Silver in PDB 5ay2: Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs

The structure of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs, PDB code: 5ay2 was solved by J.Kondo, Y.Tada, T.Dairaku, H.Saneyoshi, I.Okamoto, Y.Tanaka, A.Ono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.480, 46.860, 89.940, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 18.9

The structure of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Silver atom in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs (pdb code 5ay2). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 4 binding sites of Silver where determined in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs, PDB code: 5ay2:
Jump to Silver binding site number: 1; 2; 3; 4;

Silver binding site 1 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:11.5 occ:1.00 N3 A:C9 2.2 10.9 1.0 N3 B:C4 2.2 11.6 1.0 C2 A:C9 2.9 11.9 1.0 O2 A:C9 2.9 12.8 1.0 C2 B:C4 3.0 11.4 1.0 O2 B:C4 3.0 10.9 1.0 C4 A:C9 3.2 11.7 1.0 C4 B:C4 3.2 12.7 1.0 N4 A:C9 3.4 12.3 1.0 O4 A:U10 3.4 14.7 1.0 N4 B:C4 3.4 14.4 1.0 N6 A:A8 3.4 11.4 1.0 C4 A:U10 3.5 14.5 1.0 N3 A:U10 3.6 14.2 1.0 N6 B:A3 3.6 14.3 1.0 O4 B:U5 3.6 11.6 1.0 N3 B:U5 3.7 10.4 1.0 C4 B:U5 3.7 10.2 1.0 C6 A:A8 3.8 10.9 1.0 N1 A:A8 3.8 11.1 1.0 O A:HOH262 3.8 20.1 1.0 N1 B:A3 4.0 12.9 1.0 C6 B:A3 4.0 13.4 1.0 O B:HOH128 4.1 15.5 0.5 N1 A:C9 4.3 12.2 1.0 N1 B:C4 4.3 10.8 1.0 C5 A:U10 4.4 13.6 1.0 C2 A:U10 4.4 13.7 1.0 C2 B:U5 4.4 12.7 1.0 C5 A:C9 4.5 11.3 1.0 C5 B:C4 4.5 12.7 1.0 C5 B:U5 4.6 11.7 1.0 C2 A:A8 4.8 11.6 1.0 C5 A:A8 4.8 11.7 1.0 O2 B:U5 4.9 13.5 1.0 C6 A:C9 4.9 12.3 1.0 C6 B:C4 4.9 12.1 1.0 O2 A:U10 4.9 13.7 1.0 C2 B:A3 5.0 13.1 1.0

Silver binding site 2 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:12.4 occ:1.00 N3 A:C4 2.2 11.3 1.0 N3 B:C9 2.2 12.7 1.0 C2 A:C4 3.0 12.8 1.0 C2 B:C9 3.0 12.5 1.0 O2 A:C4 3.0 12.8 1.0 O2 B:C9 3.0 14.1 1.0 C4 A:C4 3.1 10.9 1.0 C4 B:C9 3.2 12.8 1.0 N4 A:C4 3.3 11.1 1.0 N4 B:C9 3.3 14.2 1.0 N6 A:A3 3.5 11.2 1.0 N6 B:A8 3.5 12.8 1.0 O4 A:U5 3.5 12.6 1.0 O4 B:U10 3.6 11.6 1.0 N3 B:U10 3.7 11.8 1.0 C4 B:U10 3.7 11.8 1.0 C4 A:U5 3.7 12.9 1.0 N3 A:U5 3.9 13.8 1.0 O B:HOH155 3.9 16.8 0.5 C6 A:A3 3.9 11.2 1.0 O B:HOH167 3.9 17.8 1.0 N1 A:A3 3.9 10.6 1.0 C6 B:A8 4.0 12.6 1.0 O B:HOH132 4.1 20.9 0.5 N1 B:A8 4.1 13.3 1.0 N1 A:C4 4.3 11.9 1.0 N1 B:C9 4.3 12.6 1.0 C2 B:U10 4.4 12.9 1.0 C5 A:U5 4.5 14.1 1.0 C5 B:U10 4.5 12.2 1.0 C5 A:C4 4.5 10.5 1.0 C5 B:C9 4.5 13.4 1.0 C2 A:U5 4.7 17.1 1.0 C2 A:A3 4.9 10.7 1.0 C6 A:C4 4.9 12.4 1.0 O2 B:U10 4.9 13.3 1.0 C6 B:C9 4.9 12.5 1.0 C5 A:A3 4.9 10.4 1.0 C5 B:A8 4.9 12.1 1.0

Silver binding site 3 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag101 b:11.5 occ:1.00 N3 D:C4 2.2 10.6 1.0 N3 C:C9 2.2 13.0 1.0 C2 C:C9 2.9 12.1 1.0 C2 D:C4 2.9 11.2 1.0 O2 C:C9 2.9 13.3 1.0 O2 D:C4 2.9 10.7 1.0 C4 D:C4 3.2 10.8 1.0 C4 C:C9 3.2 11.8 1.0 O4 C:U10 3.3 12.0 1.0 O4 D:U5 3.3 12.5 1.0 N4 D:C4 3.4 11.8 1.0 N4 C:C9 3.4 11.6 1.0 C4 D:U5 3.5 11.5 1.0 N6 D:A3 3.5 11.8 1.0 C4 C:U10 3.5 11.5 1.0 N3 D:U5 3.6 10.9 1.0 N6 C:A8 3.6 12.4 1.0 N3 C:U10 3.7 10.9 1.0 O C:HOH259 3.7 19.1 1.0 N1 C:A8 4.0 12.4 1.0 C6 D:A3 4.1 11.2 1.0 N1 D:A3 4.1 10.7 1.0 C6 C:A8 4.1 11.6 1.0 N1 D:C4 4.3 10.1 1.0 N1 C:C9 4.3 13.5 1.0 C5 D:U5 4.3 11.2 1.0 C5 C:U10 4.4 13.1 1.0 C2 D:U5 4.4 12.6 1.0 C5 D:C4 4.5 10.9 1.0 C5 C:C9 4.5 13.0 1.0 C2 C:U10 4.5 11.7 1.0 O A:HOH204 4.8 32.9 1.0 C6 D:C4 4.9 10.3 1.0 C6 C:C9 4.9 13.6 1.0 O2 D:U5 5.0 13.7 1.0 C6 D:U5 5.0 11.9 1.0

Silver binding site 4 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag102 b:22.0 occ:1.00 N3 C:C4 2.2 22.4 1.0 N3 D:C9 2.3 24.2 1.0 O2 D:C9 3.0 25.2 1.0 C2 D:C9 3.0 24.7 1.0 C2 C:C4 3.1 23.3 1.0 O2 C:C4 3.1 25.3 1.0 C4 C:C4 3.2 22.0 1.0 C4 D:C9 3.3 23.9 1.0 N6 C:A3 3.3 23.7 1.0 N4 C:C4 3.3 21.9 1.0 N6 D:A8 3.4 16.4 1.0 O4 D:U10 3.5 23.1 1.0 N4 D:C9 3.5 22.6 1.0 C4 D:U10 3.6 22.4 1.0 N3 D:U10 3.7 24.5 1.0 O4 C:U5 3.7 21.9 1.0 N3 C:U5 3.8 20.9 1.0 C4 C:U5 3.8 22.1 1.0 C6 D:A8 3.8 17.4 1.0 C6 C:A3 3.9 26.0 1.0 N1 D:A8 3.9 17.1 1.0 N1 C:A3 4.0 25.3 1.0 O C:HOH265 4.1 22.4 1.0 N1 D:C9 4.4 25.4 1.0 N1 C:C4 4.4 24.7 1.0 C5 D:U10 4.4 24.0 1.0 C2 D:U10 4.5 26.2 1.0 C2 C:U5 4.5 23.0 1.0 C5 C:C4 4.6 22.6 1.0 C5 D:C9 4.6 24.2 1.0 C5 C:U5 4.7 21.9 1.0 C5 D:A8 4.8 17.7 1.0 C5 C:A3 4.8 26.9 1.0 C2 D:A8 4.8 17.6 1.0 O2 C:U5 5.0 23.4 1.0 C6 C:C4 5.0 22.5 1.0 C2 C:A3 5.0 27.2 1.0

J.Kondo, Y.Tada, T.Dairaku, H.Saneyoshi, I.Okamoto, Y.Tanaka, A.Ono. 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. V. 54 13323 2015.
ISSN: ESSN 1521-3773
PubMed: 26448329
DOI: 10.1002/ANIE.201507894