Bromine in PDB 5ndi: The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop

The structure of The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop, PDB code: 5ndi 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)	40.34 / 2.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.476, 48.185, 153.066, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.8

The structure of The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Bromine atom in the The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop (pdb code 5ndi). 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 E.Coli Guanidine II Riboswitch P1 Stem-Loop, PDB code: 5ndi:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the The Structure of the E.Coli Guanidine II Riboswitch P1 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 E.Coli Guanidine II Riboswitch P1 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Br17 b:75.3 occ:1.00 BR A:CBV17 0.0 75.3 1.0 C5 A:CBV17 1.9 58.2 1.0 HN42 A:CBV17 2.6 80.1 1.0 C4 A:CBV17 2.9 60.8 1.0 H3' A:G16 3.0 86.7 1.0 C6 A:CBV17 3.0 60.7 1.0 H6 A:CBV17 3.1 72.8 1.0 N4 A:CBV17 3.1 66.8 1.0 O3P A:CBV17 3.5 63.2 1.0 C8 A:G16 3.6 60.2 1.0 N7 A:G16 3.6 65.4 1.0 H5'' A:G16 3.8 88.1 1.0 C5 A:G16 3.8 63.1 1.0 N9 A:G16 3.8 59.3 1.0 H8 A:G16 3.9 72.3 1.0 C3' A:G16 3.9 72.2 1.0 HN41 A:CBV17 3.9 80.1 1.0 C4 A:G16 4.0 61.5 1.0 H2' A:G16 4.0 79.1 1.0 N3 A:CBV17 4.3 63.8 1.0 N1 A:CBV17 4.3 58.4 1.0 C2' A:G16 4.4 66.0 1.0 O5' A:CBV17 4.4 69.5 1.0 P A:CBV17 4.5 73.8 1.0 C6 A:G16 4.5 60.6 1.0 C1' A:G16 4.6 64.5 1.0 C5' A:G16 4.7 73.4 1.0 O3' A:G16 4.7 83.5 1.0 C4' A:G16 4.7 71.0 1.0 H62 A:A18 4.8 77.8 1.0 N3 A:G16 4.8 64.4 1.0 C2 A:CBV17 4.8 63.6 1.0 O4' A:G16 4.9 67.4 1.0

Bromine binding site 2 out of 4 in the The Structure of the E.Coli Guanidine II Riboswitch P1 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 E.Coli Guanidine II Riboswitch P1 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Br17 b:66.7 occ:1.00 BR B:CBV17 0.0 66.7 1.0 C5 B:CBV17 1.9 58.3 1.0 HN42 B:CBV17 2.6 77.1 1.0 C4 B:CBV17 2.9 59.4 1.0 C6 B:CBV17 3.0 62.0 1.0 H6 B:CBV17 3.1 74.3 1.0 N4 B:CBV17 3.1 64.2 1.0 H3' B:G16 3.2 88.0 1.0 N7 B:G16 3.5 67.2 1.0 C8 B:G16 3.6 69.3 1.0 O3P B:CBV17 3.6 61.0 1.0 C5 B:G16 3.6 67.4 1.0 N9 B:G16 3.8 68.2 1.0 C4 B:G16 3.9 68.1 1.0 H8 B:G16 3.9 83.2 1.0 HN41 B:CBV17 3.9 77.1 1.0 H5'' B:G16 4.0 82.0 1.0 C3' B:G16 4.1 73.3 1.0 H2' B:G16 4.1 81.3 1.0 N3 B:CBV17 4.2 66.3 1.0 C6 B:G16 4.3 66.0 1.0 N1 B:CBV17 4.3 62.6 1.0 C2' B:G16 4.5 67.8 1.0 O5' B:CBV17 4.6 71.5 1.0 P B:CBV17 4.6 71.2 1.0 N3 B:G16 4.7 69.0 1.0 C1' B:G16 4.7 68.0 1.0 O6 B:G16 4.7 65.2 1.0 C2 B:CBV17 4.8 70.2 1.0 H62 B:A18 4.8 82.5 1.0 C5' B:G16 4.9 68.4 1.0 N1 B:G16 4.9 68.1 1.0 O3' B:G16 4.9 86.5 1.0 C4' B:G16 4.9 66.0 1.0

Bromine binding site 3 out of 4 in the The Structure of the E.Coli Guanidine II Riboswitch P1 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 E.Coli Guanidine II Riboswitch P1 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ C:Br17 b:68.4 occ:1.00 BR C:CBV17 0.0 68.4 1.0 C5 C:CBV17 1.9 64.8 1.0 HN42 C:CBV17 2.8 83.3 1.0 C6 C:CBV17 2.9 67.5 1.0 C4 C:CBV17 2.9 60.6 1.0 H3' C:G16 3.0 77.4 1.0 H6 C:CBV17 3.0 80.9 1.0 N4 C:CBV17 3.2 69.4 1.0 O2P C:CBV17 3.5 71.3 1.0 N7 C:G16 3.5 62.5 1.0 C8 C:G16 3.6 65.9 1.0 C5 C:G16 3.7 66.9 1.0 N9 C:G16 3.8 69.6 1.0 H5'' C:G16 3.8 83.8 1.0 C4 C:G16 3.9 69.5 1.0 H8 C:G16 3.9 79.1 1.0 C3' C:G16 4.0 64.5 1.0 H2' C:G16 4.0 80.7 1.0 HN41 C:CBV17 4.1 83.3 1.0 N3 C:CBV17 4.3 60.3 1.0 N1 C:CBV17 4.3 69.0 1.0 C6 C:G16 4.3 63.7 1.0 C2' C:G16 4.4 67.2 1.0 O5' C:CBV17 4.5 80.0 1.0 P C:CBV17 4.5 78.1 1.0 C1' C:G16 4.6 69.5 1.0 N3 C:G16 4.6 67.7 1.0 C5' C:G16 4.7 69.8 1.0 O3' C:G16 4.7 69.7 1.0 C4' C:G16 4.8 59.1 1.0 H62 C:A18 4.8 79.2 1.0 C2 C:CBV17 4.8 68.3 1.0 O6 C:G16 4.8 66.3 1.0 N1 C:G16 4.9 60.7 1.0 O4' C:G16 5.0 64.3 1.0

Bromine binding site 4 out of 4 in the The Structure of the E.Coli Guanidine II Riboswitch P1 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 E.Coli Guanidine II Riboswitch P1 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ D:Br17 b:63.5 occ:1.00 BR D:CBV17 0.0 63.5 1.0 C5 D:CBV17 1.9 62.5 1.0 HN42 D:CBV17 2.8 73.5 1.0 C6 D:CBV17 2.9 67.5 1.0 C4 D:CBV17 3.0 55.7 1.0 H6 D:CBV17 3.0 80.9 1.0 H3' D:G16 3.1 79.2 1.0 N4 D:CBV17 3.2 61.3 1.0 N7 D:G16 3.4 55.7 1.0 O2P D:CBV17 3.5 60.4 1.0 C8 D:G16 3.5 62.7 1.0 H8 D:G16 3.7 75.2 1.0 C5 D:G16 3.7 64.1 1.0 N9 D:G16 3.9 65.9 1.0 H5'' D:G16 4.0 78.8 1.0 C4 D:G16 4.0 65.3 1.0 C3' D:G16 4.0 66.0 1.0 H2' D:G16 4.0 83.6 1.0 HN41 D:CBV17 4.0 73.5 1.0 N1 D:CBV17 4.3 65.1 1.0 N3 D:CBV17 4.3 57.6 1.0 C6 D:G16 4.4 59.3 1.0 C2' D:G16 4.5 69.6 1.0 O5' D:CBV17 4.5 71.9 1.0 P D:CBV17 4.5 77.9 1.0 C1' D:G16 4.7 70.5 1.0 O3' D:G16 4.8 84.7 1.0 C5' D:G16 4.8 65.7 1.0 C2 D:CBV17 4.8 62.4 1.0 N3 D:G16 4.9 65.3 1.0 C4' D:G16 4.9 66.4 1.0 O6 D:G16 4.9 52.9 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