Bromine in PDB 5lqt: Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs, PDB code: 5lqt was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.58 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	34.340, 34.340, 103.170, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 22.7

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Bromine atom in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs (pdb code 5lqt). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs, PDB code: 5lqt:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:35.5 occ:1.00 BR A:CBV2 0.0 35.5 1.0 C5 A:CBV2 1.9 29.1 1.0 C4 A:CBV2 2.9 29.0 1.0 C6 A:CBV2 2.9 28.1 1.0 N4 A:CBV2 3.2 30.8 1.0 O3P A:CBV2 3.5 45.3 1.0 C5 A:G1 3.6 30.1 1.0 O A:HOH204 3.6 46.2 1.0 N7 A:G1 3.7 36.5 1.0 O A:HOH202 3.7 35.9 1.0 C4 A:G1 3.8 32.9 1.0 C8 A:G1 3.8 34.2 1.0 N9 A:G1 3.9 34.1 1.0 C6 A:G1 4.1 33.0 1.0 C3' A:G1 4.2 35.8 1.0 N3 A:CBV2 4.3 28.4 1.0 N1 A:CBV2 4.3 25.8 1.0 N3 A:G1 4.4 31.1 1.0 C2' A:G1 4.4 35.3 1.0 O5' A:CBV2 4.4 34.2 1.0 O5' A:G1 4.5 40.7 1.0 P A:CBV2 4.6 34.8 1.0 N1 A:G1 4.6 30.3 1.0 O6 A:G1 4.6 34.2 1.0 C2 A:G1 4.7 32.7 1.0 C1' A:G1 4.8 31.8 1.0 N4 A:C3 4.8 28.4 1.0 C2 A:CBV2 4.8 30.7 1.0 O2P A:CBV2 4.8 56.6 1.0 O3' A:G1 4.9 36.9 1.0 C5 A:C3 5.0 29.6 1.0

Bromine binding site 2 out of 2 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:37.1 occ:1.00 BR B:CBV2 0.0 37.1 1.0 C5 B:CBV2 1.9 31.9 1.0 C4 B:CBV2 2.9 29.9 1.0 C6 B:CBV2 2.9 35.6 1.0 N4 B:CBV2 3.2 31.9 1.0 O B:HOH202 3.4 40.7 1.0 O2P B:CBV2 3.6 45.8 1.0 O B:HOH217 3.6 39.8 1.0 N7 B:G1 3.6 34.0 1.0 C5 B:G1 3.6 30.2 1.0 O B:HOH212 3.6 39.8 1.0 O B:HOH206 3.7 40.8 1.0 C8 B:G1 3.7 31.5 1.0 C4 B:G1 3.8 29.1 1.0 N9 B:G1 3.8 30.7 1.0 C3' B:G1 4.1 32.0 1.0 C6 B:G1 4.2 32.8 1.0 N3 B:CBV2 4.3 32.9 1.0 N1 B:CBV2 4.3 33.3 1.0 C2' B:G1 4.3 32.7 1.0 O5' B:G1 4.4 36.9 1.0 O5' B:CBV2 4.5 39.3 1.0 N3 B:G1 4.5 30.0 1.0 P B:CBV2 4.6 38.3 1.0 N4 B:C3 4.6 38.2 1.0 C1' B:G1 4.6 31.5 1.0 O6 B:G1 4.8 33.4 1.0 N1 B:G1 4.8 30.9 1.0 C5 B:C3 4.8 35.6 1.0 C2 B:CBV2 4.8 33.2 1.0 O3' B:G1 4.8 35.8 1.0 C2 B:G1 4.9 28.5 1.0 O3P B:CBV2 4.9 62.0 1.0

L.Huang, S.Ashraf, J.Wang, D.M.Lilley. Control of Box C/D Snornp Assembly By N(6)-Methylation of Adenine. Embo Rep. V. 18 1631 2017.
ISSN: ESSN 1469-3178
PubMed: 28623187
DOI: 10.15252/EMBR.201743967