5AY2 image
Deposition Date 2015-08-06
Release Date 2015-10-21
Last Version Date 2024-03-20
Entry Detail
PDB ID:
5AY2
Keywords:
RNA
Title:
Crystal structure of RNA duplex containing C-Ag(I)-C base pairs
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.30 Å
R-Value Free:
0.18
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
5AY2 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')
Chain IDs:A, B, C, D
Chain Length:12
Number of Molecules:4
Biological Source:synthetic construct
Ligand Molecules
AG
Primary Citation
High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs
Angew.Chem.Int.Ed.Engl. 54 13323 13326 (2015)
PMID: 26448329 DOI: 10.1002/anie.201507894

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5AY3
5AY4