PDBsum entry 1v9g

DNA

PDB id

1v9g

Contents

			DNA/RNA

			Ligands

					SPW


					DOD ×44

References listed in PDB file

Key reference

Title

The hydration structure of a z-Dna hexameric duplex determined by a neutron diffraction technique.

Authors

T.Chatake, I.Tanaka, H.Umino, S.Arai, N.Niimura.

Ref.

Acta Crystallogr D Biol Crystallogr, 2005, 61, 1088-1098. [DOI no: 10.1107/S0907444905015581]

PubMed id

16041074

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.



	Figure 7. Figure 7 A schematic diagram showing the complicated hydration structure in the minor groove between the Gua4-Cyt9 and Gua6-Cyt7 base pairs. The three D[2]O molecules with underlined labels (D[2]O121, D[2]O137 and D[2]O113) are located at the bottom of the minor groove. This diagram includes all covalent bonds within a radius of 7 Å from the O atom of D[2]O137. Yellow broken lines show hydrogen bonds.		Figure 9. Figure 9 A schematic diagram of the hydrogen-bonding networks in the minor groove of the Z-DNA hexamer. (a) Hydrogen bonds bridging N2 amino groups from guanine bases and phosphate groups in the backbone. Arrows show the directions of the hydrogen bonds (from proton donor to acceptor). Broken lines are electrostatic interactions weaker than the hydrogen bond defined in the text. A symmetry-related atom is marked #. (b) Hydrogen bonds bridging O2 keto groups from cytosine bases. Wavy lines represent the connection of the Z-DNA duplex. D[2]O124 has a spherical contour in the neutron 2\|F[o]\| - \|F[c]\| Fourier map; therefore, the interaction between this D[2]O molecule and Z-DNA was ambiguously observed. Note that the hydrogen-bonding scheme in the lower region differs from that in the upper region because the D[2]O113, D[2]O137, D[2]O121 and D[2]O141 molecules mimic the second spermine molecule in the Spr crystal (containing two spermine molecules) as shown in Fig. 4-.

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