PDBsum entry 1dn4

DNA

PDB id: 1dn4

Contents

DNA/RNA

Waters ×61

PDB id:

1dn4

Name:

DNA

Title:

Solvation of the left-handed hexamer d(5brc-g-5brc-g-5brc-g) in crystals grown at two temperatures

Structure:

DNA (5'-d( (Cbr)p Gp (Cbr)p Gp (Cbr)p G)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.133

Authors:

B.Chevrier,A.C.Dock,B.Hartmann,M.Leng,D.Moras,M.T.Thuong,E.Westhof

Key ref:

B.Chevrier et al. (1986). Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures. J Mol Biol, 188, 707-719. PubMed id: 3735433 DOI: 10.1016/S0022-2836(86)80016-X

Date:

01-Dec-86 Release date: 16-Apr-87

DNA/RNA chains

CBR-G-CBR-G-CBR-G 6 bases

CBR-G-CBR-G-CBR-G 6 bases

DOI no: 10.1016/S0022-2836(86)80016-X

J Mol Biol 188:707-719 (1986)

PubMed id: 3735433

Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures.

B.Chevrier, A.C.Dock, B.Hartmann, M.Leng, D.Moras, M.T.Thuong, E.Westhof.

ABSTRACT

Crystals of the hexadeoxyoligomer d(5BrC-G-5BrC-G-5BrC-G) were grown at different temperatures (5 degrees C, 18 degrees C and 37 degrees C) in the absence of divalent cations. The crystals grown at 5 degrees C did not diffract X-rays, while those grown at 18 degrees C and 37 degrees C did. The oligomer adopts the left-handed ZI conformation in both crystals. The main difference resides in a more extensive hydration shell in the crystal grown at high temperature than in the crystal grown at low temperature. The high-temperature crystal displays a spine of hydration running deep in the minor groove and linking exocyclic O-2 atoms of the pyrimidine rings. In both crystalline forms, a hydrated sodium ion bound to the N-7 of a guanine ring was found. Strings of water molecules bridging phosphate anionic oxygen atoms are found along the backbone. The absolute values of the propeller-twist are also different in both structures although the values of the twist are very similar. The results point to the importance of the crystallization conditions when analysing fine structural details like solvation properties of oligomers.

Selected figure(s)

Figure 9.
Figure 9. Stereo iew of the 2 entral bse-pairs with the solvent molecules at 4-0 A from the 2 bromine atoms. Note the 2 water molecules H-bonding to the -4 of the cytosines.

Figure 10.
Figure 10. Stereo view of the C7 to G12 strand with the chai of water molecules bridging the phosphate aninic oxygen atoms.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1986, 188, 707-719) copyright 1986.

Figures were selected by an automated process.