Bromine in PDB 5o62: The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine.

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine., PDB code: 5o62 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)	36.38 / 2.12
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.016, 84.016, 67.445, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 25.5

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine. also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Bromine atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine. (pdb code 5o62). 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 Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine., PDB code: 5o62:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine.


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 Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:76.8 occ:1.00 BR A:CBV2 0.0 76.8 1.0 C5 A:CBV2 1.9 60.9 1.0 HN42 A:CBV2 2.7 53.9 1.0 C4 A:CBV2 3.0 50.1 1.0 C6 A:CBV2 3.0 60.0 1.0 H6 A:CBV2 3.1 72.0 1.0 N4 A:CBV2 3.2 44.9 1.0 O1P A:CBV2 3.6 62.7 1.0 C5 A:C1 3.6 58.1 1.0 C6 A:C1 3.8 58.1 1.0 C4 A:C1 3.9 54.7 1.0 O5' A:C1 3.9 90.2 1.0 HN41 A:CBV2 4.0 53.9 1.0 N1 A:C1 4.2 67.2 1.0 C3' A:C1 4.3 84.6 1.0 N3 A:CBV2 4.3 59.2 1.0 N1 A:CBV2 4.3 57.0 1.0 N3 A:C1 4.3 64.6 1.0 C2 A:C1 4.4 68.4 1.0 N4 A:C1 4.5 49.5 1.0 O5' A:CBV2 4.6 61.0 1.0 P A:CBV2 4.6 66.8 1.0 C2' A:C1 4.8 80.6 1.0 C2 A:CBV2 4.8 49.9 1.0 O3' A:C1 5.0 83.1 1.0 C1' A:C1 5.0 76.3 1.0

Bromine binding site 2 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine.


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 Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br39 b:44.1 occ:1.00 BR A:CBV39 0.0 44.1 1.0 C5 A:CBV39 1.9 37.4 1.0 HN42 A:CBV39 2.8 40.1 1.0 C6 A:CBV39 2.9 32.3 1.0 C4 A:CBV39 3.0 31.1 1.0 H6 A:CBV39 3.0 38.8 1.0 N4 A:CBV39 3.3 33.4 1.0 N7 A:G38 3.5 34.7 1.0 C5 A:G38 3.6 33.5 1.0 O1P A:CBV39 3.8 41.8 1.0 O4 A:U11 3.8 29.0 1.0 C8 A:G38 3.8 35.5 1.0 C4 A:G38 4.0 33.5 1.0 C6 A:G38 4.0 38.3 1.0 HN41 A:CBV39 4.1 40.1 1.0 N9 A:G38 4.1 33.3 1.0 N1 A:CBV39 4.2 31.1 1.0 N3 A:CBV39 4.3 33.4 1.0 O6 A:G38 4.4 30.7 1.0 C3' A:G38 4.5 43.0 1.0 O5' A:CBV39 4.5 38.5 1.0 N2 A:G10 4.6 34.5 1.0 N1 A:G38 4.7 35.7 1.0 N3 A:G38 4.7 32.6 1.0 C2' A:G38 4.8 37.7 1.0 P A:CBV39 4.8 39.9 1.0 C2 A:CBV39 4.8 33.5 1.0 N1 A:G10 4.9 28.6 1.0 C2 A:G38 5.0 41.8 1.0

Bromine binding site 3 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine.


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 Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:1.0 occ:1.00 BR B:CBV2 0.0 1.0 1.0 C5 B:CBV2 1.9 0.5 1.0 HN41 B:CBV2 2.9 0.8 1.0 C6 B:CBV2 3.0 0.9 1.0 H6 B:CBV2 3.0 0.3 1.0 C4 B:CBV2 3.0 0.5 1.0 N4 B:CBV2 3.3 0.3 1.0 C5 B:C1 3.5 0.5 1.0 C6 B:C1 3.6 1.0 1.0 O2P B:CBV2 3.7 0.5 1.0 C4 B:C1 3.8 0.2 1.0 O5' B:C1 3.9 97.1 1.0 N1 B:C1 4.0 0.6 1.0 N3 B:C1 4.2 0.5 1.0 HN42 B:CBV2 4.2 0.8 1.0 C3' B:C1 4.3 0.2 1.0 C2 B:C1 4.3 0.8 1.0 N1 B:CBV2 4.3 0.8 1.0 N4 B:C1 4.3 1.0 1.0 N3 B:CBV2 4.3 0.7 1.0 O5' B:CBV2 4.6 1.0 1.0 P B:CBV2 4.7 0.0 1.0 C2' B:C1 4.7 0.0 1.0 O3P B:CBV2 4.8 96.4 1.0 C1' B:C1 4.9 0.7 1.0 C2 B:CBV2 4.9 0.3 1.0

Bromine binding site 4 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine.


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 Thermobifida Fusca Guanidine III Riboswitch with 1-Ethylguanidine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br39 b:57.7 occ:1.00 BR B:CBV39 0.0 57.7 1.0 C5 B:CBV39 1.9 54.6 1.0 HN42 B:CBV39 2.7 64.5 1.0 C4 B:CBV39 3.0 53.9 1.0 C6 B:CBV39 3.0 43.4 1.0 H6 B:CBV39 3.1 52.1 1.0 N4 B:CBV39 3.2 53.8 1.0 N7 B:G38 3.5 66.0 1.0 C5 B:G38 3.5 67.6 1.0 C8 B:G38 3.7 67.6 1.0 O4 B:U11 3.9 61.0 1.0 C4 B:G38 3.9 63.2 1.0 O2P B:CBV39 4.0 63.0 1.0 C6 B:G38 4.0 63.4 1.0 N9 B:G38 4.0 69.1 1.0 HN41 B:CBV39 4.0 64.5 1.0 N3 B:CBV39 4.3 56.7 1.0 N1 B:CBV39 4.3 54.6 1.0 O6 B:G38 4.3 61.8 1.0 C3' B:G38 4.5 62.0 1.0 N2 B:G10 4.6 79.4 1.0 N1 B:G38 4.6 69.3 1.0 N3 B:G38 4.6 58.7 1.0 O5' B:CBV39 4.6 54.1 1.0 C2' B:G38 4.7 61.4 1.0 C2 B:CBV39 4.9 58.9 1.0 N1 B:G10 4.9 82.0 1.0 C2 B:G38 4.9 67.5 1.0 P B:CBV39 4.9 61.6 1.0 C1' B:G38 5.0 64.8 1.0

L.Huang, J.Wang, T.J.Wilson, D.M.J.Lilley. Structure of the Guanidine III Riboswitch. Cell Chem Biol V. 24 1407 2017.
ISSN: ESSN 2451-9456
PubMed: 28988949
DOI: 10.1016/J.CHEMBIOL.2017.08.021