3GOM

Barium bound to the Holliday junction sequence d(TCGGCGCCGA)4

Summary for 3GOM

• Entry DOI: 10.2210/pdb3gom/pdb
• Related: 1NVY 1P4Y
• Descriptor: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3', BARIUM ION (3 entities in total)
• Functional Keywords: holliday junction structure, dna
• Total number of polymer chains: 2
• Total formula weight: 6778.62

Authors

Naseer, A.,Cardin, C.J. (deposition date: 2009-03-19, release date: 2009-04-07, Last modification date: 2023-09-06)

Primary citation

Hall, J.P.,O'Sullivan, K.,Naseer, A.,Smith, J.A.,Kelly, J.M.,Cardin, C.J.
Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.
Proc.Natl.Acad.Sci.USA, 108:17610-17614, 2011

PubMed Abstract: We describe a crystal structure, at atomic resolution (1.1 Å, 100 K), of a ruthenium polypyridyl complex bound to duplex DNA, in which one ligand acts as a wedge in the minor groove, resulting in the 51° kinking of the double helix. The complex cation Λ-[Ru(1,4,5,8-tetraazaphenanthrene)(2)(dipyridophenazine)](2+) crystallizes in a 11 ratio with the oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. Each complex binds to one duplex by intercalation of the dipyridophenazine ligand and also by semiintercalation of one of the orthogonal tetraazaphenanthrene ligands into a second symmetrically equivalent duplex. The result is noncovalent cross-linking and marked kinking of DNA.

PubMed: 21969542
DOI: 10.1073/pnas.1108685108

Experimental method

X-RAY DIFFRACTION (2.3 Å)