446D

STRUCTURE OF THE OLIGONUCLEOTIDE D(CGTATATACG) AS A SITE SPECIFIC COMPLEX WITH NICKEL IONS

Summary for 446D

• Entry DOI: 10.2210/pdb446d/pdb
• Descriptor: DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3'), NICKEL (II) ION (3 entities in total)
• Functional Keywords: triple helix, nickel binding, dna
• Total number of polymer chains: 4
• Total formula weight: 12704.30

Authors

Abrescia, N.G.A.,Malinina, L.,Gonzaga, L.F.,Huynh-Dinh, T.,Neidle, S.,Subirana, J.A. (deposition date: 1999-01-15, release date: 1999-03-18, Last modification date: 2024-02-28)

Primary citation

Abrescia, N.G.,Malinina, L.,Fernandez, L.G.,Huynh-Dinh, T.,Neidle, S.,Subirana, J.A.
Structure of the oligonucleotide d(CGTATATACG) as a site-specific complex with nickel ions.
Nucleic Acids Res., 27:1593-1599, 1999

PubMed Abstract: In this paper we explore the application of Ni2+to the crystallization of oligonucleotides. We have determined in this way the structure of a fully alternating (Y-R) decanucleotide d(CGTATATACG) by single crystal X-ray diffraction. This is the first oligonucleotide crystal structure with an alternating 5'-(TA)3-3' central part. Alternating oligonucleotides have a particular interest since they often have a unique structure. In this case the general conformation is B-like with an alternating twist and an end-to-end interaction which involves terminal guanines. The crystal belongs to space group P41212 with a = b = 52.46, c = 101.49 A. This packing imposes a 90 degrees crossing of the symmetry related helices. This is a new way of packing for decamers. The oligonucleotide structure is characterized by the specific association with seven nickel ions, involving the N7 atom of every guanine. One of the Ni2+ions is shared between two guanines of symmetry related molecules. Until now no oligonucleotide has been crystallized in the presence of this metal ion. A novel C.A.T triplet structure has also been tentatively identified.

PubMed: 10075989
DOI: 10.1093/nar/27.7.1593

Experimental method

X-RAY DIFFRACTION (3 Å)