192D

RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)

Summary for 192D

• Entry DOI: 10.2210/pdb192d/pdb
• Descriptor: DNA (5'-D(*CP*CP*GP*CP*GP*G)-3'), SODIUM ION (3 entities in total)
• Functional Keywords: z-dna, double helix, flipped-out bases, dna
• Total number of polymer chains: 2
• Total formula weight: 3643.40

Authors

Malinina, L.,Urpi, L.,Salas, X.,Huynh-Dinh, T.,Subirana, J.A. (deposition date: 1994-09-22, release date: 1995-02-07, Last modification date: 2024-02-07)

Primary citation

Malinina, L.,Urpi, L.,Salas, X.,Huynh-Dinh, T.,Subirana, J.A.
Recombination-like structure of d(CCGCGG).
J.Mol.Biol., 243:484-493, 1994

PubMed Abstract: We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.

PubMed: 7966274
DOI: 10.1006/jmbi.1994.1674

Experimental method

X-RAY DIFFRACTION (1.92 Å)