Silver in PDB 7ecn: Rna Duplex Containing C-Ag-A Base Pairs

The structure of Rna Duplex Containing C-Ag-A Base Pairs, PDB code: 7ecn was solved by J.Kondo, A.Tsudura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.97 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.784, 41.482, 45.934, 90, 102.24, 90
R / Rfree (%)	17 / 20.3

The binding sites of Silver atom in the Rna Duplex Containing C-Ag-A Base Pairs (pdb code 7ecn). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 4 binding sites of Silver where determined in the Rna Duplex Containing C-Ag-A Base Pairs, PDB code: 7ecn:
Jump to Silver binding site number: 1; 2; 3; 4;

Silver binding site 1 out of 4 in the Rna Duplex Containing C-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Rna Duplex Containing C-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:17.9 occ:1.00 N1 B:A9 2.1 15.3 1.0 N3 A:C4 2.1 15.7 1.0 O B:HOH245 2.8 24.1 1.0 C2 B:A9 2.9 15.2 1.0 C2 A:C4 2.9 15.2 1.0 O2 A:C4 3.0 13.8 1.0 N4 A:C5 3.0 15.7 1.0 O6 A:G3 3.1 15.3 1.0 C4 A:C4 3.1 17.9 1.0 C6 B:A9 3.1 15.7 1.0 N4 A:C4 3.3 19.2 1.0 N6 B:A9 3.3 18.0 1.0 C4 A:C5 3.4 13.6 1.0 C6 A:G3 3.6 14.0 1.0 N4 B:C10 3.8 14.9 1.0 N1 A:G3 3.9 14.6 1.0 N3 A:C5 4.0 14.1 1.0 C5 A:C5 4.0 13.4 1.0 N3 B:C10 4.0 13.9 1.0 O6 B:G8 4.1 14.5 1.0 C4 B:C10 4.2 12.2 1.0 N3 B:A9 4.2 14.2 1.0 N1 A:C4 4.3 14.2 1.0 C5 B:A9 4.4 14.1 1.0 O A:HOH217 4.4 23.2 1.0 C5 A:C4 4.5 17.5 1.0 C5 A:G3 4.6 15.8 1.0 O A:HOH236 4.6 24.3 1.0 C4 B:A9 4.7 15.0 1.0 O B:HOH238 4.8 20.0 1.0 C6 A:C4 4.9 16.2 1.0 C6 B:G8 4.9 15.1 1.0 C2 A:C5 4.9 15.2 1.0 C6 A:C5 4.9 14.8 1.0 C2 B:C10 5.0 13.4 1.0 C2 A:G3 5.0 15.0 1.0

Silver binding site 2 out of 4 in the Rna Duplex Containing C-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Rna Duplex Containing C-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag101 b:20.1 occ:1.00 N1 A:A9 2.1 15.0 1.0 N3 B:C4 2.1 17.0 1.0 O2 B:C4 2.8 19.4 1.0 C2 B:C4 2.9 16.9 1.0 C2 A:A9 2.9 16.2 1.0 O B:HOH227 3.0 25.2 1.0 C6 A:A9 3.1 15.5 1.0 C4 B:C4 3.1 17.6 1.0 N4 B:C5 3.3 17.1 1.0 N6 A:A9 3.3 17.1 1.0 N4 B:C4 3.3 19.6 1.0 C4 B:C5 3.4 16.8 1.0 O6 B:G3 3.4 16.6 1.0 N4 A:C10 3.7 15.3 1.0 N3 A:C10 3.7 18.0 1.0 N3 B:C5 3.8 15.6 1.0 C6 B:G3 3.8 15.6 1.0 N1 B:G3 3.9 17.0 1.0 C5 B:C5 3.9 15.9 1.0 C4 A:C10 3.9 16.3 1.0 N1 B:C4 4.2 17.3 1.0 N3 A:A9 4.2 16.0 1.0 O6 A:G8 4.4 15.3 1.0 O B:HOH207 4.4 25.5 1.0 C5 A:A9 4.4 15.4 1.0 C5 B:C4 4.4 19.9 1.0 C2 B:C5 4.5 17.0 1.0 C2 A:C10 4.6 17.6 1.0 O B:HOH240 4.6 22.7 1.0 C6 B:C5 4.6 18.6 1.0 C4 A:A9 4.7 17.4 1.0 C6 B:C4 4.8 17.4 1.0 C2 B:G3 4.9 17.2 1.0 C5 B:G3 4.9 16.5 1.0 N1 B:C5 4.9 17.1 1.0 O2 A:C10 4.9 18.9 1.0

Silver binding site 3 out of 4 in the Rna Duplex Containing C-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Rna Duplex Containing C-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag101 b:26.7 occ:0.88 N3 C:C4 2.1 18.4 1.0 N1 D:A9 2.1 15.9 1.0 C2 C:C4 2.9 17.9 1.0 O2 C:C4 2.9 23.1 1.0 C6 D:A9 3.0 21.1 1.0 O C:HOH217 3.0 28.5 1.0 C2 D:A9 3.0 19.2 1.0 N6 D:A9 3.1 20.9 1.0 C4 C:C4 3.1 20.7 1.0 O6 C:G3 3.1 19.7 1.0 N4 C:C5 3.3 23.3 1.0 C4 C:C5 3.3 21.6 1.0 N4 C:C4 3.3 24.8 1.0 N3 C:C5 3.5 21.8 1.0 C6 C:G3 3.5 17.8 1.0 N1 C:G3 3.7 15.4 1.0 N3 D:C10 3.9 16.5 1.0 C5 C:C5 3.9 18.7 1.0 N4 D:C10 3.9 18.5 1.0 O6 D:G8 4.1 13.5 1.0 C4 D:C10 4.2 14.6 1.0 C2 C:C5 4.2 14.7 1.0 N1 C:C4 4.2 21.9 1.0 C5 D:A9 4.3 18.5 1.0 N3 D:A9 4.3 17.5 1.0 C5 C:C4 4.4 22.4 1.0 N1 D:G8 4.5 16.0 1.0 C5 C:G3 4.5 17.0 1.0 C6 C:C5 4.5 17.8 1.0 C6 D:G8 4.6 14.6 1.0 O C:HOH221 4.6 22.5 1.0 N1 C:C5 4.7 14.9 1.0 C2 C:G3 4.7 15.2 1.0 C2 D:C10 4.7 17.6 1.0 C4 D:A9 4.7 18.3 1.0 C6 C:C4 4.8 21.2 1.0 O2 C:C5 4.9 18.8 1.0 O2 D:C10 5.0 19.1 1.0

Silver binding site 4 out of 4 in the Rna Duplex Containing C-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Rna Duplex Containing C-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag101 b:22.0 occ:0.89 N1 C:A9 2.1 19.4 1.0 N3 D:C4 2.1 19.6 1.0 C2 D:C4 2.9 19.5 1.0 O2 D:C4 2.9 20.5 1.0 C2 C:A9 2.9 18.2 1.0 O6 D:G3 3.0 17.7 1.0 O C:HOH235 3.0 28.6 1.0 C6 C:A9 3.1 17.3 1.0 C4 D:C4 3.1 18.4 1.0 N4 D:C5 3.2 22.0 1.0 N6 C:A9 3.3 19.8 1.0 C4 D:C5 3.3 20.5 1.0 N4 D:C4 3.3 22.4 1.0 C6 D:G3 3.4 18.6 1.0 N3 D:C5 3.6 18.7 1.0 N1 D:G3 3.6 17.5 1.0 O6 C:G8 3.9 18.1 1.0 N3 C:C10 3.9 17.6 1.0 N4 C:C10 4.0 17.1 1.0 C5 D:C5 4.0 20.6 1.0 C4 C:C10 4.2 15.7 1.0 N1 D:C4 4.2 21.8 1.0 N3 C:A9 4.2 17.9 1.0 C5 D:G3 4.3 16.8 1.0 O D:HOH203 4.3 28.6 1.0 C5 C:A9 4.4 17.5 1.0 C2 D:C5 4.4 22.0 1.0 C5 D:C4 4.4 18.6 1.0 C6 C:G8 4.6 16.8 1.0 C2 D:G3 4.6 17.9 1.0 N1 C:G8 4.7 16.8 1.0 C6 D:C5 4.7 20.9 1.0 C2 C:C10 4.7 17.8 1.0 C4 C:A9 4.7 15.9 1.0 C6 D:C4 4.8 20.8 1.0 N1 D:C5 4.9 20.1 1.0 O2 C:C10 5.0 19.2 1.0

J.Kondo, A.Tsudura. Rna Duplex Containing C-Ag-A Base Pairs To Be Published.