Bromine in PDB 6ylb: Crystal Structure of the Sam-Sah Riboswitch with Sam

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sam, PDB code: 6ylb was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.46 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.113, 147.937, 74.839, 90.00, 91.71, 90.00
R / Rfree (%)	22.5 / 26.3

The binding sites of Bromine atom in the Crystal Structure of the Sam-Sah Riboswitch with Sam (pdb code 6ylb). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of the Sam-Sah Riboswitch with Sam, PDB code: 6ylb:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the Crystal Structure of the Sam-Sah Riboswitch with Sam


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the Sam-Sah Riboswitch with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Br10 b:67.4 occ:1.00 BR A:CBV10 0.0 67.4 1.0 C5 A:CBV10 1.9 71.3 1.0 HN42 A:CBV10 2.6 91.6 1.0 C4 A:CBV10 2.9 68.1 1.0 C6 A:CBV10 2.9 70.1 1.0 H6 A:CBV10 3.1 85.1 1.0 N4 A:CBV10 3.1 75.5 1.0 H3' A:U9 3.5 0.5 1.0 C5 A:U9 3.6 77.0 1.0 C4 A:U9 3.6 71.1 1.0 O2P A:CBV10 3.6 67.2 1.0 H5 A:U9 3.9 93.3 1.0 C6 A:U9 3.9 79.9 1.0 N3 A:U9 3.9 55.1 1.0 O4 A:U9 4.1 57.0 1.0 HN41 A:CBV10 4.1 91.6 1.0 O A:HOH218 4.1 47.4 1.0 N1 A:CBV10 4.1 94.3 1.0 N3 A:CBV10 4.1 68.9 1.0 N1 A:U9 4.2 78.6 1.0 C2 A:U9 4.2 65.4 1.0 H6 A:U9 4.3 96.9 1.0 H3 A:U9 4.3 67.0 1.0 C3' A:U9 4.4 0.4 1.0 H5'' A:U9 4.5 0.1 1.0 H2' A:U9 4.5 0.8 1.0 C2 A:CBV10 4.6 59.7 1.0 O5' A:CBV10 4.7 92.6 1.0 O A:HOH201 4.7 66.2 1.0 P A:CBV10 4.7 65.6 1.0 C2' A:U9 4.9 0.1 1.0 O2 A:U9 5.0 60.2 1.0

Bromine binding site 2 out of 6 in the Crystal Structure of the Sam-Sah Riboswitch with Sam


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the Sam-Sah Riboswitch with Sam within 5.0Å range: probe atom residue distance (Å) B Occ C:Br10 b:0.3 occ:1.00 BR C:CBV10 0.0 0.3 1.0 C5 C:CBV10 1.9 0.6 1.0 HN41 C:CBV10 2.7 90.7 1.0 C6 C:CBV10 2.9 0.2 1.0 C4 C:CBV10 2.9 0.7 1.0 H6 C:CBV10 3.0 0.0 1.0 N4 C:CBV10 3.2 79.6 1.0 C5 C:U9 3.5 1.0 1.0 H5 C:U9 3.6 0.6 1.0 H3' C:U9 3.8 1.0 1.0 O2P C:CBV10 3.8 0.1 1.0 C6 C:U9 3.8 1.0 1.0 C4 C:U9 3.8 0.1 1.0 H6 C:U9 4.0 0.5 1.0 N1 C:CBV10 4.1 0.2 1.0 HN42 C:CBV10 4.2 90.7 1.0 N3 C:CBV10 4.2 0.1 1.0 O4 C:U9 4.3 83.6 1.0 H2' C:U9 4.3 0.9 1.0 N3 C:U9 4.3 0.3 1.0 N1 C:U9 4.4 0.6 1.0 O5' C:CBV10 4.6 0.8 1.0 C2 C:U9 4.6 0.7 1.0 C2 C:CBV10 4.7 0.0 1.0 OP2 C:U9 4.7 90.1 1.0 C3' C:U9 4.7 0.8 1.0 P C:CBV10 4.8 0.3 1.0 H61 C:A11 4.8 87.2 1.0 H3 C:U9 4.8 0.3 1.0 C2' C:U9 4.9 0.6 1.0 O5' C:U9 4.9 0.2 1.0

Bromine binding site 3 out of 6 in the Crystal Structure of the Sam-Sah Riboswitch with Sam


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the Sam-Sah Riboswitch with Sam within 5.0Å range: probe atom residue distance (Å) B Occ F:Br10 b:88.3 occ:1.00 BR F:CBV10 0.0 88.3 1.0 C5 F:CBV10 1.9 0.3 1.0 HN41 F:CBV10 2.6 0.4 1.0 C6 F:CBV10 2.8 85.9 1.0 C4 F:CBV10 2.9 0.2 1.0 H6 F:CBV10 3.0 0.1 1.0 N4 F:CBV10 3.1 0.8 1.0 C5 F:U9 3.7 60.8 1.0 C4 F:U9 3.8 61.4 1.0 H5 F:U9 3.8 73.9 1.0 O F:HOH210 3.9 54.1 1.0 C6 F:U9 3.9 72.0 1.0 H3' F:U9 3.9 0.6 1.0 O2P F:CBV10 4.0 65.9 1.0 O F:HOH217 4.0 61.5 1.0 HN42 F:CBV10 4.1 0.4 1.0 N1 F:CBV10 4.1 94.5 1.0 N3 F:CBV10 4.1 90.8 1.0 N3 F:U9 4.1 55.7 1.0 H2' F:U9 4.2 97.0 1.0 O4 F:U9 4.2 51.8 1.0 H6 F:U9 4.3 87.4 1.0 N1 F:U9 4.3 83.9 1.0 O F:HOH218 4.4 63.7 1.0 C2 F:U9 4.4 75.9 1.0 H3 F:U9 4.5 67.8 1.0 C2 F:CBV10 4.5 64.9 1.0 O5' F:CBV10 4.6 81.8 1.0 C3' F:U9 4.8 0.8 1.0 C2' F:U9 4.8 80.0 1.0 P F:CBV10 4.9 75.7 1.0

Bromine binding site 4 out of 6 in the Crystal Structure of the Sam-Sah Riboswitch with Sam


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the Sam-Sah Riboswitch with Sam within 5.0Å range: probe atom residue distance (Å) B Occ I:Br10 b:0.5 occ:1.00 BR I:CBV10 0.0 0.5 1.0 C5 I:CBV10 1.9 0.1 1.0 HN41 I:CBV10 2.7 0.2 1.0 C6 I:CBV10 2.9 1.0 1.0 C4 I:CBV10 2.9 0.4 1.0 H6 I:CBV10 3.0 0.9 1.0 N4 I:CBV10 3.1 0.4 1.0 C5 I:U9 3.4 78.7 1.0 C4 I:U9 3.5 85.2 1.0 H5 I:U9 3.6 95.4 1.0 C6 I:U9 3.7 0.0 1.0 N3 I:U9 3.9 0.6 1.0 O4 I:U9 4.0 78.3 1.0 H3' I:U9 4.0 0.4 1.0 H6 I:U9 4.1 0.0 1.0 N1 I:CBV10 4.1 0.6 1.0 N1 I:U9 4.1 0.9 1.0 H2' I:U9 4.1 0.7 1.0 N3 I:CBV10 4.1 0.8 1.0 HN42 I:CBV10 4.1 0.2 1.0 C2 I:U9 4.2 0.3 1.0 O2P I:CBV10 4.3 0.4 1.0 H3 I:U9 4.3 0.3 1.0 C2 I:CBV10 4.6 1.0 1.0 O5' I:CBV10 4.7 0.4 1.0 C2' I:U9 4.8 0.2 1.0 C3' I:U9 4.8 0.0 1.0 H61 I:A11 4.9 81.2 1.0

Bromine binding site 5 out of 6 in the Crystal Structure of the Sam-Sah Riboswitch with Sam


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the Sam-Sah Riboswitch with Sam within 5.0Å range: probe atom residue distance (Å) B Occ M:Br10 b:0.1 occ:1.00 BR M:CBV10 0.0 0.1 1.0 C5 M:CBV10 1.9 0.7 1.0 HN41 M:CBV10 2.7 0.2 1.0 C6 M:CBV10 2.8 0.8 1.0 H6 M:CBV10 2.9 0.4 1.0 C4 M:CBV10 2.9 0.6 1.0 N4 M:CBV10 3.2 0.2 1.0 C5 M:U9 3.7 64.7 1.0 O M:HOH218 3.7 62.6 1.0 O2P M:CBV10 3.8 57.1 1.0 C4 M:U9 3.8 48.3 1.0 H5 M:U9 3.8 78.6 1.0 H3' M:U9 3.9 0.0 1.0 C6 M:U9 3.9 80.6 1.0 N1 M:CBV10 4.1 0.1 1.0 O M:HOH220 4.1 46.1 1.0 N3 M:U9 4.1 55.9 1.0 N3 M:CBV10 4.2 0.5 1.0 H2' M:U9 4.2 0.2 1.0 HN42 M:CBV10 4.2 0.2 1.0 O4 M:U9 4.2 52.9 1.0 N1 M:U9 4.3 89.5 1.0 H6 M:U9 4.3 97.7 1.0 C2 M:U9 4.4 63.7 1.0 H3 M:U9 4.5 68.1 1.0 O5' M:CBV10 4.6 76.6 1.0 C2 M:CBV10 4.6 99.8 1.0 C3' M:U9 4.7 94.2 1.0 P M:CBV10 4.8 72.7 1.0 C2' M:U9 4.8 0.1 1.0

Bromine binding site 6 out of 6 in the Crystal Structure of the Sam-Sah Riboswitch with Sam


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the Sam-Sah Riboswitch with Sam within 5.0Å range: probe atom residue distance (Å) B Occ O:Br10 b:0.1 occ:1.00 BR O:CBV10 0.0 0.1 1.0 C5 O:CBV10 1.9 0.6 1.0 HN42 O:CBV10 2.7 0.3 1.0 C6 O:CBV10 2.8 0.9 1.0 C4 O:CBV10 2.9 0.2 1.0 H6 O:CBV10 3.0 0.6 1.0 N4 O:CBV10 3.2 0.5 1.0 C5 O:U9 3.4 76.2 1.0 H5 O:U9 3.5 86.6 1.0 C4 O:U9 3.6 77.1 1.0 C6 O:U9 3.7 0.3 1.0 H3' O:U9 3.7 0.6 1.0 O2P O:CBV10 4.0 0.8 1.0 H6 O:U9 4.0 0.2 1.0 N3 O:U9 4.0 0.1 1.0 O4 O:U9 4.0 0.1 1.0 N1 O:CBV10 4.1 0.7 1.0 N1 O:U9 4.1 0.3 1.0 N3 O:CBV10 4.2 74.5 1.0 HN41 O:CBV10 4.2 0.3 1.0 H2' O:U9 4.3 0.0 1.0 C2 O:U9 4.3 0.8 1.0 H3 O:U9 4.4 0.1 1.0 O5' O:CBV10 4.6 0.7 1.0 C3' O:U9 4.6 0.8 1.0 C2 O:CBV10 4.6 92.2 1.0 OP2 O:U9 4.8 0.5 1.0 O5' O:U9 4.8 0.7 1.0 C2' O:U9 4.8 0.5 1.0 P O:CBV10 4.9 0.1 1.0

L.Huang, T.W.Liao, J.Wang, T.Ha, D.M.J.Lilley. Crystal Structure and Ligand-Induced Folding of the Sam/Sah Riboswitch. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 32520325
DOI: 10.1093/NAR/GKAA493