Bromine 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:

Silver

(Ag)

21 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Bromine 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 Bromine atom.
In total 12 binding sites of Bromine where determined in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs, PDB code: 7eck:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br6 b:66.2 occ:1.00 BR A:CBR6 0.0 66.2 1.0 C5 A:CBR6 1.9 46.4 1.0 C6 A:CBR6 2.9 46.6 1.0 C4 A:CBR6 2.9 44.9 1.0 N4 A:CBR6 3.1 43.7 1.0 C5 A:U5 3.5 52.8 1.0 C6 A:U5 3.6 53.6 1.0 C4 A:U5 3.7 43.8 1.0 OP2 A:CBR6 3.8 46.4 1.0 N1 A:U5 4.0 56.6 1.0 N3 A:U5 4.0 44.5 1.0 N3 A:CBR6 4.1 44.0 1.0 N1 A:CBR6 4.1 48.5 1.0 O4 A:U5 4.2 37.5 1.0 C2 A:U5 4.2 52.8 1.0 C3' A:U5 4.5 52.5 1.0 N7 A:G7 4.5 41.7 1.0 C2' A:U5 4.6 53.3 1.0 O5' A:CBR6 4.6 46.3 1.0 C2 A:CBR6 4.7 46.1 1.0 P A:CBR6 4.8 57.0 1.0 C1' A:U5 4.9 55.4 1.0

Bromine binding site 2 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 B:Br6 b:72.4 occ:1.00 BR B:CBR6 0.0 72.4 1.0 C5 B:CBR6 1.9 56.4 1.0 C6 B:CBR6 2.9 56.7 1.0 C4 B:CBR6 2.9 51.2 1.0 N4 B:CBR6 3.1 50.5 1.0 N3 B:U5 3.6 55.6 1.0 C2 B:U5 3.6 57.3 1.0 C4 B:U5 3.7 64.2 1.0 N1 B:U5 3.8 64.8 1.0 OP2 B:CBR6 3.8 57.8 1.0 C5 B:U5 3.9 69.3 1.0 C6 B:U5 3.9 68.2 1.0 C2' B:U5 4.1 63.9 1.0 O2 B:U5 4.2 57.0 1.0 N1 B:CBR6 4.2 57.5 1.0 N3 B:CBR6 4.2 50.6 1.0 AG A:AG102 4.3 64.4 1.0 O4 B:U5 4.3 67.2 1.0 C1' B:U5 4.5 66.2 1.0 C3' B:U5 4.7 64.8 1.0 C2 B:CBR6 4.7 52.4 1.0 O5' B:CBR6 4.9 40.1 1.0 P B:CBR6 4.9 57.9 1.0

Bromine binding site 3 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 C:Br6 b:79.0 occ:1.00 BR C:CBR6 0.0 79.0 1.0 C5 C:CBR6 1.9 50.8 1.0 C6 C:CBR6 2.9 49.0 1.0 C4 C:CBR6 2.9 49.4 1.0 N4 C:CBR6 3.1 45.9 1.0 C5 C:U5 3.6 49.4 1.0 C6 C:U5 3.6 46.3 1.0 C4 C:U5 3.7 51.3 1.0 OP2 C:CBR6 3.7 46.4 1.0 N3 C:U5 3.8 50.7 1.0 N1 C:U5 3.8 47.3 1.0 C2 C:U5 4.0 48.4 1.0 N1 C:CBR6 4.2 57.6 1.0 N3 C:CBR6 4.2 45.6 1.0 O4 C:U5 4.2 45.2 1.0 C2' C:U5 4.3 51.8 1.0 C3' C:U5 4.4 49.1 1.0 O5' C:CBR6 4.6 59.8 1.0 O2 C:U5 4.7 44.4 1.0 C1' C:U5 4.7 52.5 1.0 C2 C:CBR6 4.7 52.1 1.0 P C:CBR6 4.7 57.2 1.0

Bromine binding site 4 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 D:Br6 b:87.8 occ:1.00 BR D:CBR6 0.0 87.8 1.0 C5 D:CBR6 2.0 44.4 1.0 C6 D:CBR6 2.9 47.4 1.0 C4 D:CBR6 3.0 48.5 1.0 N4 D:CBR6 3.3 52.3 1.0 C6 D:U5 3.6 49.3 1.0 C5 D:U5 3.7 47.1 1.0 N1 D:U5 3.7 51.6 1.0 C4 D:U5 3.9 43.0 1.0 C2 D:U5 3.9 45.7 1.0 N3 D:U5 4.0 38.3 1.0 C2' D:U5 4.0 59.3 1.0 OP2 D:CBR6 4.1 64.8 1.0 N1 D:CBR6 4.2 52.9 1.0 O5' D:CBR6 4.3 44.5 1.0 C3' D:U5 4.3 59.5 1.0 N3 D:CBR6 4.3 48.4 1.0 C1' D:U5 4.4 55.4 1.0 O4 D:U5 4.6 37.5 1.0 O2 D:U5 4.6 45.1 1.0 P D:CBR6 4.8 72.0 1.0 C2 D:CBR6 4.8 50.0 1.0 O4' D:CBR6 5.0 59.9 1.0

Bromine binding site 5 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 E:Br6 b:50.1 occ:1.00 BR E:CBR6 0.0 50.1 1.0 C5 E:CBR6 1.9 26.9 1.0 C6 E:CBR6 2.8 27.9 1.0 C4 E:CBR6 2.9 29.0 1.0 N4 E:CBR6 3.2 28.5 1.0 C6 E:U5 3.6 27.1 1.0 C5 E:U5 3.6 24.3 1.0 N1 E:U5 3.6 33.5 1.0 C4 E:U5 3.7 25.9 1.0 N3 E:U5 3.7 27.0 1.0 C2 E:U5 3.7 30.3 1.0 OP2 E:CBR6 3.7 25.4 1.0 C2' E:U5 4.0 27.7 1.0 N1 E:CBR6 4.1 32.7 1.0 N3 E:CBR6 4.2 31.8 1.0 C3' E:U5 4.2 27.2 1.0 O5' E:CBR6 4.2 27.9 1.0 O4 E:U5 4.3 27.6 1.0 O2 E:U5 4.4 27.0 1.0 C1' E:U5 4.4 36.0 1.0 P E:CBR6 4.5 32.6 1.0 C2 E:CBR6 4.7 32.3 1.0 N7 E:G7 4.7 28.6 1.0 O3' E:U5 4.9 29.6 1.0

Bromine binding site 6 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 F:Br6 b:61.4 occ:1.00 BR F:CBR6 0.0 61.4 1.0 C5 F:CBR6 1.9 44.0 1.0 C4 F:CBR6 2.8 41.2 1.0 C6 F:CBR6 2.9 43.1 1.0 N4 F:CBR6 3.0 42.0 1.0 C4 F:U5 3.6 47.4 1.0 C5 F:U5 3.6 51.0 1.0 OP2 F:CBR6 3.7 40.4 1.0 N3 F:U5 3.7 48.6 1.0 C6 F:U5 3.7 51.0 1.0 N1 F:U5 3.9 50.4 1.0 C2 F:U5 3.9 48.2 1.0 O4 F:U5 4.1 43.6 1.0 N3 F:CBR6 4.1 39.7 1.0 N1 F:CBR6 4.2 43.8 1.0 C2' F:U5 4.4 47.2 1.0 C3' F:U5 4.5 47.9 1.0 O5' F:CBR6 4.5 46.1 1.0 O2 F:U5 4.6 44.9 1.0 AG E:AG102 4.6 50.4 0.6 P F:CBR6 4.7 49.0 1.0 C2 F:CBR6 4.7 41.9 1.0 C1' F:U5 4.8 48.3 1.0

Bromine binding site 7 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 G:Br6 b:72.9 occ:1.00 BR G:CBR6 0.0 72.9 1.0 C5 G:CBR6 1.9 53.2 1.0 C6 G:CBR6 2.9 52.8 1.0 C4 G:CBR6 2.9 51.1 1.0 N4 G:CBR6 3.1 43.0 1.0 OP2 G:CBR6 3.7 51.2 1.0 N3 G:U5 3.8 45.1 1.0 C4 G:U5 3.8 44.7 1.0 C2 G:U5 3.9 46.9 1.0 C5 G:U5 3.9 44.2 1.0 N1 G:U5 3.9 47.6 1.0 C6 G:U5 3.9 46.1 1.0 N1 G:CBR6 4.1 54.5 1.0 N3 G:CBR6 4.2 52.4 1.0 C2' G:U5 4.3 48.6 1.0 C3' G:U5 4.4 47.5 1.0 O4 G:U5 4.4 44.9 1.0 O2 G:U5 4.4 51.1 1.0 O5' G:CBR6 4.5 42.2 1.0 C1' G:U5 4.7 51.8 1.0 P G:CBR6 4.7 54.0 1.0 C2 G:CBR6 4.7 54.7 1.0 AG G:AG102 4.8 66.6 0.6

Bromine binding site 8 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 H:Br6 b:61.4 occ:1.00 BR H:CBR6 0.0 61.4 1.0 C5 H:CBR6 1.9 42.5 1.0 C4 H:CBR6 2.9 47.2 1.0 C6 H:CBR6 2.9 39.3 1.0 N4 H:CBR6 3.1 44.4 1.0 OP2 H:CBR6 3.6 38.9 1.0 N1 H:U5 3.8 36.7 1.0 C6 H:U5 3.8 39.2 1.0 C5 H:U5 3.8 39.9 1.0 C2 H:U5 3.8 37.4 1.0 N3 H:U5 3.9 37.2 1.0 C4 H:U5 3.9 38.9 1.0 N3 H:CBR6 4.2 47.5 1.0 N1 H:CBR6 4.2 42.0 1.0 C3' H:U5 4.2 44.6 1.0 C2' H:U5 4.2 42.1 1.0 O5' H:CBR6 4.3 39.7 1.0 O2 H:U5 4.4 40.0 1.0 O4 H:U5 4.5 39.8 1.0 P H:CBR6 4.5 52.3 1.0 C1' H:U5 4.5 42.0 1.0 C2 H:CBR6 4.7 45.0 1.0 O3' H:U5 4.9 50.1 1.0 O6 H:G7 4.9 47.5 1.0

Bromine binding site 9 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 I:Br6 b:46.5 occ:1.00 BR I:CBR6 0.0 46.5 1.0 C5 I:CBR6 1.9 26.6 1.0 C6 I:CBR6 2.8 29.0 1.0 C4 I:CBR6 2.9 27.4 1.0 N4 I:CBR6 3.1 26.7 1.0 N3 I:U5 3.6 26.8 1.0 C4 I:U5 3.7 27.6 1.0 C5 I:U5 3.7 29.6 1.0 C6 I:U5 3.7 28.0 1.0 C2 I:U5 3.7 31.4 1.0 N1 I:U5 3.7 27.9 1.0 OP2 I:CBR6 3.8 24.1 1.0 N1 I:CBR6 4.1 30.8 1.0 C2' I:U5 4.1 30.1 1.0 N3 I:CBR6 4.1 29.8 1.0 O4 I:U5 4.2 28.0 1.0 C3' I:U5 4.3 29.5 1.0 O2 I:U5 4.3 31.9 1.0 O5' I:CBR6 4.4 23.7 1.0 C1' I:U5 4.5 31.6 1.0 N7 I:G7 4.6 36.1 1.0 C2 I:CBR6 4.6 31.5 1.0 P I:CBR6 4.7 24.8 1.0

Bromine binding site 10 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 J:Br6 b:58.8 occ:1.00 BR J:CBR6 0.0 58.8 1.0 C5 J:CBR6 1.9 31.3 1.0 C6 J:CBR6 2.8 27.9 1.0 C4 J:CBR6 2.9 30.0 1.0 N4 J:CBR6 3.1 25.4 1.0 C4 J:U5 3.3 29.9 1.0 N3 J:U5 3.4 31.6 1.0 C5 J:U5 3.5 31.4 1.0 C2 J:U5 3.7 31.4 1.0 C6 J:U5 3.7 27.3 1.0 OP2 J:CBR6 3.8 24.1 1.0 N1 J:U5 3.8 28.9 1.0 O4 J:U5 3.8 29.8 1.0 N1 J:CBR6 4.1 29.0 1.0 N3 J:CBR6 4.2 30.7 1.0 O2 J:U5 4.4 31.2 1.0 C3' J:U5 4.6 26.1 1.0 C2' J:U5 4.6 24.9 1.0 AG J:AG102 4.6 41.4 0.5 C2 J:CBR6 4.7 29.9 1.0 O5' J:CBR6 4.7 22.9 1.0 C1' J:U5 4.8 25.3 1.0 P J:CBR6 4.9 33.5 1.0

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