Bromine in PDB 5ndh: The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh 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)	50.17 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.727, 57.825, 100.862, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 22.2

The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	4 atoms

The binding sites of Bromine atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop (pdb code 5ndh). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop


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 P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:53.7 occ:1.00 BR A:CBV2 0.0 53.7 1.0 C5 A:CBV2 1.9 46.0 1.0 HN42 A:CBV2 2.7 52.5 1.0 C4 A:CBV2 2.9 45.0 1.0 C6 A:CBV2 3.0 43.0 1.0 H6 A:CBV2 3.1 51.6 1.0 N4 A:CBV2 3.1 43.8 1.0 H3' A:G1 3.3 1.0 1.0 O A:HOH202 3.3 56.4 1.0 O2P A:CBV2 3.5 45.9 1.0 N7 A:G1 3.6 47.2 1.0 C5 A:G1 3.7 46.7 1.0 C8 A:G1 3.7 49.9 1.0 H2' A:G1 3.9 79.3 1.0 C4 A:G1 3.9 47.5 1.0 N9 A:G1 4.0 48.5 1.0 HN41 A:CBV2 4.0 52.5 1.0 H8 A:G1 4.1 59.9 1.0 C3' A:G1 4.2 95.8 1.0 C6 A:G1 4.2 38.6 1.0 N3 A:CBV2 4.3 39.8 1.0 N1 A:CBV2 4.3 47.8 1.0 O5' A:G1 4.3 54.3 1.0 C2' A:G1 4.4 66.1 1.0 O5' A:CBV2 4.5 60.1 1.0 P A:CBV2 4.5 59.3 1.0 N3 A:G1 4.6 42.2 1.0 O6 A:G1 4.7 39.4 1.0 N7 A:G3 4.7 37.3 1.0 C1' A:G1 4.8 62.4 1.0 N1 A:G1 4.8 38.1 1.0 O3' A:G1 4.8 81.5 1.0 C2 A:CBV2 4.9 44.0 1.0

Bromine binding site 2 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:66.3 occ:1.00 BR B:CBV2 0.0 66.3 1.0 C5 B:CBV2 1.9 46.3 1.0 HN42 B:CBV2 2.8 48.3 1.0 C6 B:CBV2 2.9 36.8 1.0 C4 B:CBV2 3.0 35.2 1.0 H6 B:CBV2 3.0 44.1 1.0 N4 B:CBV2 3.2 40.3 1.0 H3' B:G1 3.4 69.3 1.0 HO5' B:G1 3.5 64.9 1.0 N7 B:G1 3.5 52.5 1.0 C5 B:G1 3.7 46.1 1.0 C8 B:G1 3.7 50.3 1.0 O1P B:CBV2 3.7 40.1 1.0 C4 B:G1 4.0 45.0 1.0 N9 B:G1 4.0 48.8 1.0 H2' B:G1 4.0 66.8 1.0 H8 B:G1 4.1 60.4 1.0 HN41 B:CBV2 4.1 48.3 1.0 C6 B:G1 4.2 45.6 1.0 O5' B:G1 4.3 54.1 1.0 C3' B:G1 4.3 57.7 1.0 N1 B:CBV2 4.3 36.1 1.0 N3 B:CBV2 4.3 34.7 1.0 C2' B:G1 4.5 55.6 1.0 O5' B:CBV2 4.6 40.2 1.0 NA B:NA102 4.6 58.5 1.0 O6 B:G1 4.7 40.0 1.0 N3 B:G1 4.7 40.7 1.0 P B:CBV2 4.7 56.4 1.0 C1' B:G1 4.8 58.1 1.0 C2 B:CBV2 4.8 38.6 1.0 N1 B:G1 4.9 40.0 1.0

Bromine binding site 3 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ C:Br2 b:43.0 occ:1.00 BR C:CBV2 0.0 43.0 1.0 C5 C:CBV2 1.9 41.0 1.0 HN42 C:CBV2 2.8 47.5 1.0 C4 C:CBV2 2.9 37.9 1.0 C6 C:CBV2 3.0 36.2 1.0 H6 C:CBV2 3.0 43.4 1.0 N4 C:CBV2 3.2 39.6 1.0 H3' C:G1 3.5 64.7 1.0 O3P C:CBV2 3.5 68.5 1.0 N7 C:G1 3.6 43.6 1.0 C5 C:G1 3.7 43.3 1.0 C8 C:G1 3.8 41.8 1.0 O C:HOH212 3.9 50.0 1.0 H2' C:G1 3.9 59.5 1.0 C4 C:G1 4.0 41.2 1.0 N9 C:G1 4.0 44.3 1.0 HN41 C:CBV2 4.0 47.5 1.0 O C:HOH201 4.1 51.7 1.0 H8 C:G1 4.2 50.2 1.0 C6 C:G1 4.3 44.7 1.0 N3 C:CBV2 4.3 37.4 1.0 N1 C:CBV2 4.3 36.4 1.0 C3' C:G1 4.3 53.9 1.0 O5' C:CBV2 4.4 44.5 1.0 P C:CBV2 4.5 49.3 1.0 C2' C:G1 4.5 49.6 1.0 O5' C:G1 4.7 46.6 1.0 N3 C:G1 4.7 43.6 1.0 O6 C:G1 4.7 43.6 1.0 O2P C:CBV2 4.7 80.1 1.0 C2 C:CBV2 4.8 41.2 1.0 N1 C:G1 4.9 41.4 1.0 C1' C:G1 4.9 49.0 1.0 O3' C:G1 4.9 56.3 1.0

Bromine binding site 4 out of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ D:Br2 b:47.5 occ:1.00 BR D:CBV2 0.0 47.5 1.0 C5 D:CBV2 1.9 43.8 1.0 HN42 D:CBV2 2.7 50.4 1.0 C4 D:CBV2 2.9 34.7 1.0 C6 D:CBV2 2.9 43.2 1.0 H6 D:CBV2 3.0 51.9 1.0 N4 D:CBV2 3.2 42.0 1.0 H3' D:G1 3.3 63.7 1.0 O1P D:CBV2 3.5 56.0 1.0 HO5' D:G1 3.5 66.4 1.0 N7 D:G1 3.6 40.2 1.0 C5 D:G1 3.7 38.0 1.0 C8 D:G1 3.8 37.8 1.0 C4 D:G1 4.0 41.9 1.0 N9 D:G1 4.0 41.6 1.0 O2P D:CBV2 4.0 49.4 1.0 HN41 D:CBV2 4.0 50.4 1.0 H2' D:G1 4.0 61.4 1.0 H8 D:G1 4.2 45.4 1.0 C3' D:G1 4.2 53.1 1.0 N3 D:CBV2 4.3 35.2 1.0 O D:HOH208 4.3 54.7 1.0 C6 D:G1 4.3 45.7 1.0 N1 D:CBV2 4.3 40.0 1.0 O5' D:G1 4.3 55.3 1.0 O5' D:CBV2 4.5 43.3 1.0 C2' D:G1 4.6 51.1 1.0 P D:CBV2 4.6 46.6 1.0 N3 D:G1 4.7 43.6 1.0 O6 D:G1 4.7 39.3 1.0 C2 D:CBV2 4.8 36.5 1.0 C1' D:G1 4.9 45.7 1.0 N1 D:G1 4.9 47.2 1.0 O3' D:G1 4.9 58.0 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