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Entry Detail
PDB ID:
8CMM
Keywords:
DNA
Title:
Re-pairing DNA - binding of a ruthenium phi complex to a double mismatch
Biological Source:
Source Organism:
synthetic construct
PDB Version:
Deposition Date:
2023-02-20
Release Date:
2024-03-06
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
0.90 Å
R-Value Free:
0.15
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
I 21 21 21
8CMM validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*GP*CP*TP*AP*TP*AP*AP*TP*GP*CP*G)-3')
Chain IDs:A
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
K
LI
V70
V7F
Primary Citation
Re-pairing DNA: binding of a ruthenium phi complex to a double mismatch.
Chem Sci 15 9096 9103 (2024)
PMID: 38903237 DOI: 10.1039/d4sc01448k

Abstact

We report a crystal structure at atomic resolution (0.9 Å) of a ruthenium complex bound to a consecutive DNA double mismatch, which results in a TA basepair with flipped out thymine, together with the formation of an adenine bulge. The structure shows a form of metalloinsertion interaction of the Λ-[Ru(phen)2phi]2+ (phi = 9,10-phenanthrenediimine) complex at the bulge site. The metal complex interacts with the DNA via the major groove, where specific interactions between the adenines of the DNA and the phen ligands of the complex are formed. One Δ-[Ru(phen)2phi]2+ complex interacts via the minor groove, which shows sandwiching of its phi ligand between the phi ligands of the other two ruthenium complexes, and no interaction of its phen ligands with DNA. To our knowledge, this binding model represents a new form of metalloinsertion in showing major rather than minor groove insertion.

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Primary Citation of related structures
8CMM