Bromine in PDB 1j6s: Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads

The structure of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads, PDB code: 1j6s was solved by B.Pan, Y.Xiong, K.Shi, J.Deng, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.40
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	37.984, 37.984, 82.195, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.4

The structure of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads also contains other interesting chemical elements:

Barium	(Ba)	8 atoms
Sodium	(Na)	8 atoms

The binding sites of Bromine atom in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads (pdb code 1j6s). 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 Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads, PDB code: 1j6s:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


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 Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1 b:14.4 occ:1.00 BR A:BRU1 0.0 14.4 1.0 C5 A:BRU1 1.9 9.8 1.0 C6 A:BRU1 2.8 10.2 1.0 C4 A:BRU1 2.8 10.5 1.0 O4 A:BRU1 3.1 9.6 1.0 OP1 C:A15 3.4 8.1 1.0 O5' C:A15 3.6 7.0 1.0 C5' C:A15 3.7 7.1 1.0 O C:HOH377 3.8 22.3 1.0 C4' C:A15 3.9 6.7 1.0 N3 A:BRU1 4.1 9.3 1.0 O3' C:A15 4.1 6.8 1.0 N1 A:BRU1 4.1 9.6 1.0 P C:A15 4.2 8.1 1.0 O A:HOH388 4.6 26.1 1.0 O5' A:BRU1 4.6 9.7 1.0 C2 A:BRU1 4.7 9.6 1.0 C3' C:A15 4.7 7.1 1.0 OP1 C:G16 4.8 7.7 1.0 O A:HOH319 5.0 17.8 1.0 O A:HOH355 5.0 11.2 1.0 O3' C:G14 5.0 7.0 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


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 Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range: probe atom residue distance (Å) B Occ B:Br7 b:8.4 occ:1.00 BR B:BRU7 0.0 8.4 1.0 C5 B:BRU7 1.9 6.4 1.0 C6 B:BRU7 2.8 6.4 1.0 C4 B:BRU7 2.9 6.9 1.0 O4 B:BRU7 3.2 6.2 1.0 O C:HOH333 3.5 18.2 1.0 O B:HOH353 4.1 19.4 1.0 N1 B:BRU7 4.1 6.7 1.0 N3 B:BRU7 4.1 6.3 1.0 O5' B:BRU7 4.1 9.0 1.0 C2 B:BRU7 4.7 6.4 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


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 Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range: probe atom residue distance (Å) B Occ C:Br13 b:12.4 occ:1.00 BR C:BRU13 0.0 12.4 1.0 C5 C:BRU13 1.9 9.3 1.0 C6 C:BRU13 2.8 9.4 1.0 C4 C:BRU13 2.9 9.3 1.0 O4 C:BRU13 3.1 9.6 1.0 O C:HOH390 4.1 24.5 1.0 N1 C:BRU13 4.1 9.1 1.0 N3 C:BRU13 4.1 9.3 1.0 O5' C:BRU13 4.4 14.5 1.0 C2 C:BRU13 4.7 9.4 1.0 O C:HOH370 4.8 27.4 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


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 Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range: probe atom residue distance (Å) B Occ D:Br19 b:7.6 occ:1.00 BR D:BRU19 0.0 7.6 1.0 C5 D:BRU19 1.9 5.7 1.0 C6 D:BRU19 2.8 5.8 1.0 C4 D:BRU19 2.8 5.9 1.0 O4 D:BRU19 3.1 5.8 1.0 N3 D:BRU19 4.1 6.0 1.0 N1 D:BRU19 4.1 5.7 1.0 O5' D:BRU19 4.2 7.8 1.0 C2 D:BRU19 4.7 6.3 1.0

B.Pan, Y.Xiong, K.Shi, J.Deng, M.Sundaralingam. Crystal Structure of An Rna Purine-Rich Tetraplex Containing Adenine Tetrads: Implications For Specific Binding in Rna Tetraplexes Structure V. 11 815 2003.
ISSN: ISSN 0969-2126
PubMed: 12842044
DOI: 10.1016/S0969-2126(03)00107-2