Silver in PDB 7ecl: Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair

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

Resolution Low / High (Å)	42.11 / 3.01
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.252, 43.252, 378.967, 90, 90, 120
R / Rfree (%)	21.8 / 29.3

The structure of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair also contains other interesting chemical elements:

Bromine

(Br)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Silver atom in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair (pdb code 7ecl). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 23 binding sites of Silver where determined in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair, PDB code: 7ecl:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


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 and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:72.7 occ:0.76 N1 B:A9 1.8 45.2 1.0 N3 A:C4 2.2 55.4 1.0 N6 A:A3 2.5 41.0 1.0 C6 B:A9 2.7 48.2 1.0 N6 B:A9 2.8 50.4 1.0 C2 B:A9 2.8 44.8 1.0 N4 A:C4 2.8 56.2 1.0 C4 A:C4 2.9 54.5 1.0 C6 A:A3 3.1 47.4 1.0 O4 A:U5 3.1 47.2 1.0 C2 A:C4 3.3 55.5 1.0 C4 A:U5 3.5 53.8 1.0 O2 A:C4 3.5 54.1 1.0 O4 B:U10 3.5 50.2 1.0 N1 A:A3 3.5 46.5 1.0 N6 B:A8 4.0 49.0 1.0 C5 B:A9 4.0 45.4 1.0 C5 A:A3 4.0 51.9 1.0 C5 A:U5 4.0 54.3 1.0 C4 B:U10 4.1 48.8 1.0 N3 B:A9 4.1 47.4 1.0 N3 A:U5 4.2 50.5 1.0 N3 B:U10 4.2 48.1 1.0 C5 A:C4 4.3 55.2 1.0 N1 B:A8 4.4 44.3 1.0 C4 B:A9 4.4 46.4 1.0 N1 A:C4 4.5 54.0 1.0 C6 B:A8 4.5 47.9 1.0 N7 A:A3 4.6 52.0 1.0 C2 A:A3 4.6 51.2 1.0 C6 A:C4 4.9 54.4 1.0 C6 A:U5 4.9 54.2 1.0 C4 A:A3 5.0 50.4 1.0

Silver binding site 2 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


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 and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag101 b:69.8 occ:1.00 N3 B:C4 2.0 55.1 1.0 N1 A:A9 2.0 53.1 1.0 C4 B:C4 2.7 62.6 1.0 N4 B:C4 2.7 58.8 1.0 N3 B:U5 2.8 48.7 1.0 C6 A:A9 2.9 52.8 1.0 C2 A:A9 2.9 49.9 1.0 C2 B:C4 3.0 60.3 1.0 N6 A:A9 3.0 58.2 1.0 AG B:AG102 3.1 72.5 1.0 AG B:AG103 3.1 77.1 0.6 O2 B:C4 3.2 62.6 1.0 C2 B:U5 3.3 55.0 1.0 C4 B:U5 3.4 59.6 1.0 O2 B:U5 3.5 54.2 1.0 O4 B:U5 3.7 68.2 1.0 O4 A:U10 3.9 50.1 1.0 C5 B:C4 4.1 66.2 1.0 N1 B:U5 4.1 63.8 1.0 C5 A:A9 4.1 52.9 1.0 N3 A:A9 4.2 43.5 1.0 N1 B:C4 4.2 65.5 1.0 C5 B:U5 4.2 66.5 1.0 N6 B:A3 4.3 61.8 1.0 C4 A:U10 4.4 51.0 1.0 C6 B:U5 4.5 65.9 1.0 C4 A:A9 4.6 50.0 1.0 N1 A:A8 4.6 47.8 1.0 N3 A:U10 4.6 54.8 1.0 C6 B:C4 4.7 66.8 1.0 C6 B:A3 4.8 58.7 1.0 N1 B:A3 4.9 55.3 1.0

Silver binding site 3 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


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 and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag102 b:72.5 occ:0.99 N3 B:U5 2.1 48.7 1.0 N1 A:A8 2.1 47.8 1.0 O2 B:U5 2.7 54.2 1.0 C2 B:U5 2.8 55.0 1.0 C2 A:A8 3.0 48.9 1.0 AG B:AG101 3.1 69.8 1.0 C6 A:A8 3.1 50.9 1.0 N6 A:A8 3.2 63.0 1.0 C4 B:U5 3.2 59.6 1.0 O4 B:U5 3.4 68.2 1.0 N4 B:CBR6 3.5 58.6 1.0 N1 A:A9 3.5 53.1 1.0 C6 A:A9 3.5 52.8 1.0 C4 B:CBR6 3.6 53.0 1.0 N6 A:A9 3.7 58.2 1.0 N3 B:CBR6 3.9 52.8 1.0 C5 B:CBR6 4.0 53.1 1.0 C2 A:A9 4.1 49.9 1.0 N1 B:U5 4.1 63.8 1.0 C5 A:A9 4.2 52.9 1.0 N3 A:A8 4.3 46.4 1.0 C5 A:A8 4.4 48.4 1.0 C5 B:U5 4.4 66.5 1.0 BR B:CBR6 4.6 80.2 1.0 C4 A:A9 4.6 50.0 1.0 N4 B:C4 4.7 58.8 1.0 N3 B:C4 4.7 55.1 1.0 C2 B:CBR6 4.7 50.6 1.0 C6 B:CBR6 4.7 54.5 1.0 O6 A:G7 4.7 52.6 1.0 N3 A:A9 4.7 43.5 1.0 C6 B:U5 4.8 65.9 1.0 C4 A:A8 4.8 48.0 1.0 N7 A:A9 5.0 53.2 1.0 N1 B:CBR6 5.0 54.7 1.0

Silver binding site 4 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


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 and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag103 b:77.1 occ:0.61 N1 B:A3 2.2 55.3 1.0 O4 A:U10 2.2 50.1 1.0 N6 B:A3 2.5 61.8 1.0 N3 A:U10 2.6 54.8 1.0 C6 B:A3 2.6 58.7 1.0 C4 A:U10 2.8 51.0 1.0 N3 B:C4 3.0 55.1 1.0 AG B:AG101 3.1 69.8 1.0 C2 B:A3 3.3 57.0 1.0 N1 A:A9 3.3 53.1 1.0 C2 B:C4 3.4 60.3 1.0 O2 B:C4 3.4 62.6 1.0 C4 B:C4 3.7 62.6 1.0 C2 A:U10 3.8 49.4 1.0 C5 B:A3 3.9 60.5 1.0 C2 A:A9 3.9 49.9 1.0 N4 B:C4 4.0 58.8 1.0 C6 A:A9 4.1 52.8 1.0 N6 A:A9 4.1 58.2 1.0 N4 A:C11 4.1 50.7 1.0 C4 A:C11 4.2 53.6 1.0 C5 A:U10 4.2 50.0 1.0 N3 A:C11 4.2 56.0 1.0 O2 A:U10 4.2 41.7 1.0 N1 B:C4 4.4 65.5 1.0 N3 B:A3 4.4 63.8 1.0 O6 B:G2 4.5 58.3 1.0 C4 B:A3 4.6 64.0 1.0 C5 B:C4 4.7 66.2 1.0 C5 A:C11 4.8 51.6 1.0 C2 A:C11 4.8 49.3 1.0 N1 A:U10 4.9 45.3 1.0 C6 B:C4 5.0 66.8 1.0 N1 B:G2 5.0 54.5 1.0 C6 A:U10 5.0 45.1 1.0

Silver binding site 5 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


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 C-Ag-A and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag101 b:69.0 occ:0.73 N3 D:U5 2.2 46.0 1.0 O4 D:U5 2.6 52.6 1.0 N1 C:A8 2.6 48.0 1.0 N6 C:A8 2.7 43.7 1.0 C4 D:U5 2.8 46.3 1.0 N1 C:A9 3.0 39.3 1.0 C6 C:A9 3.1 35.1 1.0 C6 C:A8 3.1 46.9 1.0 N4 D:CBR6 3.2 56.8 1.0 C2 C:A9 3.2 45.8 1.0 C2 D:U5 3.3 50.3 1.0 C4 D:CBR6 3.4 54.1 1.0 C5 C:A9 3.5 44.5 1.0 N3 D:CBR6 3.6 56.1 1.0 O2 D:U5 3.6 47.0 1.0 N6 C:A9 3.6 35.7 1.0 N3 C:A9 3.6 42.9 1.0 C4 C:A9 3.6 44.0 1.0 C2 C:A8 3.8 49.7 1.0 C5 D:CBR6 4.1 50.9 1.0 C5 D:U5 4.2 46.3 1.0 AG D:AG101 4.3 52.4 1.0 N7 C:A9 4.3 49.2 1.0 N1 C:G7 4.4 56.0 1.0 C2 D:CBR6 4.4 55.9 1.0 O6 C:G7 4.5 59.9 1.0 N1 D:U5 4.5 56.3 1.0 C5 C:A8 4.5 52.3 1.0 N9 C:A9 4.6 46.9 1.0 C6 D:U5 4.8 53.9 1.0 C6 C:G7 4.8 58.9 1.0 C6 D:CBR6 4.9 56.7 1.0 C8 C:A9 4.9 47.4 1.0 BR D:CBR6 4.9 77.1 1.0

Silver binding site 6 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


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 C-Ag-A and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag102 b:94.4 occ:0.67 N1 D:A9 2.0 74.5 1.0 N3 C:C4 2.1 70.5 1.0 N6 D:A9 2.4 73.2 1.0 C6 D:A9 2.5 73.5 1.0 N4 C:C4 2.7 67.3 1.0 C4 C:C4 2.8 66.2 1.0 C2 D:A9 3.1 75.3 1.0 N3 D:U10 3.2 60.1 1.0 C2 C:C4 3.2 66.7 1.0 AG D:AG103 3.3 102.0 0.7 C4 C:U5 3.3 61.5 1.0 N3 C:U5 3.4 64.5 1.0 O4 C:U5 3.4 66.1 1.0 AG D:AG102 3.4 68.3 0.6 O2 C:C4 3.5 63.6 1.0 O4 D:U10 3.5 66.0 1.0 C4 D:U10 3.5 60.0 1.0 C5 C:U5 3.8 62.5 1.0 C5 D:A9 3.9 71.3 1.0 C2 D:U10 3.9 65.8 1.0 C2 C:U5 4.0 71.1 1.0 O2 D:U10 4.2 65.1 1.0 C5 C:C4 4.2 64.3 1.0 N3 D:A9 4.3 72.8 1.0 N1 C:A3 4.4 59.8 1.0 C6 C:U5 4.4 61.5 1.0 N1 C:U5 4.5 67.9 1.0 N1 C:C4 4.5 61.9 1.0 C4 D:A9 4.5 72.5 1.0 C5 D:U10 4.6 66.6 1.0 N6 D:A8 4.6 66.6 1.0 O2 C:U5 4.7 70.9 1.0 N1 D:A8 4.8 69.1 1.0 N1 D:U10 4.8 68.1 1.0 C6 C:C4 4.9 65.1 1.0 C2 C:A3 4.9 60.5 1.0

Silver binding site 7 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag101 b:52.4 occ:1.00 N3 D:C4 2.1 39.4 1.0 N1 C:A9 2.1 39.3 1.0 N6 C:A9 2.4 35.7 1.0 O2 D:C4 2.6 43.8 1.0 C6 C:A9 2.7 35.1 1.0 C2 D:C4 2.7 39.1 1.0 O4 D:U5 2.8 52.6 1.0 C4 D:U5 2.9 46.3 1.0 O4 C:U10 2.9 36.6 1.0 C5 D:U5 3.2 46.3 1.0 C4 D:C4 3.2 49.3 1.0 N6 D:A3 3.2 41.5 1.0 C2 C:A9 3.2 45.8 1.0 C4 C:U10 3.4 41.2 1.0 N4 D:C4 3.5 54.7 1.0 N3 D:U5 3.7 46.0 1.0 N3 C:U10 3.7 40.7 1.0 C6 D:A3 3.8 46.4 1.0 C6 D:U5 4.0 53.9 1.0 N1 D:A3 4.0 48.6 1.0 C5 C:A9 4.0 44.5 1.0 N1 D:C4 4.1 50.8 1.0 C5 C:U10 4.2 43.1 1.0 AG C:AG101 4.3 69.0 0.7 N3 C:A9 4.5 42.9 1.0 C2 D:U5 4.5 50.3 1.0 C5 D:C4 4.5 49.3 1.0 N1 D:U5 4.6 56.3 1.0 C4 C:A9 4.7 44.0 1.0 C2 C:U10 4.7 40.9 1.0 C6 D:C4 4.8 51.0 1.0 C5 D:A3 4.8 43.4 1.0

Silver binding site 8 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag102 b:68.3 occ:0.62 N3 D:U10 2.1 60.1 1.0 N1 C:A3 2.1 59.8 1.0 C2 C:A3 2.4 60.5 1.0 O4 D:U10 2.4 66.0 1.0 C4 D:U10 2.6 60.0 1.0 C4 D:C11 3.0 54.1 1.0 N4 D:C11 3.0 50.9 1.0 C2 D:U10 3.2 65.8 1.0 N3 D:C11 3.3 49.8 1.0 O6 C:G2 3.3 56.4 1.0 C6 C:A3 3.4 67.7 1.0 N3 C:C4 3.4 70.5 1.0 AG C:AG102 3.4 94.4 0.7 O2 D:U10 3.5 65.1 1.0 C5 D:C11 3.6 53.1 1.0 C4 C:C4 3.6 66.2 1.0 N3 C:A3 3.7 65.6 1.0 N4 C:C4 3.7 67.3 1.0 C5 D:U10 3.9 66.6 1.0 N6 C:A3 4.0 77.6 1.0 C2 D:C11 4.0 47.4 1.0 C2 C:C4 4.1 66.7 1.0 C6 C:G2 4.1 54.8 1.0 C6 D:C11 4.2 52.2 1.0 N1 C:G2 4.3 52.4 1.0 N1 D:U10 4.3 68.1 1.0 N6 D:A9 4.3 73.2 1.0 N1 D:C11 4.4 46.9 1.0 N1 D:A9 4.4 74.5 1.0 C5 C:C4 4.4 64.3 1.0 C5 C:A3 4.5 70.4 1.0 C4 C:A3 4.5 70.6 1.0 O2 C:C4 4.5 63.6 1.0 C6 D:U10 4.6 68.6 1.0 C6 D:A9 4.7 73.5 1.0 O2 D:C11 4.7 47.0 1.0 N1 C:C4 4.8 61.9 1.0 C6 C:C4 4.9 65.1 1.0

Silver binding site 9 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag103 b:102.0 occ:0.68 N3 C:U5 2.1 64.5 1.0 O4 C:U5 2.2 66.1 1.0 N1 D:A8 2.3 69.1 1.0 C4 C:U5 2.5 61.5 1.0 N6 D:A8 2.7 66.6 1.0 C6 D:A8 2.9 66.4 1.0 AG C:AG102 3.3 94.4 0.7 C2 C:U5 3.3 71.1 1.0 N1 D:A9 3.4 74.5 1.0 N6 D:A9 3.4 73.2 1.0 C2 D:A8 3.4 68.4 1.0 C6 D:A9 3.4 73.5 1.0 O2 C:U5 3.7 70.9 1.0 N4 C:CBR6 3.8 60.9 1.0 C4 C:CBR6 3.9 64.8 1.0 C5 C:U5 3.9 62.5 1.0 N3 C:CBR6 4.1 64.7 1.0 C2 D:A9 4.1 75.3 1.0 O6 D:G7 4.2 58.7 1.0 C5 D:A9 4.2 71.3 1.0 C5 D:A8 4.3 63.5 1.0 C5 C:CBR6 4.4 59.0 1.0 N1 C:U5 4.4 67.9 1.0 N1 D:G7 4.6 60.3 1.0 N4 C:C4 4.6 67.3 1.0 C6 C:U5 4.6 61.5 1.0 N3 D:A8 4.7 65.7 1.0 C6 D:G7 4.7 61.8 1.0 N3 C:C4 4.7 70.5 1.0 C4 D:A9 4.8 72.5 1.0 C2 C:CBR6 4.8 62.2 1.0 N3 D:A9 4.9 72.8 1.0 C4 D:A8 4.9 65.2 1.0

Silver binding site 10 out of 23 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ E:Ag101 b:60.2 occ:0.75 N3 E:C4 2.1 45.7 1.0 N1 F:A9 2.2 45.7 1.0 N4 E:C4 2.6 58.1 1.0 N6 F:A9 2.6 45.3 1.0 C4 E:C4 2.7 50.5 1.0 C6 F:A9 2.8 46.3 1.0 N6 E:A3 3.0 46.0 1.0 C2 E:C4 3.2 50.6 1.0 O4 E:U5 3.2 43.0 1.0 O4 F:U10 3.2 42.1 1.0 C2 F:A9 3.4 46.9 1.0 C4 E:U5 3.4 42.0 1.0 O2 E:C4 3.5 49.2 1.0 C6 E:A3 3.5 45.4 1.0 C4 F:U10 3.7 43.0 1.0 N1 E:A3 3.8 44.0 1.0 N3 F:U10 3.9 40.7 1.0 C5 E:U5 3.9 40.8 1.0 N3 E:U5 4.0 39.7 1.0 N6 F:A8 4.0 33.8 1.0 C5 E:C4 4.1 55.6 1.0 C5 F:A9 4.2 49.2 1.0 N1 E:C4 4.4 55.9 1.0 C5 E:A3 4.4 47.9 1.0 N3 F:A9 4.6 50.0 1.0 C5 F:U10 4.6 43.9 1.0 C6 E:U5 4.7 39.5 1.0 C6 E:C4 4.8 56.1 1.0 C2 E:A3 4.8 46.0 1.0 C2 E:U5 4.8 45.4 1.0 C4 F:A9 4.9 47.1 1.0 C2 F:U10 4.9 46.7 1.0 C6 F:A8 5.0 37.5 1.0

J.Kondo, Y.Uchida. Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair To Be Published.