1V9G

Neutron Crystallographic analysis of the Z-DNA hexamer CGCGCG

1V9G の概要

• エントリーDOI: 10.2210/pdb1v9g/pdb
• 関連するPDBエントリー: 1IOT
• 分子名称: 5'-D(*CP*GP*CP*GP*CP*G)-3', N,N'-BIS(3-AMMONIOPROPYL)BUTANE-1,4-DIAMINIUM (3 entities in total)
• 機能のキーワード: z-dna, hydrogen, hydration, h/d exchange, neutron, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3836.84

構造登録者

Chatake, T.,Tanaka, I.,Niimura, N. (登録日: 2004-01-26, 公開日: 2005-01-26, 最終更新日: 2023-10-25)

主引用文献

Chatake, T.,Tanaka, I.,Umino, H.,Arai, S.,Niimura, N.
The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique.
Acta Crystallogr.,Sect.D, 61:1088-1098, 2005

PubMed Abstract: In order to reveal the hydration structure of Z-DNA, a neutron diffraction study has been carried out at 1.8 A resolution on a Z-DNA hexamer d(CGCGCG). Neutron diffraction data were collected with the BIX-3 single-crystal diffractometer at the JRR-3 reactor in the Japan Atomic Energy Research Institute (JAERI) using a large crystal (1.6 mm3) obtained from D2O solution. It has been found that almost all the guanine bases have participated in H/D exchange at the C8-H8 group, consistent with the acidic nature of this bond. 44 water molecules were found in the nuclear density maps, of which 29 showed the entire contour of all three atoms (D-O-D). The remaining 15 water molecules had a simple spherical shape, indicating that they were rotationally disordered. An interesting relationship was found between the orientational disorder of the water molecules and their locations. Almost all water molecules in the minor groove were well ordered in the crystal, while 40% of the water molecules in the major groove were rotationally disordered. The hydrogen-bonding networks in the hydration shells have two structural aspects: flexibility and regularity.

PubMed: 16041074
DOI: 10.1107/S0907444905015581

実験手法

NEUTRON DIFFRACTION (1.8 Å)