5AY2

Crystal structure of RNA duplex containing C-Ag(I)-C base pairs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs

Kondo, J.Tada, Y.Dairaku, T.Saneyoshi, H.Okamoto, I.Tanaka, Y.Ono, A.

(2015) Angew Chem Int Ed Engl 54: 13323-13326

  • DOI: 10.1002/anie.201507894
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pair ...

    Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices.


    Organizational Affiliation

    Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686 (Japan).



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')A, B,C,D12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG
Query on AG

Download CCD File 
A, C
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.48α = 90
b = 46.86β = 90
c = 89.94γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations