5WSQ

Crystal structure of C-Hg-T pair containing DNA duplex

  • Classification: DNA
  • Organism(s): unidentified

  • Deposited: 2016-12-08 Released: 2017-02-08 
  • Deposition Author(s): Gan, J.H., Liu, H.H.
  • Funding Organization(s): the Key Research and Development Project of China; National Natural Science Foundation of China 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex

Liu, H.H.Cai, C.Haruehanroengra, P.Yao, Q.Q.Chen, Y.Q.Yang, C.Luo, Q.Wu, B.X.Li, J.X.Ma, J.B.Sheng, J.Gan, J.H.

(2017) Nucleic Acids Res. 45: 2910-2918

  • DOI: 10.1093/nar/gkw1296
  • Primary Citation of Related Structures:  5WSP, 5WSR, 5WSS, 5GSK

  • PubMed Abstract: 
  • Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural b ...

    Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-HgII-T containing duplex, three T-HgII-T containing duplexes and one native duplex containing T-T pair without HgII. Our structures suggest that both C-T and T-T pairs are flexible in interacting with the HgII ion with various binding modes including N3-HgII-N3, N4-HgII-N3, O2-HgII-N3 and N3-HgII-O4. Our studies also reveal that the overall conformations of the C-HgII-T and T-HgII-T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C-HgII-T or T-HgII-T containing DNA nanodevices in the future.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*CP*GP*TP*GP*C)-3')A,B8unidentified
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PDO
Query on PDO

Download SDF File 
Download CCD File 
B
1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 37.848α = 90.00
b = 51.138β = 90.00
c = 21.593γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
REFMACrefinement
SHELXDEphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-12-08 
  • Released Date: 2017-02-08 
  • Deposition Author(s): Gan, J.H., Liu, H.H.

Funding OrganizationCountryGrant Number
the Key Research and Development Project of ChinaChina2016YFA0500600
National Natural Science Foundation of ChinaChina31370728

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Data collection