Bromine in PDB 5nex: The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine, PDB code: 5nex was solved by L.Huang, J.Wang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.42 / 1.72
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	55.639, 55.639, 135.927, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 23.3

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Bromine atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine (pdb code 5nex). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total only one binding site of Bromine was determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine, PDB code: 5nex:

Bromine binding site 1 out of 1 in the The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of The Structure of the G. Violaceus Guanidine II Riboswitch P1 Stem-Loop with Agmatine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br17 b:74.9 occ:1.00 BR A:CBV17 0.0 74.9 1.0 C5 A:CBV17 1.9 33.8 1.0 HN42 A:CBV17 2.7 34.6 1.0 C6 A:CBV17 2.9 24.3 1.0 C4 A:CBV17 3.0 28.4 1.0 H6 A:CBV17 3.0 29.1 1.0 N4 A:CBV17 3.1 28.8 1.0 H3' A:A16 3.4 30.9 1.0 N7 A:A16 3.5 31.6 1.0 C8 A:A16 3.6 29.2 1.0 C5 A:A16 3.6 26.9 1.0 O1P A:CBV17 3.6 30.5 1.0 H2' A:A16 3.7 26.9 1.0 O A:HOH209 3.8 46.9 1.0 N9 A:A16 3.8 26.5 1.0 C4 A:A16 3.8 28.9 1.0 H8 A:A16 4.0 35.0 1.0 HN41 A:CBV17 4.0 34.6 1.0 O A:HOH207 4.2 49.9 1.0 C3' A:A16 4.2 25.7 1.0 C6 A:A16 4.2 29.2 1.0 N1 A:CBV17 4.2 26.0 1.0 N3 A:CBV17 4.3 25.4 1.0 C2' A:A16 4.3 22.4 1.0 O5' A:CBV17 4.4 25.7 1.0 H5 A:C18 4.5 39.6 1.0 N3 A:A16 4.6 24.6 1.0 P A:CBV17 4.6 30.6 1.0 C1' A:A16 4.6 26.5 1.0 H62 A:A16 4.7 36.7 1.0 H41 A:C18 4.7 40.9 1.0 N6 A:A16 4.7 30.6 1.0 C2 A:CBV17 4.8 27.4 1.0 N1 A:A16 4.8 24.3 1.0 O3' A:A16 4.9 29.0 1.0 C2 A:A16 4.9 26.0 1.0 O5' A:A16 5.0 28.4 1.0

L.Huang, J.Wang, D.M.J.Lilley. The Structure of the Guanidine-II Riboswitch. Cell Chem Biol V. 24 695 2017.
ISSN: ESSN 2451-9456
PubMed: 28529131
DOI: 10.1016/J.CHEMBIOL.2017.05.014