdb
• Related: 167D 1WQZ
• Descriptor: 5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3' (2 entities in total)
• Functional Keywords: b-dna, hydration, hydrogen, dna
• Total number of polymer chains: 2
• Total formula weight: 6088.03

Authors

Arai, S.,Chatake, T.,Ohhara, T.,Kurihara, K.,Tanaka, I.,Suzuki, N.,Fujimoto, Z.,Mizuno, H.,Niimura, N. (deposition date: 2004-10-07, release date: 2005-06-21, Last modification date: 2023-10-25)

Primary citation

Arai, S.,Chatake, T.,Ohhara, T.,Kurihara, K.,Tanaka, I.,Suzuki, N.,Fujimoto, Z.,Mizuno, H.,Niimura, N.
Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements
Nucleic Acids Res., 33:3017-3024, 2005

PubMed Abstract: It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 A resolution X-ray and 3.0 A resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.

PubMed: 15914673
DOI: 10.1093/nar/gki616

Experimental method

X-RAY DIFFRACTION (2 Å)