1V9G

Neutron Crystallographic analysis of the Z-DNA hexamer CGCGCG

Summary for 1V9G

• Entry DOI: 10.2210/pdb1v9g/pdb
• Related: 1IOT
• Descriptor: 5'-D(*CP*GP*CP*GP*CP*G)-3', N,N'-BIS(3-AMMONIOPROPYL)BUTANE-1,4-DIAMINIUM (3 entities in total)
• Functional Keywords: z-dna, hydrogen, hydration, h/d exchange, neutron, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 3836.84

Authors

Chatake, T.,Tanaka, I.,Niimura, N. (deposition date: 2004-01-26, release date: 2005-01-26, Last modification date: 2023-10-25)

Primary citation

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

Experimental method

NEUTRON DIFFRACTION (1.8 Å)