Bromine in PDB 5ay3: Crystal Structure of Rna Duplex Containing C-C Base Pairs

The structure of Crystal Structure of Rna Duplex Containing C-C Base Pairs, PDB code: 5ay3 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)	25.80 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.160, 44.460, 27.370, 90.00, 109.43, 90.00
R / Rfree (%)	18.4 / 19.9

The binding sites of Bromine atom in the Crystal Structure of Rna Duplex Containing C-C Base Pairs (pdb code 5ay3). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Rna Duplex Containing C-C Base Pairs, PDB code: 5ay3:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of Rna Duplex Containing C-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-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:17.9 occ:1.00 BR A:CBR6 0.0 17.9 1.0 C5 A:CBR6 1.9 12.5 1.0 C6 A:CBR6 2.8 13.3 1.0 C4 A:CBR6 2.9 11.5 1.0 N4 A:CBR6 3.1 10.6 1.0 O A:HOH134 3.2 34.1 1.0 O A:HOH121 3.6 11.2 0.3 OP2 A:CBR6 3.6 19.6 1.0 C5 A:U5 3.6 12.2 1.0 O A:HOH169 3.6 22.5 1.0 C6 A:U5 3.8 13.8 1.0 C4 A:U5 3.8 12.3 1.0 O A:HOH137 3.8 25.5 1.0 O A:HOH156 3.9 11.3 0.3 O A:HOH164 4.0 19.7 0.3 N3 A:U5 4.0 13.3 1.0 N1 A:U5 4.0 15.7 1.0 N1 A:CBR6 4.1 11.9 1.0 C2 A:U5 4.1 15.5 1.0 N3 A:CBR6 4.2 11.3 1.0 O4 A:U5 4.3 11.7 1.0 C3' A:U5 4.3 17.3 1.0 O5' A:CBR6 4.4 16.1 1.0 C2' A:U5 4.5 17.1 1.0 O A:HOH104 4.6 34.8 1.0 P A:CBR6 4.6 17.6 1.0 C2 A:CBR6 4.7 12.3 1.0 C1' A:U5 4.8 16.6 1.0 O2 A:U5 4.9 16.8 1.0 O A:HOH141 5.0 27.0 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of Rna Duplex Containing C-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-C Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br6 b:15.1 occ:1.00 BR B:CBR6 0.0 15.1 1.0 C5 B:CBR6 1.9 10.1 1.0 O B:HOH167 2.3 21.0 0.5 O B:HOH129 2.8 38.1 1.0 C6 B:CBR6 2.8 10.5 1.0 C4 B:CBR6 2.9 9.2 1.0 N4 B:CBR6 3.1 11.1 1.0 O B:HOH161 3.4 15.8 0.5 O B:HOH125 3.5 15.8 1.0 OP2 B:CBR6 3.5 11.9 1.0 O B:HOH156 3.5 36.4 1.0 C6 B:U5 3.7 11.5 1.0 C5 B:U5 3.7 12.2 1.0 O B:HOH158 3.8 22.8 1.0 N1 B:U5 3.9 12.6 1.0 C4 B:U5 3.9 11.9 1.0 O B:HOH116 4.0 20.3 1.0 C3' B:U5 4.1 11.4 1.0 N1 B:CBR6 4.1 9.3 1.0 N3 B:U5 4.1 13.5 1.0 N3 B:CBR6 4.1 10.3 1.0 C2 B:U5 4.2 10.4 1.0 O B:HOH174 4.2 50.4 1.0 C2' B:U5 4.3 12.5 1.0 O5' B:CBR6 4.4 11.3 1.0 P B:CBR6 4.5 10.6 1.0 O4 B:U5 4.6 13.9 1.0 N7 B:G7 4.6 9.6 1.0 C2 B:CBR6 4.6 9.6 1.0 C1' B:U5 4.7 12.1 1.0 O3' B:U5 4.8 10.9 1.0 O5' B:U5 4.8 13.7 1.0 O2 B:U5 4.9 13.3 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