Bromine in PDB 5ay4: Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II)

The structure of Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II), PDB code: 5ay4 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)	26.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.000, 44.540, 27.550, 90.00, 109.10, 90.00
R / Rfree (%)	16 / 19.6

The structure of Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Bromine atom in the Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II) (pdb code 5ay4). 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 Obtained in the Presence of Hg(II), PDB code: 5ay4:
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 Obtained in the Presence of Hg(II)


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 Obtained in the Presence of Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:22.4 occ:1.00 BR A:CBR6 0.0 22.4 1.0 C5 A:CBR6 1.9 17.0 1.0 C6 A:CBR6 2.8 18.3 1.0 C4 A:CBR6 2.9 16.2 1.0 N4 A:CBR6 3.1 14.4 1.0 O A:HOH117 3.2 44.6 0.5 O A:HOH144 3.3 40.5 0.5 C5 A:U5 3.6 16.8 1.0 O A:HOH125 3.7 29.1 1.0 O A:HOH179 3.7 43.5 1.0 C6 A:U5 3.7 17.7 1.0 O A:HOH163 3.8 25.1 1.0 C4 A:U5 3.8 16.3 1.0 OP2 A:CBR6 3.8 25.2 1.0 O A:HOH150 3.8 25.7 1.0 O A:HOH167 3.9 35.3 1.0 N3 A:U5 4.0 15.8 1.0 N1 A:U5 4.0 19.7 1.0 C2 A:U5 4.1 18.5 1.0 N1 A:CBR6 4.1 17.7 1.0 N3 A:CBR6 4.2 15.3 1.0 O4 A:U5 4.3 14.0 1.0 C3' A:U5 4.4 23.0 1.0 O5' A:CBR6 4.5 24.2 1.0 C2' A:U5 4.5 22.1 1.0 C2 A:CBR6 4.7 17.1 1.0 P A:CBR6 4.7 25.3 1.0 O A:HOH116 4.8 29.9 1.0 C1' A:U5 4.8 20.6 1.0 O2 A:U5 4.8 19.2 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II)


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 Obtained in the Presence of Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Br6 b:17.6 occ:1.00 BR B:CBR6 0.0 17.6 1.0 C5 B:CBR6 1.9 13.1 1.0 C6 B:CBR6 2.8 12.5 1.0 C4 B:CBR6 2.9 13.0 1.0 N4 B:CBR6 3.1 12.5 1.0 O B:HOH246 3.2 20.9 0.5 O B:HOH227 3.4 15.1 1.0 O B:HOH264 3.5 34.6 1.0 OP2 B:CBR6 3.5 12.9 1.0 C5 B:U5 3.6 15.9 1.0 C6 B:U5 3.6 14.7 1.0 O B:HOH208 3.7 17.7 0.5 O B:HOH257 3.8 28.1 1.0 C4 B:U5 3.8 15.9 1.0 N1 B:U5 3.9 14.5 1.0 O B:HOH212 3.9 18.6 1.0 N3 B:U5 4.0 14.6 1.0 C2 B:U5 4.0 13.7 1.0 N1 B:CBR6 4.1 11.8 1.0 C3' B:U5 4.1 14.1 1.0 N3 B:CBR6 4.2 11.5 1.0 C2' B:U5 4.2 15.1 1.0 O5' B:CBR6 4.4 12.6 1.0 O4 B:U5 4.4 16.2 1.0 P B:CBR6 4.5 11.9 1.0 C1' B:U5 4.6 13.7 1.0 N7 B:G7 4.6 12.5 1.0 C2 B:CBR6 4.7 12.9 1.0 O2 B:U5 4.8 13.5 1.0 O3' B:U5 4.9 14.3 1.0 O5' B:U5 4.9 14.7 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