Bromine in PDB 5vjb: Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa

The structure of Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa, PDB code: 5vjb was solved by C.W.Reiss, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.234, 60.540, 71.914, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 23.8

The structure of Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Bromine atom in the Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa (pdb code 5vjb). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa, PDB code: 5vjb:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Br14 b:61.1 occ:1.00 BR A:5BU14 0.0 61.1 1.0 C5 A:5BU14 1.9 35.2 1.0 C6 A:5BU14 2.8 42.3 1.0 C4 A:5BU14 2.9 38.7 1.0 O4 A:5BU14 3.1 40.6 1.0 OP2 A:5BU14 3.4 48.5 1.0 C6 A:C13 3.6 40.6 1.0 C5 A:C13 3.6 37.6 1.0 C3' A:C13 3.9 50.2 1.0 N1 A:C13 3.9 41.9 1.0 N1 A:5BU14 4.1 42.8 1.0 C4 A:C13 4.1 37.5 1.0 N3 A:5BU14 4.1 37.5 1.0 O5' A:5BU14 4.2 46.3 1.0 C2' A:C13 4.3 47.7 1.0 O5' A:C13 4.3 42.6 1.0 C2 A:C13 4.3 40.5 1.0 P A:5BU14 4.4 49.8 1.0 N3 A:C13 4.4 38.7 1.0 C2 A:5BU14 4.6 39.5 1.0 C1' A:C13 4.6 47.5 1.0 O3' A:C13 4.7 56.1 1.0 OP2 A:C13 4.7 47.7 1.0 N4 A:C13 4.8 36.9 1.0 C4' A:C13 5.0 49.0 1.0

Bromine binding site 2 out of 4 in the Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Br14 b:48.8 occ:1.00 BR B:5BU14 0.0 48.8 1.0 C5 B:5BU14 1.9 42.4 1.0 C6 B:5BU14 2.8 38.2 1.0 C4 B:5BU14 2.9 39.0 1.0 O4 B:5BU14 3.1 34.8 1.0 OP2 B:5BU14 3.5 37.8 1.0 C6 B:C13 3.6 35.3 1.0 C5 B:C13 3.7 37.3 1.0 C7 B:SPM102 3.9 73.8 1.0 C9 B:SPM102 3.9 64.7 1.0 N1 B:5BU14 4.1 39.6 1.0 C3' B:C13 4.1 38.0 1.0 N1 B:C13 4.1 33.5 1.0 N3 B:5BU14 4.1 37.4 1.0 O5' B:C13 4.2 46.1 1.0 C4 B:C13 4.2 34.8 1.0 OP2 B:C13 4.3 38.2 1.0 N10 B:SPM102 4.5 55.6 1.0 O5' B:5BU14 4.5 39.5 1.0 C8 B:SPM102 4.5 72.2 1.0 P B:5BU14 4.5 42.2 1.0 C2 B:C13 4.6 40.5 1.0 C2 B:5BU14 4.6 38.8 1.0 C2' B:C13 4.6 39.1 1.0 N3 B:C13 4.6 36.2 1.0 C1' B:C13 4.8 33.4 1.0 O3' B:C13 4.8 39.5 1.0 N4 B:C13 4.9 37.3 1.0 P B:C13 4.9 42.6 1.0

Bromine binding site 3 out of 4 in the Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Br14 b:54.2 occ:1.00 BR C:5BU14 0.0 54.2 1.0 C5 C:5BU14 1.9 40.0 1.0 C6 C:5BU14 2.8 39.6 1.0 C4 C:5BU14 2.9 39.9 1.0 O4 C:5BU14 3.1 38.9 1.0 OP2 C:5BU14 3.3 49.1 1.0 C6 C:C13 3.6 45.9 1.0 C5 C:C13 3.7 36.8 1.0 C3' C:C13 4.0 45.2 1.0 N1 C:C13 4.0 40.5 1.0 N1 C:5BU14 4.1 39.8 1.0 O5' C:5BU14 4.2 45.1 1.0 N3 C:5BU14 4.2 38.1 1.0 C4 C:C13 4.2 36.5 1.0 O5' C:C13 4.3 44.8 1.0 P C:5BU14 4.3 45.2 1.0 C2' C:C13 4.3 43.8 1.0 C2 C:C13 4.5 41.0 1.0 N3 C:C13 4.5 35.1 1.0 OP2 C:C13 4.6 43.9 1.0 C2 C:5BU14 4.6 41.0 1.0 O3' C:C13 4.7 45.2 1.0 C1' C:C13 4.7 42.9 1.0 N4 C:C13 4.9 32.4 1.0

Bromine binding site 4 out of 4 in the Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Guanidine-II Riboswitch P2 Hairpin Dimer with 5-Bromou Substitution From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Br14 b:50.2 occ:1.00 BR D:5BU14 0.0 50.2 1.0 C5 D:5BU14 1.8 42.4 1.0 C6 D:5BU14 2.8 42.3 1.0 C4 D:5BU14 2.8 44.1 1.0 O4 D:5BU14 3.0 46.0 1.0 OP2 D:5BU14 3.5 50.1 1.0 C5 D:C13 3.6 42.4 1.0 C6 D:C13 3.6 44.2 1.0 N1 D:5BU14 4.0 43.0 1.0 N1 D:C13 4.0 44.0 1.0 C4 D:C13 4.0 40.0 1.0 N3 D:5BU14 4.0 43.0 1.0 C3' D:C13 4.1 42.7 1.0 N3 D:C13 4.3 36.3 1.0 C2 D:C13 4.3 41.3 1.0 O5' D:5BU14 4.3 43.5 1.0 P D:5BU14 4.4 50.9 1.0 C2' D:C13 4.4 42.3 1.0 C2 D:5BU14 4.5 43.6 1.0 O5' D:C13 4.5 41.9 1.0 N4 D:C13 4.7 40.5 1.0 OP2 D:C13 4.7 36.1 1.0 C1' D:C13 4.7 41.7 1.0 O3' D:C13 4.8 45.9 1.0

C.W.Reiss, S.A.Strobel. Structural Basis For Ligand Binding to the Guanidine-II Riboswitch. Rna V. 23 1338 2017.
ISSN: ESSN 1469-9001
PubMed: 28600356
DOI: 10.1261/RNA.061804.117