1G3V

CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2

Summary for 1G3V

• Entry DOI: 10.2210/pdb1g3v/pdb
• Descriptor: 5'-D(*CP*GP*TP*GP*TP*AP*CP*AP*CP*G)-3', NICKEL (II) ION (3 entities in total)
• Functional Keywords: nickel binding, b-dna, dna
• Total number of polymer chains: 4
• Total formula weight: 12649.56

Authors

Subirana, J.A.,Abrescia, N.G.A. (deposition date: 2000-10-25, release date: 2002-01-11, Last modification date: 2024-02-07)

Primary citation

Abrescia, N.A.,Huynh-Dinh, T.,Subirana, J.A.
Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2.
J.Biol.Inorg.Chem., 7:195-199, 2002

PubMed Abstract: The aim of this study was to clarify whether Ni2+ ions could bind to guanine bases in a standard B-DNA duplex and eventually induce a B-->Z transition. We have determined by X-ray crystallography at 3.1 A resolution the structure of the alternating deoxynucleotide d(CGTGTACACG), which contains both internal and terminal guanines. The duplex is in the B form. It is shown that nickel ions bind selectively to the N7 atom of guanine 10, which is in an extra-helical position, and guanine 2, which is in the terminal position of the duplex. It does not bind to guanine 4, which lies within a standard B-DNA tract. This simple but unambiguous result proves that nickel ions select between different guanines via steric accessibility. Guanine-Ni2+-guanine bridges among symmetry-related duplexes have also been found. These bridges may explain why Ni2+ ions may act either as a precipitant or a renaturing agent for DNA under certain conditions. The biochemical interaction of nickel with DNA can thus be related to its capacity to specifically bind to B-DNA regions with exposed guanines. Also, from the structural point of view, we have found a terminal cytosine, which forms a C.G:C reverse-Hoogsteen triple structure with a base pair of a neighbor duplex. This type of triplet is seldom found and is here described for the first time for a DNA structure.

PubMed: 11862555
DOI: 10.1007/s007750100286

Experimental method

X-RAY DIFFRACTION (3.1 Å)