5XUV

Crystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4-thiothymine base pairs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine-2Ag(i)-4-thiothymine

Kondo, J.Sugawara, T.Saneyoshi, H.Ono, A.

(2017) Chem. Commun. (Camb.) 53: 11747-11750

  • DOI: 10.1039/c7cc06153f

  • PubMed Abstract: 
  • Herein, we determined a high-resolution crystal structure of a B-form DNA duplex containing consecutive dinuclear metal ion-mediated base pairs, namely, 4-thiothymine-2Ag(i)-4-thiothymine (S-2Ag(i)-S), and four Ag(i) ions form a rectangular network a ...

    Herein, we determined a high-resolution crystal structure of a B-form DNA duplex containing consecutive dinuclear metal ion-mediated base pairs, namely, 4-thiothymine-2Ag(i)-4-thiothymine (S-2Ag(i)-S), and four Ag(i) ions form a rectangular network and the distances between the Ag(i) ions are 2.8-3.2 Å, which may indicate the existence of metallophilic attractions.


    Organizational Affiliation

    Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, 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*(8RO)P*(8RO)P*TP*CP*GP*CP*G)-3')A,B12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
AG
Query on AG

Download SDF File 
Download CCD File 
A, B
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8RO
Query on 8RO
A, B
DNA linkingC10 H15 N2 O6 P SDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.213α = 90.00
b = 40.487β = 90.00
c = 66.432γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
MEXTJapan17H03033

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references