PDBsum entry 1v9g

DNA

PDB id: 1v9g

Contents

DNA/RNA

Ligands

SPW

DOD ×44

PDB id:

1v9g

Name:

DNA

Title:

Neutron crystallographic analysis of the z-DNA hexamer cgcgcg

Structure:

5'-d( Cp Gp Cp Gp Cp G)-3'. Chain: a, b. Engineered: yes. Other_details: z-DNA duplex

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Authors:

T.Chatake,I.Tanaka,N.Niimura

Key ref:

T.Chatake et al. (2005). The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique. Acta Crystallogr D Biol Crystallogr, 61, 1088-1098. PubMed id: 16041074 DOI: 10.1107/S0907444905015581

Date:

26-Jan-04 Release date: 26-Jan-05

DNA/RNA chains

C-G-C-G-C-G 6 bases

C-G-C-G-C-G 6 bases

DOI no: 10.1107/S0907444905015581

Acta Crystallogr D Biol Crystallogr 61:1088-1098 (2005)

PubMed id: 16041074

The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique.

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

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.

Selected figure(s)

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-.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1088-1098) copyright 2005.

Figures were selected by the author.