Bromine in PDB 1j9h: Crystal Structure of An Rna Duplex with Uridine Bulges

The structure of Crystal Structure of An Rna Duplex with Uridine Bulges, PDB code: 1j9h was solved by Y.Xiong, J.Deng, C.Sudarsanakumar, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.40
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.180, 47.180, 80.040, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 23.4

The structure of Crystal Structure of An Rna Duplex with Uridine Bulges also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Bromine atom in the Crystal Structure of An Rna Duplex with Uridine Bulges (pdb code 1j9h). 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 An Rna Duplex with Uridine Bulges, PDB code: 1j9h:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of An Rna Duplex with Uridine Bulges


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 An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ A:Br7 b:16.4 occ:1.00 BR A:CBR7 0.0 16.4 1.0 C5 A:CBR7 1.9 13.4 1.0 C6 A:CBR7 2.8 14.2 1.0 C4 A:CBR7 2.9 12.4 1.0 N4 A:CBR7 3.1 11.2 1.0 O A:HOH195 3.3 24.5 1.0 OP2 A:G6 3.5 18.4 1.0 C8 A:G6 3.5 14.6 1.0 N7 A:G6 3.6 14.2 1.0 OP2 A:CBR7 3.6 22.4 1.0 O5' A:G6 3.6 16.3 1.0 O A:HOH202 3.7 24.6 1.0 O A:HOH159 3.7 17.6 1.0 C3' A:G6 4.0 16.6 1.0 N1 A:CBR7 4.1 13.9 1.0 N9 A:G6 4.1 15.2 1.0 N3 A:CBR7 4.1 12.8 1.0 P A:G6 4.2 17.1 1.0 O A:HOH127 4.2 18.5 1.0 C5 A:G6 4.2 13.7 1.0 O5' A:CBR7 4.4 19.3 1.0 P A:CBR7 4.5 22.4 1.0 C4 A:G6 4.5 14.8 1.0 C2 A:CBR7 4.6 13.6 1.0 C5' A:G6 4.7 15.0 1.0 C2' A:G6 4.7 16.5 1.0 O3' A:G6 4.8 19.2 1.0 C4' A:G6 4.8 16.6 1.0 C1' A:G6 4.9 16.8 1.0 N7 A:A8 4.9 13.3 1.0 OP1 A:G6 4.9 21.9 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of An Rna Duplex with Uridine Bulges


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 An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:Br16 b:13.2 occ:1.00 BR B:CBR16 0.0 13.2 1.0 C5 B:CBR16 1.9 11.9 1.0 C6 B:CBR16 2.8 11.2 1.0 C4 B:CBR16 2.9 10.3 1.0 N4 B:CBR16 3.1 12.2 1.0 O A:HOH211 3.4 24.4 1.0 OP2 B:CBR16 3.5 15.7 1.0 OP2 B:G15 3.6 18.1 1.0 C8 B:G15 3.6 14.2 1.0 O B:HOH111 3.6 15.9 1.0 O B:HOH114 3.7 15.6 1.0 N7 B:G15 3.7 14.1 1.0 O5' B:G15 3.7 15.4 1.0 O B:HOH242 3.7 32.3 1.0 O B:HOH162 3.8 21.8 1.0 O B:HOH186 4.1 21.9 1.0 C3' B:G15 4.1 14.3 1.0 N3 B:CBR16 4.1 10.1 1.0 N1 B:CBR16 4.1 11.5 1.0 N9 B:G15 4.2 12.2 1.0 P B:G15 4.2 17.4 1.0 O B:HOH180 4.2 20.6 1.0 C5 B:G15 4.3 12.8 1.0 O5' B:CBR16 4.4 14.4 1.0 P B:CBR16 4.5 15.2 1.0 C4 B:G15 4.5 13.7 1.0 C2 B:CBR16 4.6 11.5 1.0 C5' B:G15 4.8 11.7 1.0 C2' B:G15 4.8 14.9 1.0 O3' B:G15 4.8 14.8 1.0 OP1 B:G15 4.8 16.0 1.0 C4' B:G15 4.9 14.8 1.0 C1' B:G15 4.9 14.7 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of An Rna Duplex with Uridine Bulges


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 An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ C:Br25 b:12.2 occ:1.00 BR C:CBR25 0.0 12.2 1.0 C5 C:CBR25 1.9 10.8 1.0 C6 C:CBR25 2.8 10.2 1.0 C4 C:CBR25 2.9 9.9 1.0 N4 C:CBR25 3.1 9.8 1.0 OP2 C:CBR25 3.5 13.8 1.0 C8 C:G24 3.6 12.8 1.0 OP2 C:G24 3.6 12.4 1.0 O C:HOH197 3.6 24.0 1.0 N7 C:G24 3.6 11.7 1.0 O C:HOH138 3.6 16.0 1.0 O C:HOH124 3.7 16.2 1.0 O5' C:G24 3.7 13.9 1.0 O C:HOH121 3.8 16.3 1.0 O C:HOH160 3.9 19.1 1.0 N1 C:CBR25 4.1 9.7 1.0 N3 C:CBR25 4.1 10.1 1.0 C3' C:G24 4.1 12.9 1.0 N9 C:G24 4.2 11.9 1.0 P C:G24 4.2 13.5 1.0 C5 C:G24 4.3 11.0 1.0 O5' C:CBR25 4.4 12.8 1.0 O C:HOH225 4.4 24.3 1.0 P C:CBR25 4.5 13.1 1.0 C4 C:G24 4.6 11.1 1.0 C2 C:CBR25 4.6 10.5 1.0 C5' C:G24 4.8 12.7 1.0 O3' C:G24 4.8 11.6 1.0 C2' C:G24 4.8 13.9 1.0 OP1 C:G24 4.9 14.5 1.0 C4' C:G24 4.9 13.2 1.0 C1' C:G24 5.0 14.0 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of An Rna Duplex with Uridine Bulges


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 An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ D:Br34 b:13.3 occ:1.00 BR D:CBR34 0.0 13.3 1.0 C5 D:CBR34 1.9 10.8 1.0 C6 D:CBR34 2.8 11.8 1.0 C4 D:CBR34 2.9 9.6 1.0 N4 D:CBR34 3.1 10.9 1.0 OP2 D:G33 3.5 13.2 1.0 OP2 D:CBR34 3.5 15.9 1.0 C8 D:G33 3.5 11.7 1.0 O5' D:G33 3.6 13.1 1.0 O D:HOH112 3.6 16.6 1.0 N7 D:G33 3.7 12.8 1.0 O D:HOH221 3.7 26.5 1.0 O D:HOH161 3.7 17.9 1.0 O D:HOH203 3.7 23.1 1.0 C3' D:G33 4.1 14.2 1.0 N1 D:CBR34 4.1 11.0 1.0 P D:G33 4.1 12.4 1.0 N3 D:CBR34 4.1 10.7 1.0 N9 D:G33 4.2 11.9 1.0 O D:HOH137 4.2 17.6 1.0 C5 D:G33 4.3 10.5 1.0 O5' D:CBR34 4.3 15.5 1.0 P D:CBR34 4.5 15.7 1.0 C4 D:G33 4.6 11.1 1.0 C2 D:CBR34 4.6 10.4 1.0 C5' D:G33 4.7 14.2 1.0 OP1 D:G33 4.7 14.3 1.0 C2' D:G33 4.8 14.2 1.0 O3' D:G33 4.8 14.6 1.0 C4' D:G33 4.8 11.4 1.0 N7 D:A35 4.9 12.6 1.0 O D:HOH215 4.9 29.1 1.0 C1' D:G33 4.9 13.8 1.0 O4' D:G33 5.0 13.7 1.0

Y.Xiong, J.Deng, C.Sudarsanakumar, M.Sundaralingam. Crystal Structure of An Rna Duplex R(Gugucgcac)(2) with Uridine Bulges. J.Mol.Biol. V. 313 573 2001.
ISSN: ISSN 0022-2836
PubMed: 11676540
DOI: 10.1006/JMBI.2001.5045