PDBsum entry 1m6r

DNA

PDB id: 1m6r

Contents

DNA/RNA

Waters ×63

PDB id:

1m6r

Name:

DNA

Title:

Crystal structure of rgd(cgcgcg) forming hexamer z-DNA duplex with 5'- (rg) overhang

Structure:

5'-r( G)d( Cp Gp Cp Gp Cp G)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

1.54Å R-factor: 0.162 R-free: 0.191

Authors:

B.Pan,M.Sundaralingam

Key ref:

B.Pan and M.Sundaralingam (2003). Crystal structure of rGd(CGCGCG): a Z-DNA hexamer duplex with a 5'-(rG) overhang. Acta Crystallogr D Biol Crystallogr, 59, 433-437. PubMed id: 12595699 DOI: 10.1107/S0907444902022655

Date:

17-Jul-02 Release date: 25-Feb-03

DNA/RNA chains

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

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

DOI no: 10.1107/S0907444902022655

Acta Crystallogr D Biol Crystallogr 59:433-437 (2003)

PubMed id: 12595699

Crystal structure of rGd(CGCGCG): a Z-DNA hexamer duplex with a 5'-(rG) overhang.

B.Pan, M.Sundaralingam.

ABSTRACT

The crystal structure of the heptamer rGd(CGCGCG) has been determined at 1.54 A resolution with R(work) and R(free) of 0.191 and 0.235, respectively. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 17.96, b = 31.47, c = 44.73 A and two independent strands in the asymmetric unit. The chimera forms a Z-DNA hexamer duplex d(CGCGCG)(2), with the 5'-overhang rG invisible in the density. The replacement of rG in the 5' terminus of d(GCGCGCG) changes the reverse Hoogsteen G.G base pairing of the 5'-overhang dG (Pan et al., 1997). However, the replacement does not change the helix from Z-form to A-form or the water-structure motifs in the Z-DNA double-helical structure.

Selected figure(s)

Figure 1.
Figure 1 (a) A-form duplex (gCGCGC)[2], (b) Z-form duplex (CGCGCG)[2].

Figure 4.
Figure 4 Hydration of the heptamer structure gCGCGCG. (a) Water structure in the minor groove. The backbones of the heptamer are shown in dark lines as zigzag chains, while hydrogen bonds are shown as dotted lines. (b) Water structure in the major groove. (c) Three different hydration patterns for the phosphate groups.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 433-437) copyright 2003.

Figures were selected by an automated process.