Bromine in PDB 5ay2: Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs

The structure of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs, PDB code: 5ay2 was solved by J.Kondo, Y.Tada, T.Dairaku, H.Saneyoshi, I.Okamoto, Y.Tanaka, A.Ono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.480, 46.860, 89.940, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 18.9

The structure of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs also contains other interesting chemical elements:

Silver

(Ag)

4 atoms

The binding sites of Bromine atom in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs (pdb code 5ay2). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs, PDB code: 5ay2:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:19.2 occ:1.00 BR A:CBR6 0.0 19.2 1.0 C5 A:CBR6 1.9 17.2 1.0 C6 A:CBR6 2.8 15.8 1.0 C4 A:CBR6 2.9 15.7 1.0 N4 A:CBR6 3.1 13.5 1.0 O A:HOH240 3.3 24.4 1.0 O A:HOH258 3.5 41.5 1.0 C5 A:U5 3.6 14.1 1.0 OP2 A:CBR6 3.6 19.1 1.0 O A:HOH249 3.7 24.9 1.0 O A:HOH245 3.8 21.0 1.0 C4 A:U5 3.8 12.9 1.0 C6 A:U5 3.8 15.4 1.0 O A:HOH287 3.9 36.0 1.0 O A:HOH226 4.0 18.5 1.0 O A:HOH290 4.0 36.4 1.0 O B:HOH185 4.1 34.5 1.0 N3 A:U5 4.1 13.8 1.0 N1 A:CBR6 4.1 15.9 1.0 N3 A:CBR6 4.2 15.4 1.0 N1 A:U5 4.2 16.2 1.0 O4 A:U5 4.3 12.6 1.0 C2 A:U5 4.3 17.1 1.0 O5' A:CBR6 4.5 18.6 1.0 C3' A:U5 4.5 17.2 1.0 O A:HOH207 4.6 18.0 0.5 O A:HOH243 4.6 18.5 0.5 P A:CBR6 4.6 18.5 1.0 C2 A:CBR6 4.7 15.7 1.0 C2' A:U5 4.7 17.5 1.0 O A:HOH244 5.0 16.5 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br6 b:16.1 occ:1.00 BR B:CBR6 0.0 16.1 1.0 C5 B:CBR6 1.9 14.1 1.0 C6 B:CBR6 2.8 13.8 1.0 C4 B:CBR6 2.9 12.3 1.0 N4 B:CBR6 3.1 11.0 1.0 O B:HOH162 3.4 43.6 1.0 O B:HOH172 3.5 29.1 1.0 C5 B:U5 3.6 11.7 1.0 O B:HOH140 3.6 19.0 0.5 O B:HOH137 3.6 19.3 1.0 C6 B:U5 3.7 11.8 1.0 C4 B:U5 3.7 10.2 1.0 OP2 B:CBR6 3.8 14.4 1.0 O B:HOH116 3.8 16.6 0.5 O A:HOH286 3.8 44.5 1.0 N3 B:U5 4.0 10.4 1.0 N1 B:U5 4.0 12.1 1.0 O B:HOH118 4.1 28.2 1.0 N1 B:CBR6 4.1 13.3 1.0 C2 B:U5 4.2 12.7 1.0 N3 B:CBR6 4.2 12.8 1.0 O B:HOH111 4.2 42.7 1.0 O4 B:U5 4.3 11.6 1.0 C3' B:U5 4.4 12.8 1.0 O5' B:CBR6 4.5 14.6 1.0 C2' B:U5 4.6 12.2 1.0 O A:HOH279 4.6 41.0 1.0 C2 B:CBR6 4.7 13.5 1.0 P B:CBR6 4.7 14.8 1.0 C1' B:U5 4.9 11.3 1.0 O2 B:U5 4.9 13.5 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Br6 b:22.1 occ:1.00 BR C:CBR6 0.0 22.1 1.0 C5 C:CBR6 1.9 20.1 1.0 C6 C:CBR6 2.8 18.6 1.0 C4 C:CBR6 2.9 18.7 1.0 N4 C:CBR6 3.1 17.3 1.0 O C:HOH262 3.5 44.0 1.0 O C:HOH201 3.6 45.2 1.0 O C:HOH210 3.6 32.2 1.0 O C:HOH253 3.6 35.5 1.0 OP2 C:CBR6 3.6 25.1 1.0 C5 C:U5 3.7 21.9 1.0 C6 C:U5 3.8 22.0 1.0 C4 C:U5 3.8 22.1 1.0 O C:HOH216 3.9 24.7 1.0 N3 C:U5 4.1 20.9 1.0 N1 C:CBR6 4.1 16.7 1.0 N1 C:U5 4.1 22.4 1.0 N3 C:CBR6 4.2 15.7 1.0 C2 C:U5 4.3 23.0 1.0 O4 C:U5 4.3 21.9 1.0 O5' C:CBR6 4.4 22.7 1.0 C3' C:U5 4.4 24.6 1.0 C2' C:U5 4.6 24.4 1.0 P C:CBR6 4.6 23.0 1.0 C2 C:CBR6 4.7 17.4 1.0 C1' C:U5 4.9 23.9 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Rna Duplex Containing C-Ag(I)-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Br6 b:14.2 occ:1.00 BR D:CBR6 0.0 14.2 1.0 C5 D:CBR6 1.9 11.6 1.0 C6 D:CBR6 2.8 12.7 1.0 C4 D:CBR6 2.9 11.4 1.0 N4 D:CBR6 3.1 10.0 1.0 O D:HOH246 3.4 27.4 1.0 O D:HOH212 3.5 26.4 1.0 O D:HOH223 3.6 19.4 1.0 C5 D:U5 3.6 11.2 1.0 O D:HOH247 3.6 45.6 1.0 C6 D:U5 3.7 11.9 1.0 OP2 D:CBR6 3.7 13.4 1.0 C4 D:U5 3.7 11.5 1.0 O D:HOH214 3.8 18.3 1.0 N3 D:U5 3.8 10.9 1.0 N1 D:U5 3.9 10.8 1.0 C2 D:U5 4.0 12.6 1.0 O D:HOH207 4.0 26.3 1.0 O D:HOH271 4.0 44.5 1.0 N1 D:CBR6 4.1 13.1 1.0 N3 D:CBR6 4.2 12.6 1.0 C3' D:U5 4.2 11.6 1.0 O4 D:U5 4.3 12.5 1.0 O C:HOH270 4.3 27.1 1.0 C2' D:U5 4.3 10.8 1.0 O5' D:CBR6 4.4 11.9 1.0 O C:HOH269 4.4 49.0 1.0 P D:CBR6 4.6 13.1 1.0 O2 D:U5 4.7 13.7 1.0 C2 D:CBR6 4.7 11.2 1.0 C1' D:U5 4.7 12.8 1.0 N7 D:G7 4.9 13.4 1.0 O3' D:U5 5.0 11.5 1.0

J.Kondo, Y.Tada, T.Dairaku, H.Saneyoshi, I.Okamoto, Y.Tanaka, A.Ono. High-Resolution Crystal Structure of A Silver(I)-Rna Hybrid Duplex Containing Watson-Crick-Like Csilver(I)C Metallo-Base Pairs Angew.Chem.Int.Ed.Engl. V. 54 13323 2015.
ISSN: ESSN 1521-3773
PubMed: 26448329
DOI: 10.1002/ANIE.201507894