4L24

Crystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs

Kondo, J.Yamada, T.Hirose, C.Okamoto, I.Tanaka, Y.Ono, A.

(2014) Angew.Chem.Int.Ed.Engl. 53: 2385-2388

  • DOI: 10.1002/anie.201309066
  • Primary Citation of Related Structures:  4L25, 4L26

  • PubMed Abstract: 
  • The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containin ...

    The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials.


    Organizational Affiliation

    Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo (Japan). j.kondo@sophia.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')A,B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.500α = 90.00
b = 41.270β = 90.00
c = 64.560γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
CrystalCleardata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release