Silver in PDB 7ecp: Rna Duplex Containing C-Ag-U

The structure of Rna Duplex Containing C-Ag-U, PDB code: 7ecp 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)	31.45 / 2.91
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	88.968, 88.968, 33.326, 90, 90, 90
R / Rfree (%)	15.4 / 22.6

The binding sites of Silver atom in the Rna Duplex Containing C-Ag-U (pdb code 7ecp). 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-U, PDB code: 7ecp:
Jump to Silver binding site number: 1; 2; 3; 4;

Silver binding site 1 out of 4 in the Rna Duplex Containing C-Ag-U


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-U within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:13.7 occ:1.00 N3 A:U9 2.1 13.1 1.0 N3 B:C4 2.1 9.0 1.0 O2 B:C5 2.8 15.2 1.0 C4 A:U9 2.8 12.2 1.0 O4 A:U9 2.9 13.3 1.0 N4 B:C4 2.9 6.3 1.0 C4 B:C4 2.9 9.1 1.0 O2 A:C10 2.9 6.3 1.0 C2 A:U9 3.0 11.3 1.0 C2 B:C4 3.1 10.5 1.0 C2 B:C5 3.2 11.1 1.0 C2 A:C10 3.2 7.0 1.0 O2 A:U9 3.2 10.9 1.0 N3 B:C5 3.3 13.6 1.0 O2 B:C4 3.3 17.6 1.0 N3 A:C10 3.4 6.3 1.0 N1 A:C10 4.0 10.6 1.0 N1 A:G8 4.1 14.7 1.0 N1 B:G3 4.1 10.3 1.0 C5 A:U9 4.2 16.5 1.0 N1 B:C5 4.2 11.7 1.0 N2 A:G8 4.2 14.7 1.0 N1 A:U9 4.2 13.3 1.0 C5 B:C4 4.3 11.8 1.0 C4 B:C5 4.3 13.6 1.0 C4 A:C10 4.3 8.7 1.0 N2 B:G3 4.4 12.2 1.0 N1 B:C4 4.4 14.0 1.0 C2 A:G8 4.4 13.8 1.0 C1' A:C10 4.6 12.7 1.0 C2 B:G3 4.6 10.6 1.0 C6 A:U9 4.7 16.9 1.0 C1' B:C5 4.8 15.6 1.0 C6 B:C4 4.8 12.3 1.0 C6 A:G8 4.8 17.0 1.0 C6 A:C10 4.8 11.6 1.0 C6 B:G3 4.9 9.4 1.0 N4 B:C5 4.9 10.0 1.0 O6 B:G3 4.9 8.9 1.0 C5 A:C10 5.0 13.8 1.0

Silver binding site 2 out of 4 in the Rna Duplex Containing C-Ag-U


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-U within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:20.8 occ:1.00 N3 B:U9 2.1 13.5 1.0 N3 A:C4 2.3 18.1 1.0 O4 B:U9 2.8 8.7 1.0 O2 A:C5 2.8 7.9 1.0 C4 B:U9 2.8 10.8 1.0 C2 A:C5 3.1 10.7 1.0 C2 B:U9 3.1 17.5 1.0 O2 B:C10 3.2 12.2 1.0 C2 B:C10 3.2 13.2 1.0 C2 A:C4 3.2 13.1 1.0 C4 A:C4 3.2 14.2 1.0 N4 A:C4 3.2 7.9 1.0 O2 A:C4 3.2 19.1 1.0 N3 B:C10 3.3 10.7 1.0 N3 A:C5 3.3 12.2 1.0 O2 B:U9 3.4 17.1 1.0 N1 B:G8 3.8 12.8 1.0 N2 B:G8 4.0 16.4 1.0 N1 B:C10 4.0 17.4 1.0 C4 B:C10 4.0 12.5 1.0 N1 A:C5 4.0 13.4 1.0 C2 B:G8 4.2 12.9 1.0 C5 B:U9 4.2 14.9 1.0 C4 A:C5 4.2 12.1 1.0 N1 A:G3 4.3 7.4 1.0 N1 B:U9 4.4 20.0 1.0 N1 A:C4 4.5 10.0 1.0 N2 A:G3 4.6 11.4 1.0 C5 A:C4 4.6 12.4 1.0 C6 B:G8 4.6 13.0 1.0 C6 B:C10 4.6 17.8 1.0 C1' A:C5 4.6 17.2 1.0 C1' B:C10 4.7 11.6 1.0 N4 B:C10 4.7 11.4 1.0 C5 B:C10 4.7 20.4 1.0 C6 B:U9 4.8 17.1 1.0 O6 B:G8 4.8 9.0 1.0 C2 A:G3 4.8 11.1 1.0 C6 A:C5 4.9 10.4 1.0 N4 A:C5 4.9 15.9 1.0 C6 A:G3 5.0 11.7 1.0 O6 A:G3 5.0 12.4 1.0 C5 A:C5 5.0 7.2 1.0

Silver binding site 3 out of 4 in the Rna Duplex Containing C-Ag-U


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-U within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag101 b:15.8 occ:1.00 N3 D:U9 2.0 9.7 1.0 N3 C:C4 2.2 11.6 1.0 C2 D:U9 2.8 13.8 1.0 O2 D:U9 2.8 19.6 1.0 C4 D:U9 2.9 9.6 1.0 O2 D:C10 3.0 10.3 1.0 C2 C:C4 3.0 10.3 1.0 O2 C:C4 3.0 19.7 1.0 O4 D:U9 3.0 10.4 1.0 O2 C:C5 3.1 21.2 1.0 C4 C:C4 3.1 18.2 1.0 N3 C:C5 3.1 9.2 1.0 C2 D:C10 3.2 11.0 1.0 C2 C:C5 3.2 14.9 1.0 N4 C:C4 3.2 15.4 1.0 N3 D:C10 3.4 11.4 1.0 N1 D:C10 3.9 10.3 1.0 C4 C:C5 4.0 13.3 1.0 N1 C:C5 4.0 18.1 1.0 N1 D:U9 4.1 18.3 1.0 N1 C:G3 4.2 9.4 1.0 C5 D:U9 4.2 11.9 1.0 C4 D:C10 4.2 10.8 1.0 N1 D:G8 4.3 17.1 1.0 N1 C:C4 4.3 14.4 1.0 N2 C:G3 4.4 17.5 1.0 C5 C:C4 4.4 18.6 1.0 C1' D:C10 4.5 10.5 1.0 N2 D:G8 4.5 17.4 1.0 N4 C:C5 4.5 18.6 1.0 C2 C:G3 4.6 12.9 1.0 C6 D:U9 4.6 14.0 1.0 C6 D:C10 4.7 11.6 1.0 C2 D:G8 4.7 14.8 1.0 C5 C:C5 4.7 12.8 1.0 C1' C:C5 4.7 18.7 1.0 C6 C:C5 4.7 15.6 1.0 C5 D:C10 4.8 12.1 1.0 C6 C:C4 4.9 11.9 1.0 C6 C:G3 4.9 9.1 1.0 O6 C:G3 4.9 16.5 1.0 C6 D:G8 5.0 15.4 1.0 N4 D:C10 5.0 11.0 1.0

Silver binding site 4 out of 4 in the Rna Duplex Containing C-Ag-U


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-U within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag102 b:75.5 occ:1.00 N3 C:U9 2.4 25.8 1.0 N3 D:C4 2.6 12.2 1.0 O4 C:U9 3.0 13.9 1.0 N4 D:C4 3.0 21.5 1.0 C4 C:U9 3.1 20.6 1.0 C4 D:C4 3.2 16.3 1.0 C2 C:U9 3.3 29.8 1.0 O2 D:C5 3.3 20.8 1.0 C2 D:C5 3.4 22.6 1.0 N3 C:C10 3.4 20.0 1.0 N3 D:C5 3.4 17.3 1.0 C2 C:C10 3.5 20.7 1.0 O2 C:U9 3.5 25.0 1.0 O2 C:C10 3.6 18.5 1.0 C2 D:C4 3.6 13.6 1.0 N1 D:G3 3.7 15.9 1.0 O2 D:C4 3.8 17.5 1.0 C4 C:C10 4.0 18.0 1.0 N1 C:G8 4.0 15.3 1.0 N1 D:C5 4.1 25.4 1.0 C4 D:C5 4.1 11.5 1.0 N2 D:G3 4.2 23.7 1.0 N1 C:C10 4.3 19.9 1.0 C2 D:G3 4.3 16.0 1.0 O6 D:G3 4.4 26.4 1.0 C6 D:G3 4.4 22.8 1.0 N2 C:G8 4.4 15.0 1.0 C5 C:U9 4.4 25.1 1.0 N4 C:C10 4.6 13.5 1.0 C2 C:G8 4.6 18.9 1.0 N1 C:U9 4.6 28.8 1.0 C5 D:C4 4.6 14.1 1.0 C6 C:G8 4.7 14.2 1.0 C5 C:C10 4.7 24.6 1.0 N4 D:C5 4.7 8.5 1.0 O6 C:G8 4.8 15.9 1.0 C1' D:C5 4.8 21.3 1.0 C6 D:C5 4.8 20.2 1.0 C6 C:C10 4.8 17.1 1.0 C5 D:C5 4.8 20.3 1.0 N1 D:C4 4.8 15.5 1.0 C1' C:C10 5.0 20.1 1.0 C6 C:U9 5.0 20.1 1.0

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