2RT8

Structure of metallo-dna in solution


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation.

Yamaguchi, H.Sebera, J.Kondo, J.Oda, S.Komuro, T.Kawamura, T.Dairaku, T.Kondo, Y.Okamoto, I.Ono, A.Burda, J.V.Kojima, C.Sychrovsky, V.Tanaka, Y.

(2014) Nucleic Acids Res 42: 4094-4099

  • DOI: https://doi.org/10.1093/nar/gkt1344
  • Primary Citation of Related Structures:  
    2RT8

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic, Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan, Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686 Japan, Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')10N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')10N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-06-14
    Changes: Other