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2AVH

G4T3G4 dimeric quadruplex structure

Summary for 2AVH
Entry DOI10.2210/pdb2avh/pdb
Related2AVJ
Descriptor5'-D(*GP*GP*GP*GP*TP*TP*TP*GP*GP*GP*G)-3', POTASSIUM ION (3 entities in total)
Functional Keywordsquadruplex, loop, dna
Total number of polymer chains1
Total formula weight3657.66
Authors
Hazel, P.,Parkinson, G.N.,Neidle, S. (deposition date: 2005-08-30, release date: 2006-03-28, Last modification date: 2024-04-03)
Primary citationHazel, P.,Parkinson, G.N.,Neidle, S.
Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex.
J.Am.Chem.Soc., 128:5480-5487, 2006
Cited by
PubMed Abstract: The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA sequence d(G(4)T(3)G(4)) has been determined at 1.5 A resolution, together with that of the brominated analogue d(G(4)(Br)UTTG(4)) at 2.4 A resolution. Both sequences form bimolecular intermolecular G-quadruplexes with lateral loops. d(G(4)(Br)UTTG(4)) crystallized in the monoclinic space group P2(1) with three quadruplex molecules in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and form an eight-G-quartet stack, with a linear array of seven K(+) ions between the quartets. d(G(4)T(3)G(4)) crystallized in the orthorhombic space group C222 and has a structure very similar to the head-to-tail dimer in the P2(1) unit cell. The sequence studied here is able to form several different folds; however, all four quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the analogous quadruplex with T(4) loops. A total of seven independent T(3) loops were observed in the two structures. These can be classified into two discrete conformational classes, suggesting that these represent preferred loop conformations that are independent of crystal-packing forces.
PubMed: 16620121
DOI: 10.1021/ja058577+
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.5 Å)
Structure validation

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