2RT8 image
Deposition Date 2013-06-18
Release Date 2014-03-05
Last Version Date 2024-05-15
Entry Detail
PDB ID:
2RT8
Keywords:
DNA
Title:
Structure of metallo-dna in solution
Biological Source:
Source Organism:
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
100
Conformers Submitted:
17
Selection Criteria:
structures with the lowest energy
2RT8 validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')
Chain IDs:A
Chain Length:10
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')
Chain IDs:B
Chain Length:10
Number of Molecules:1
Biological Source:
Ligand Molecules
HG
Primary Citation
The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation.
Nucleic Acids Res. 42 4094 4099 (2014)
PMID: 24371287 DOI: 10.1093/nar/gkt1344

Abstact

We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem Hg(II)-mediated T-T base pairs (thymine-Hg(II)-thymine, T-Hg(II)-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-Hg(II)-T base pairs whose chemical structure was determined with the (15)N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson-Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T-Hg(II)-T base pair formation. The positive ΔS value arises owing to the Hg(II) dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards Hg(II) and revealed arrangement of T-Hg(II)-T base pairs in metallo-DNA.

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Primary Citation of related structures
2RT8