Silver in PDB 7eco: Rna Duplex Containing U-Ag-U Base Pairs

The structure of Rna Duplex Containing U-Ag-U Base Pairs, PDB code: 7eco 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)	36.91 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.771, 26.875, 78.944, 90, 101.69, 90
R / Rfree (%)	18.5 / 21.7

The binding sites of Silver atom in the Rna Duplex Containing U-Ag-U Base Pairs (pdb code 7eco). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 6 binding sites of Silver where determined in the Rna Duplex Containing U-Ag-U Base Pairs, PDB code: 7eco:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6;

Silver binding site 1 out of 6 in the Rna Duplex Containing U-Ag-U 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 U-Ag-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Ag101 b:24.6 occ:1.00 N3 F:U4 2.2 17.0 1.0 N3 E:U9 2.2 17.2 1.0 C2 E:U9 3.0 17.6 1.0 C2 F:U4 3.0 22.0 1.0 C4 F:U4 3.0 23.1 1.0 O2 E:U9 3.1 20.2 1.0 O4 F:U4 3.1 23.1 1.0 O2 F:U4 3.1 21.4 1.0 C4 E:U9 3.1 21.3 1.0 O4 E:U9 3.2 21.4 1.0 O6 E:G8 3.4 20.8 1.0 O6 F:G3 3.4 21.6 1.0 N3 E:C10 3.5 21.1 1.0 O F:HOH206 3.5 26.6 1.0 N4 E:C10 3.6 19.8 1.0 N3 F:C5 3.6 19.0 1.0 O E:HOH203 3.7 17.2 1.0 C4 E:C10 3.7 20.6 1.0 N4 F:C5 3.7 22.0 1.0 C6 E:G8 3.8 18.4 1.0 C4 F:C5 3.8 20.5 1.0 N1 E:G8 3.9 17.4 1.0 N1 F:G3 3.9 20.7 1.0 C6 F:G3 3.9 22.0 1.0 C2 E:C10 4.3 20.8 1.0 N1 F:U4 4.3 21.2 1.0 N1 E:U9 4.3 18.4 1.0 C5 F:U4 4.4 25.8 1.0 C2 F:C5 4.4 20.0 1.0 C5 E:U9 4.5 19.1 1.0 C5 E:C10 4.7 23.5 1.0 O2 E:C10 4.7 23.2 1.0 C6 F:U4 4.8 22.6 1.0 O2 F:C5 4.8 21.0 1.0 C5 F:C5 4.9 22.2 1.0 C6 E:U9 4.9 18.4 1.0 C2 E:G8 4.9 18.6 1.0 C5 E:G8 4.9 20.6 1.0 C2 F:G3 5.0 23.1 1.0

Silver binding site 2 out of 6 in the Rna Duplex Containing U-Ag-U 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 U-Ag-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ F:Ag101 b:21.7 occ:1.00 N3 F:U9 2.2 16.0 1.0 N3 E:U4 2.2 20.6 1.0 O4 E:U4 3.0 22.9 1.0 C4 E:U4 3.0 24.2 1.0 C4 F:U9 3.0 17.6 1.0 O4 F:U9 3.1 21.9 1.0 C2 F:U9 3.1 18.3 1.0 C2 E:U4 3.1 24.2 1.0 O2 F:U9 3.2 17.7 1.0 O2 E:U4 3.2 21.7 1.0 N3 F:C10 3.4 18.6 1.0 O E:HOH205 3.5 20.6 1.0 N4 E:C5 3.5 17.2 1.0 C4 E:C5 3.5 18.3 1.0 O6 E:G3 3.5 24.5 1.0 O6 F:G8 3.6 18.9 1.0 C4 F:C10 3.6 21.3 1.0 N3 E:C5 3.6 18.4 1.0 N4 F:C10 3.6 21.2 1.0 O F:HOH219 3.7 19.7 1.0 N1 E:G3 4.0 21.5 1.0 C6 E:G3 4.0 26.3 1.0 C2 F:C10 4.1 20.9 1.0 C6 F:G8 4.1 17.7 1.0 C5 E:C5 4.2 20.8 1.0 C2 E:C5 4.3 21.7 1.0 N1 F:G8 4.3 16.9 1.0 O E:HOH224 4.3 34.6 1.0 C5 E:U4 4.4 22.5 1.0 N1 F:U9 4.4 16.5 1.0 N1 E:U4 4.4 23.0 1.0 C5 F:U9 4.4 19.2 1.0 C5 F:C10 4.4 21.0 1.0 O2 F:C10 4.6 21.9 1.0 C6 E:C5 4.8 20.7 1.0 N1 F:C10 4.8 20.1 1.0 N1 E:C5 4.8 20.6 1.0 C6 E:U4 4.8 23.5 1.0 C6 F:U9 4.9 19.2 1.0 O2 E:C5 4.9 22.1 1.0 C6 F:C10 4.9 20.0 1.0 C2 E:G3 5.0 24.1 1.0

Silver binding site 3 out of 6 in the Rna Duplex Containing U-Ag-U 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 U-Ag-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:24.4 occ:0.68 N3 A:U4 2.1 22.8 1.0 N3 B:U9 2.2 19.5 1.0 C2 B:U9 3.0 22.1 1.0 C4 A:U4 3.0 25.1 1.0 O2 B:U9 3.0 24.2 1.0 O4 A:U4 3.0 26.3 1.0 C2 A:U4 3.0 28.0 1.0 C4 B:U9 3.1 22.4 1.0 O4 B:U9 3.1 20.7 1.0 O2 A:U4 3.2 26.7 1.0 N3 B:C10 3.3 22.4 1.0 N4 A:C5 3.3 24.3 1.0 O A:HOH202 3.5 23.0 1.0 O6 B:G8 3.6 22.2 1.0 C4 A:C5 3.6 26.4 1.0 N3 A:C5 3.6 24.9 1.0 O6 A:G3 3.6 23.3 1.0 O A:HOH201 3.6 30.1 1.0 C4 B:C10 3.7 23.6 1.0 N4 B:C10 3.8 21.3 1.0 N1 A:G3 3.8 24.5 1.0 C6 A:G3 4.0 20.2 1.0 C2 B:C10 4.0 22.6 1.0 C6 B:G8 4.1 22.0 1.0 N1 B:G8 4.2 21.4 1.0 N1 B:U9 4.3 23.8 1.0 N1 A:U4 4.3 25.2 1.0 C5 A:U4 4.3 28.6 1.0 O2 B:C10 4.3 23.5 1.0 C5 B:U9 4.4 21.0 1.0 C5 A:C5 4.5 28.7 1.0 C2 A:C5 4.5 25.2 1.0 C5 B:C10 4.7 26.1 1.0 C6 A:U4 4.7 27.6 1.0 C2 A:G3 4.8 21.4 1.0 C6 B:U9 4.8 22.0 1.0 N1 B:C10 4.9 22.4 1.0 O B:HOH217 5.0 32.4 1.0

Silver binding site 4 out of 6 in the Rna Duplex Containing U-Ag-U 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 U-Ag-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag101 b:28.9 occ:1.00 N3 B:U4 2.1 28.9 1.0 N3 A:U9 2.3 28.1 1.0 C4 B:U4 3.0 28.0 1.0 C2 B:U4 3.0 28.8 1.0 O4 B:U4 3.0 27.8 1.0 C2 A:U9 3.1 25.5 1.0 C4 A:U9 3.2 23.9 1.0 O2 B:U4 3.2 34.0 1.0 O4 A:U9 3.2 27.5 1.0 O2 A:U9 3.2 28.8 1.0 N3 A:C10 3.4 28.7 1.0 O6 B:G3 3.4 24.2 1.0 N3 B:C5 3.5 31.6 1.0 O A:HOH206 3.5 29.1 1.0 N4 B:C5 3.6 28.3 1.0 O B:HOH206 3.6 25.6 1.0 C4 B:C5 3.6 30.1 1.0 O6 A:G8 3.7 27.5 1.0 N1 B:G3 3.7 27.6 1.0 C6 B:G3 3.8 26.7 1.0 C4 A:C10 3.9 27.6 1.0 N4 A:C10 3.9 25.7 1.0 C2 A:C10 4.0 26.4 1.0 N1 A:G8 4.1 26.1 1.0 C6 A:G8 4.1 26.2 1.0 C2 B:C5 4.2 31.1 1.0 O2 A:C10 4.3 28.7 1.0 N1 B:U4 4.3 31.3 1.0 C5 B:U4 4.3 29.4 1.0 N1 A:U9 4.4 25.1 1.0 C5 A:U9 4.5 29.1 1.0 C5 B:C5 4.5 32.5 1.0 C2 B:G3 4.6 29.5 1.0 O2 B:C5 4.7 35.3 1.0 C6 B:U4 4.8 30.7 1.0 C5 B:G3 4.9 27.5 1.0 C5 A:C10 4.9 28.2 1.0 C6 A:U9 5.0 24.8 1.0 N1 B:C5 5.0 30.4 1.0

Silver binding site 5 out of 6 in the Rna Duplex Containing U-Ag-U Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Rna Duplex Containing U-Ag-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag101 b:26.3 occ:1.00 N3 C:U9 2.1 24.9 1.0 N3 D:U4 2.2 25.4 1.0 O4 C:U9 2.8 23.0 1.0 C4 C:U9 2.9 20.0 1.0 O4 D:U4 2.9 24.2 1.0 C4 D:U4 3.0 24.6 1.0 C2 C:U9 3.0 24.2 1.0 C2 D:U4 3.1 27.4 1.0 O2 C:U9 3.2 25.6 1.0 N3 C:C10 3.3 26.8 1.0 O2 D:U4 3.3 29.0 1.0 C4 C:C10 3.4 26.7 1.0 N3 D:C5 3.4 28.4 1.0 C4 D:C5 3.5 29.6 1.0 N4 D:C5 3.5 26.0 1.0 N4 C:C10 3.5 25.6 1.0 O C:HOH105 3.6 28.9 1.0 O6 C:G8 3.6 27.4 1.0 O D:HOH207 3.6 27.0 1.0 O6 D:G3 3.9 24.6 1.0 C2 C:C10 3.9 26.1 1.0 C2 D:C5 4.1 29.6 1.0 C6 C:G8 4.2 28.9 1.0 C5 C:C10 4.2 24.8 1.0 C5 C:U9 4.2 25.1 1.0 C5 D:C5 4.2 30.1 1.0 N1 D:G3 4.2 25.7 1.0 N1 C:G8 4.2 27.0 1.0 N1 C:U9 4.3 22.4 1.0 C5 D:U4 4.3 27.9 1.0 C6 D:G3 4.3 25.6 1.0 N1 D:U4 4.4 26.4 1.0 O2 C:C10 4.4 30.2 1.0 N1 C:C10 4.6 22.2 1.0 C6 C:C10 4.7 23.2 1.0 O2 D:C5 4.7 27.7 1.0 C6 C:U9 4.7 24.0 1.0 N1 D:C5 4.8 28.8 1.0 C6 D:C5 4.8 29.6 1.0 C6 D:U4 4.8 28.8 1.0

Silver binding site 6 out of 6 in the Rna Duplex Containing U-Ag-U Base Pairs


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Rna Duplex Containing U-Ag-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag102 b:32.6 occ:1.00 N3 D:U9 2.2 23.6 1.0 N3 C:U4 2.3 25.9 1.0 O2 C:U4 3.0 30.8 1.0 C2 C:U4 3.0 30.9 1.0 O4 D:U9 3.0 25.3 1.0 C4 D:U9 3.0 24.8 1.0 C2 D:U9 3.1 25.8 1.0 C4 C:U4 3.2 32.4 1.0 O2 D:U9 3.2 27.1 1.0 O4 C:U4 3.3 30.1 1.0 O6 D:G8 3.3 26.1 1.0 N3 D:C10 3.4 29.3 1.0 O6 C:G3 3.5 30.7 1.0 N4 C:C5 3.5 26.1 1.0 N3 C:C5 3.6 26.8 1.0 N4 D:C10 3.6 27.4 1.0 C4 D:C10 3.7 26.4 1.0 C4 C:C5 3.7 29.4 1.0 O D:HOH205 3.8 25.4 1.0 C6 D:G8 3.9 27.2 1.0 N1 C:G3 3.9 29.8 1.0 C6 C:G3 4.0 31.1 1.0 N1 D:G8 4.0 26.2 1.0 C2 D:C10 4.2 27.6 1.0 N1 C:U4 4.4 30.3 1.0 C5 D:U9 4.4 24.1 1.0 N1 D:U9 4.4 26.0 1.0 C2 C:C5 4.4 27.6 1.0 C5 C:U4 4.5 37.4 1.0 O2 D:C10 4.6 31.1 1.0 C5 D:C10 4.7 29.1 1.0 C5 C:C5 4.7 31.9 1.0 O2 C:C5 4.8 26.6 1.0 C6 D:U9 4.9 24.4 1.0 C6 C:U4 4.9 33.9 1.0 C2 C:G3 5.0 29.9 1.0 C5 D:G8 5.0 27.2 1.0

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