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
  • Primary Citation of Related Structures:  
    5AY2, 5AY4, 5AY3

  • 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 pairs can be easily prepared from commercially available sources ...

    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
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')A, B, C, D12synthetic construct
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    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  (Full details and data files)

    • 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