Silver in PDB 7eck: Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs

The structure of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs, PDB code: 7eck 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)	42.19 / 2.79
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.408, 43.408, 379.673, 90, 90, 120
R / Rfree (%)	22 / 29.2

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

Bromine

(Br)

12 atoms

Pages:

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

Binding sites:

The binding sites of Silver atom in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs (pdb code 7eck). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 21 binding sites of Silver where determined in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs, PDB code: 7eck:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 21 in the Rna Duplex Containing C-Ag-A and U-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 and U-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag101 b:51.9 occ:0.92 N1 B:A9 1.9 35.2 1.0 N3 A:C4 1.9 41.9 1.0 N6 B:A9 2.5 42.6 1.0 C6 B:A9 2.5 41.1 1.0 N6 A:A3 2.7 28.2 1.0 C2 A:C4 2.7 41.8 1.0 O2 A:C4 2.8 40.7 1.0 O4 A:U5 2.8 37.5 1.0 C4 A:C4 3.0 41.6 1.0 C2 B:A9 3.0 36.8 1.0 C6 A:A3 3.2 32.9 1.0 N4 A:C4 3.2 41.0 1.0 C4 A:U5 3.3 43.8 1.0 O4 B:U10 3.5 37.7 1.0 N1 A:A3 3.6 31.5 1.0 C5 A:U5 3.8 52.8 1.0 C5 B:A9 3.9 34.9 1.0 C5 A:A3 3.9 38.7 1.0 N3 A:U5 4.0 44.5 1.0 N3 B:U10 4.0 35.9 1.0 C4 B:U10 4.0 33.4 1.0 N1 A:C4 4.0 47.0 1.0 N6 B:A8 4.1 40.1 1.0 N3 B:A9 4.2 39.2 1.0 C5 A:C4 4.3 46.4 1.0 N7 A:A3 4.5 37.7 1.0 C4 B:A9 4.5 34.7 1.0 C2 A:A3 4.6 34.8 1.0 C6 A:C4 4.6 49.1 1.0 N1 B:A8 4.8 38.7 1.0 C6 A:U5 4.8 53.6 1.0 C6 B:A8 4.9 36.8 1.0 C4 A:A3 4.9 38.2 1.0 C2 A:U5 5.0 52.8 1.0

Silver binding site 2 out of 21 in the Rna Duplex Containing C-Ag-A and U-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 and U-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag102 b:64.4 occ:0.98 N3 B:U5 2.0 55.6 1.0 N1 A:A8 2.1 41.3 1.0 C2 B:U5 2.8 57.3 1.0 N6 A:A8 2.8 44.0 1.0 C6 A:A8 2.8 40.8 1.0 O2 B:U5 2.9 57.0 1.0 C4 B:U5 2.9 64.2 1.0 O4 B:U5 3.0 67.2 1.0 N6 A:A9 3.0 42.2 1.0 C2 A:A8 3.0 43.6 1.0 C6 A:A9 3.1 38.9 1.0 N1 A:A9 3.1 44.0 1.0 AG B:AG101 3.3 61.5 1.0 N4 B:CBR6 3.4 50.5 1.0 C4 B:CBR6 3.7 51.2 1.0 C2 A:A9 3.9 48.2 1.0 C5 A:A9 4.0 42.9 1.0 C5 B:CBR6 4.1 56.4 1.0 N1 B:U5 4.1 64.8 1.0 C5 A:A8 4.2 42.2 1.0 C5 B:U5 4.2 69.3 1.0 N3 B:CBR6 4.3 50.6 1.0 N3 A:A8 4.3 45.2 1.0 BR B:CBR6 4.3 72.4 1.0 C4 A:A9 4.6 46.2 1.0 C6 B:U5 4.6 68.2 1.0 N3 B:C4 4.6 58.5 1.0 N3 A:A9 4.7 48.8 1.0 C4 A:A8 4.7 41.9 1.0 N7 A:A9 4.8 43.2 1.0 N4 B:C4 4.8 68.3 1.0 O6 A:G7 4.9 47.4 1.0 C6 B:CBR6 4.9 56.7 1.0

Silver binding site 3 out of 21 in the Rna Duplex Containing C-Ag-A and U-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 and U-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Ag101 b:61.5 occ:1.00 N3 B:C4 1.9 58.5 1.0 N1 A:A9 2.0 44.0 1.0 C2 B:C4 2.6 61.1 1.0 O2 B:C4 2.7 58.2 1.0 C6 A:A9 2.9 38.9 1.0 N6 B:A3 2.9 51.5 1.0 N3 B:U5 2.9 55.6 1.0 N6 A:A9 2.9 42.2 1.0 C2 A:A9 2.9 48.2 1.0 C4 B:C4 3.0 65.4 1.0 C4 B:U5 3.1 64.2 1.0 N4 B:C4 3.2 68.3 1.0 AG A:AG102 3.3 64.4 1.0 O4 B:U5 3.3 67.2 1.0 O4 A:U10 3.5 41.1 1.0 C6 B:A3 3.5 55.8 1.0 C2 B:U5 3.6 57.3 1.0 N3 A:U10 3.9 49.1 1.0 C4 A:U10 3.9 42.1 1.0 N1 B:A3 4.0 50.3 1.0 C5 B:U5 4.0 69.3 1.0 N1 B:C4 4.0 66.7 1.0 O2 B:U5 4.0 57.0 1.0 C5 A:A9 4.2 42.9 1.0 N3 A:A9 4.2 48.8 1.0 C5 B:C4 4.2 65.9 1.0 N1 B:U5 4.3 64.8 1.0 C5 B:A3 4.4 61.0 1.0 C6 B:U5 4.4 68.2 1.0 C6 B:C4 4.6 65.2 1.0 C4 A:A9 4.6 46.2 1.0 N7 B:A3 4.9 61.0 1.0 C2 A:U10 4.9 51.6 1.0 N1 A:A8 5.0 41.3 1.0 C5 A:U10 5.0 44.0 1.0 C2 B:A3 5.0 54.1 1.0

Silver binding site 4 out of 21 in the Rna Duplex Containing C-Ag-A and U-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 and U-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Ag101 b:63.9 occ:0.83 N1 D:A9 2.0 44.6 1.0 N3 C:C4 2.0 47.2 1.0 N4 C:C4 2.1 53.2 1.0 C4 C:C4 2.4 50.6 1.0 N6 D:A9 2.7 39.6 1.0 C6 D:A9 2.7 44.8 1.0 C2 D:A9 3.1 45.7 1.0 C4 C:U5 3.3 51.3 1.0 C2 C:C4 3.3 51.2 1.0 AG D:AG102 3.3 55.8 0.5 AG D:AG103 3.3 48.0 0.4 O4 C:U5 3.3 45.2 1.0 N3 C:U5 3.5 50.7 1.0 N6 C:A3 3.7 48.8 1.0 O2 C:C4 3.8 51.1 1.0 C5 C:U5 3.8 49.4 1.0 C5 C:C4 3.8 53.7 1.0 N3 D:U10 3.8 40.9 1.0 N1 C:A3 3.9 46.8 1.0 C5 D:A9 4.0 46.1 1.0 C6 C:A3 4.1 47.8 1.0 C2 C:U5 4.2 48.4 1.0 N6 D:A8 4.2 46.4 1.0 O4 D:U10 4.2 53.9 1.0 C4 D:U10 4.3 45.8 1.0 N3 D:A9 4.3 48.0 1.0 N1 C:C4 4.4 53.0 1.0 C6 C:U5 4.4 46.3 1.0 C2 D:U10 4.5 42.9 1.0 O2 D:U10 4.5 40.1 1.0 N1 C:U5 4.6 47.3 1.0 C6 C:C4 4.6 55.1 1.0 C4 D:A9 4.6 50.5 1.0 N1 D:A8 4.7 43.9 1.0 C2 C:A3 4.8 48.7 1.0 O2 C:U5 4.8 44.4 1.0 C6 D:A8 4.9 48.3 1.0

Silver binding site 5 out of 21 in the Rna Duplex Containing C-Ag-A and U-Ag-A 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 C-Ag-A and U-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag101 b:47.8 occ:1.00 N3 D:C4 1.9 41.8 1.0 N1 C:A9 1.9 33.3 1.0 N6 C:A9 2.6 30.1 1.0 O2 D:C4 2.7 44.0 1.0 C2 D:C4 2.7 46.3 1.0 C6 C:A9 2.7 30.7 1.0 O4 D:U5 2.9 37.5 1.0 C2 C:A9 2.9 35.2 1.0 C4 D:C4 3.0 50.6 1.0 C4 D:U5 3.0 43.0 1.0 C5 D:U5 3.2 47.1 1.0 N4 D:C4 3.2 61.5 1.0 O4 C:U10 3.2 32.6 1.0 C4 C:U10 3.5 34.3 1.0 N6 D:A3 3.5 45.9 1.0 N3 C:U10 3.6 32.9 1.0 N1 D:A3 3.6 44.5 1.0 C6 D:A3 3.8 45.3 1.0 N3 D:U5 3.9 38.3 1.0 C6 D:U5 4.0 49.3 1.0 N1 D:C4 4.0 61.4 1.0 C5 C:A9 4.0 38.6 1.0 N3 C:A9 4.2 40.3 1.0 C5 D:C4 4.3 55.6 1.0 C5 C:U10 4.4 37.5 1.0 N6 C:A8 4.5 40.1 1.0 C2 C:U10 4.5 38.0 1.0 C2 D:A3 4.6 48.0 1.0 C4 C:A9 4.6 38.6 1.0 C2 D:U5 4.6 45.7 1.0 C6 D:C4 4.7 59.4 1.0 N1 D:U5 4.7 51.6 1.0 C5 D:A3 4.9 46.4 1.0

Silver binding site 6 out of 21 in the Rna Duplex Containing C-Ag-A and U-Ag-A 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 C-Ag-A and U-Ag-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag102 b:55.8 occ:0.48 N1 C:A3 1.8 46.8 1.0 N3 D:U10 1.9 40.9 1.0 N6 C:A3 2.4 48.8 1.0 C6 C:A3 2.5 47.8 1.0 C4 D:U10 2.8 45.8 1.0 C2 D:U10 2.8 42.9 1.0 O4 D:U10 2.9 53.9 1.0 O2 D:U10 2.9 40.1 1.0 C2 C:A3 3.0 48.7 1.0 N4 D:C11 3.2 42.8 1.0 AG C:AG101 3.3 63.9 0.8 C4 D:C11 3.3 39.7 1.0 O6 C:G2 3.4 40.8 1.0 N3 D:C11 3.6 39.6 1.0 N3 C:C4 3.6 47.2 1.0 N1 D:A9 3.8 44.6 1.0 C5 C:A3 3.8 50.1 1.0 C4 C:C4 3.8 50.6 1.0 N4 C:C4 3.9 53.2 1.0 C5 D:C11 4.0 39.0 1.0 N1 D:U10 4.1 47.5 1.0 C5 D:U10 4.1 50.8 1.0 N3 C:A3 4.2 54.9 1.0 N6 D:A9 4.2 39.6 1.0 C2 C:C4 4.2 51.2 1.0 C6 D:A9 4.2 44.8 1.0 C6 C:G2 4.2 46.5 1.0 C2 D:C11 4.4 40.7 1.0 C4 C:A3 4.4 53.1 1.0 C2 D:A9 4.4 45.7 1.0 N1 C:G2 4.4 47.3 1.0 O2 C:C4 4.6 51.1 1.0 C6 D:U10 4.6 49.4 1.0 C5 C:C4 4.6 53.7 1.0 C6 D:C11 4.7 38.3 1.0 N1 D:C11 4.9 39.4 1.0 N1 C:C4 4.9 53.0 1.0 N7 C:A3 5.0 57.5 1.0

Silver binding site 7 out of 21 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


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 Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ag103 b:48.0 occ:0.39 N1 D:A8 2.0 43.9 1.0 N3 C:U5 2.0 50.7 1.0 N6 D:A8 2.2 46.4 1.0 O4 C:U5 2.2 45.2 1.0 C6 D:A8 2.4 48.3 1.0 C4 C:U5 2.4 51.3 1.0 C2 C:U5 3.2 48.4 1.0 C2 D:A8 3.2 44.1 1.0 N1 D:A9 3.3 44.6 1.0 AG C:AG101 3.3 63.9 0.8 C6 D:A9 3.4 44.8 1.0 N4 C:CBR6 3.5 45.9 1.0 N6 D:A9 3.5 39.6 1.0 O2 C:U5 3.6 44.4 1.0 C4 C:CBR6 3.7 49.4 1.0 C5 D:A8 3.8 47.9 1.0 C5 C:U5 3.8 49.4 1.0 C2 D:A9 3.9 45.7 1.0 N3 C:CBR6 3.9 45.6 1.0 O6 D:G7 3.9 46.6 1.0 C5 D:A9 4.0 46.1 1.0 N1 C:U5 4.3 47.3 1.0 N3 D:A8 4.4 47.2 1.0 C5 C:CBR6 4.4 50.8 1.0 N4 C:C4 4.5 53.2 1.0 C4 D:A9 4.5 50.5 1.0 C6 C:U5 4.5 46.3 1.0 C4 D:A8 4.5 48.5 1.0 N3 D:A9 4.5 48.0 1.0 C6 D:G7 4.6 48.8 1.0 N3 C:C4 4.7 47.2 1.0 N1 D:G7 4.7 43.1 1.0 C2 C:CBR6 4.8 52.1 1.0 N7 D:A9 4.9 46.5 1.0 N7 D:A8 4.9 50.5 1.0

Silver binding site 8 out of 21 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


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 Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Ag101 b:44.7 occ:0.90 N3 E:C4 1.8 29.9 1.0 N1 F:A9 1.9 29.2 1.0 C4 E:C4 2.6 31.9 1.0 N4 E:C4 2.7 34.8 1.0 C6 F:A9 2.8 35.1 1.0 C2 E:C4 2.8 32.1 1.0 N6 F:A9 2.8 35.6 1.0 N6 E:A3 2.9 28.1 1.0 C2 F:A9 2.9 29.4 1.0 O4 E:U5 2.9 27.6 1.0 O2 E:C4 3.0 33.6 1.0 C4 E:U5 3.2 25.9 1.0 O4 F:U10 3.3 29.9 1.0 C6 E:A3 3.6 28.6 1.0 C5 E:U5 3.6 24.3 1.0 C4 F:U10 3.7 29.3 1.0 N3 E:U5 3.9 27.0 1.0 C5 E:C4 4.0 35.6 1.0 N1 E:A3 4.0 29.2 1.0 N3 F:U10 4.1 27.8 1.0 N1 E:C4 4.1 35.0 1.0 C5 F:A9 4.1 36.4 1.0 N3 F:A9 4.2 35.5 1.0 N6 F:A8 4.4 27.0 1.0 N1 F:A8 4.4 32.4 1.0 C5 E:A3 4.4 29.9 1.0 C6 E:C4 4.5 37.0 1.0 C6 E:U5 4.5 27.1 1.0 C5 F:U10 4.5 27.9 1.0 C4 F:A9 4.6 34.1 1.0 C6 F:A8 4.8 31.5 1.0 C2 E:U5 4.9 30.3 1.0 N7 E:A3 4.9 29.7 1.0

Silver binding site 9 out of 21 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


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 Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:Ag102 b:50.4 occ:0.56 N1 E:A8 1.9 34.3 1.0 N3 F:U5 1.9 48.6 1.0 N6 E:A8 2.5 34.5 1.0 C6 E:A8 2.6 33.3 1.0 C4 F:U5 2.8 47.4 1.0 O4 F:U5 2.8 43.6 1.0 C2 F:U5 2.9 48.2 1.0 N1 E:A9 3.0 37.3 1.0 O2 F:U5 3.0 44.9 1.0 C2 E:A8 3.1 36.6 1.0 AG F:AG101 3.3 46.9 1.0 C6 E:A9 3.4 37.1 1.0 N4 F:CBR6 3.4 42.0 1.0 C2 E:A9 3.6 39.5 1.0 N6 E:A9 3.6 39.9 1.0 C4 F:CBR6 3.6 41.2 1.0 C5 E:A8 3.9 31.2 1.0 N3 F:CBR6 4.0 39.7 1.0 C5 F:U5 4.1 51.0 1.0 C5 E:A9 4.1 37.4 1.0 N1 F:U5 4.1 50.4 1.0 C5 F:CBR6 4.2 44.0 1.0 N3 E:A8 4.3 37.9 1.0 N3 E:A9 4.3 41.2 1.0 C4 E:A9 4.5 40.4 1.0 C4 E:A8 4.5 32.7 1.0 N3 F:C4 4.6 43.2 1.0 O6 E:G7 4.6 29.3 1.0 C6 F:U5 4.6 51.0 1.0 BR F:CBR6 4.6 61.4 1.0 C2 F:CBR6 4.8 41.9 1.0 C6 F:CBR6 4.9 43.1 1.0

Silver binding site 10 out of 21 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


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 Pairs within 5.0Å range: probe atom residue distance (Å) B Occ F:Ag101 b:46.9 occ:1.00 N1 E:A9 1.9 37.3 1.0 N3 F:C4 2.1 43.2 1.0 C2 E:A9 2.7 39.5 1.0 O2 F:C4 2.7 45.4 1.0 N6 F:A3 2.8 44.0 1.0 C2 F:C4 2.8 46.4 1.0 C6 E:A9 3.0 37.1 1.0 C4 F:C4 3.1 42.7 1.0 N6 E:A9 3.2 39.9 1.0 N3 F:U5 3.2 48.6 1.0 C6 F:A3 3.3 42.3 1.0 AG E:AG102 3.3 50.4 0.6 N4 F:C4 3.3 52.8 1.0 N1 F:A3 3.5 43.0 1.0 C4 F:U5 3.5 47.4 1.0 O4 E:U10 3.5 37.8 1.0 O4 F:U5 3.5 43.6 1.0 N3 E:U10 3.7 45.5 1.0 C4 E:U10 3.9 40.7 1.0 C2 F:U5 3.9 48.2 1.0 N3 E:A9 4.1 41.2 1.0 N1 F:C4 4.1 46.1 1.0 C5 E:A9 4.2 37.4 1.0 C5 F:A3 4.3 42.8 1.0 O2 F:U5 4.3 44.9 1.0 C5 F:U5 4.3 51.0 1.0 C5 F:C4 4.4 40.5 1.0 C2 F:A3 4.5 44.4 1.0 N6 E:A8 4.5 34.5 1.0 C4 E:A9 4.6 40.4 1.0 N1 F:U5 4.6 50.4 1.0 C2 E:U10 4.7 50.2 1.0 N1 E:A8 4.7 34.3 1.0 C6 F:C4 4.8 44.0 1.0 C6 F:U5 4.8 51.0 1.0 N7 F:A3 5.0 44.9 1.0 O2 E:U10 5.0 54.8 1.0

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