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

The structure of Crystal Structure of the Sam-Sah Riboswitch with Amp, PDB code: 6ymk 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)	37.48 / 2.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.100, 147.847, 75.009, 90.00, 91.84, 90.00
R / Rfree (%)	22.5 / 26.4

The structure of Crystal Structure of the Sam-Sah Riboswitch with Amp also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Bromine atom in the Crystal Structure of the Sam-Sah Riboswitch with Amp (pdb code 6ymk). 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 Amp, PDB code: 6ymk:
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 Amp


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Br10 b:0.6 occ:1.00 BR A:CBV10 0.0 0.6 1.0 C5 A:CBV10 1.9 0.3 1.0 HN42 A:CBV10 2.7 0.8 1.0 C6 A:CBV10 2.9 0.3 1.0 C4 A:CBV10 2.9 0.1 1.0 H6 A:CBV10 3.0 0.7 1.0 N4 A:CBV10 3.2 0.1 1.0 H3' A:U9 3.3 80.7 1.0 C5 A:U9 3.5 99.6 1.0 O2P A:CBV10 3.5 86.0 1.0 H5 A:U9 3.7 0.0 1.0 C6 A:U9 3.7 95.8 1.0 C4 A:U9 3.8 86.5 1.0 H6 A:U9 4.0 0.5 1.0 N1 A:U9 4.1 78.6 1.0 N3 A:U9 4.1 54.6 1.0 N1 A:CBV10 4.1 70.3 1.0 N3 A:CBV10 4.2 88.4 1.0 O A:HOH215 4.2 63.0 1.0 HN41 A:CBV10 4.2 0.8 1.0 H5'' A:U9 4.2 0.8 1.0 O4 A:U9 4.2 0.2 1.0 C3' A:U9 4.2 66.8 1.0 C2 A:U9 4.3 71.2 1.0 H2' A:U9 4.4 82.8 1.0 O5' A:CBV10 4.5 71.7 1.0 P A:CBV10 4.6 65.7 1.0 H3 A:U9 4.6 66.1 1.0 C2 A:CBV10 4.7 77.2 1.0 C2' A:U9 4.8 68.5 1.0 O3' A:U9 4.9 65.2 1.0 C1' A:U9 4.9 80.4 1.0 C5' A:U9 5.0 89.4 1.0

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Br10 b:0.9 occ:1.00 BR C:CBV10 0.0 0.9 1.0 C5 C:CBV10 1.9 0.2 1.0 HN41 C:CBV10 2.7 0.9 1.0 C6 C:CBV10 2.8 0.1 1.0 C4 C:CBV10 2.9 0.0 1.0 H6 C:CBV10 3.0 0.2 1.0 N4 C:CBV10 3.2 89.5 1.0 C5 C:U9 3.4 72.3 1.0 H5 C:U9 3.6 87.3 1.0 H3' C:U9 3.6 0.0 1.0 C6 C:U9 3.6 94.8 1.0 C4 C:U9 3.8 75.7 1.0 H6 C:U9 3.9 0.3 1.0 O2P C:CBV10 3.9 0.8 1.0 H2' C:U9 4.1 0.3 1.0 N1 C:CBV10 4.1 0.6 1.0 N1 C:U9 4.1 0.4 1.0 N3 C:U9 4.2 91.6 1.0 N3 C:CBV10 4.2 86.9 1.0 HN42 C:CBV10 4.2 0.9 1.0 O4 C:U9 4.3 68.1 1.0 C2 C:U9 4.4 0.5 1.0 C3' C:U9 4.5 0.6 1.0 O5' C:CBV10 4.5 0.0 1.0 C2 C:CBV10 4.6 0.7 1.0 C2' C:U9 4.7 0.2 1.0 H3 C:U9 4.7 0.4 1.0 OP2 C:U9 4.7 85.1 1.0 O5' C:U9 4.7 0.1 1.0 P C:CBV10 4.8 0.2 1.0 H3' C:CBV10 4.9 0.7 1.0 C1' C:U9 5.0 0.6 1.0

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ F:Br10 b:94.8 occ:1.00 BR F:CBV10 0.0 94.8 1.0 C5 F:CBV10 1.9 69.6 1.0 HN41 F:CBV10 2.6 69.2 1.0 C6 F:CBV10 2.9 76.1 1.0 C4 F:CBV10 2.9 58.2 1.0 H6 F:CBV10 3.0 91.8 1.0 N4 F:CBV10 3.1 57.3 1.0 C5 F:U9 3.7 75.6 1.0 C4 F:U9 3.9 56.8 1.0 H5 F:U9 3.9 91.2 1.0 C6 F:U9 4.0 79.9 1.0 H3' F:U9 4.1 0.4 1.0 O2P F:CBV10 4.1 72.8 1.0 N1 F:CBV10 4.1 65.3 1.0 HN42 F:CBV10 4.1 69.2 1.0 N3 F:CBV10 4.1 79.4 1.0 O4 F:U9 4.2 60.3 1.0 N3 F:U9 4.2 70.2 1.0 H6 F:U9 4.4 96.4 1.0 H2' F:U9 4.4 0.9 1.0 N1 F:U9 4.4 76.4 1.0 C2 F:U9 4.6 64.9 1.0 C2 F:CBV10 4.6 88.4 1.0 O5' F:CBV10 4.6 78.0 1.0 H3 F:U9 4.6 84.8 1.0 C3' F:U9 4.9 0.9 1.0

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ I:Br10 b:0.8 occ:1.00 BR I:CBV10 0.0 0.8 1.0 C5 I:CBV10 1.9 0.2 1.0 HN41 I:CBV10 2.7 0.5 1.0 C6 I:CBV10 2.9 1.0 1.0 C4 I:CBV10 2.9 0.1 1.0 H6 I:CBV10 3.0 0.9 1.0 N4 I:CBV10 3.2 0.2 1.0 C5 I:U9 3.4 82.9 1.0 H5 I:U9 3.5 0.0 1.0 C6 I:U9 3.6 96.7 1.0 H3' I:U9 3.6 0.0 1.0 C4 I:U9 3.7 84.0 1.0 O2P I:CBV10 3.9 0.8 1.0 H6 I:U9 3.9 0.6 1.0 N1 I:CBV10 4.1 0.9 1.0 N1 I:U9 4.1 1.0 1.0 H2' I:U9 4.2 0.7 1.0 N3 I:U9 4.2 0.3 1.0 N3 I:CBV10 4.2 0.6 1.0 HN42 I:CBV10 4.2 0.5 1.0 O4 I:U9 4.2 70.3 1.0 O I:HOH207 4.4 60.1 1.0 C2 I:U9 4.4 98.8 1.0 C3' I:U9 4.5 0.6 1.0 O5' I:CBV10 4.6 0.5 1.0 C2 I:CBV10 4.6 92.4 1.0 H3 I:U9 4.7 0.7 1.0 C2' I:U9 4.7 0.8 1.0 O5' I:U9 4.7 0.6 1.0 P I:CBV10 4.8 0.5 1.0 OP2 I:U9 4.8 94.9 1.0 C1' I:U9 5.0 98.8 1.0

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ M:Br10 b:0.2 occ:1.00 BR M:CBV10 0.0 0.2 1.0 C5 M:CBV10 1.9 0.5 1.0 HN41 M:CBV10 2.7 0.7 1.0 C6 M:CBV10 2.9 0.7 1.0 C4 M:CBV10 2.9 0.3 1.0 H6 M:CBV10 3.0 0.5 1.0 N4 M:CBV10 3.2 0.1 1.0 O M:HOH221 3.6 73.6 1.0 C5 M:U9 3.8 60.0 1.0 C4 M:U9 3.9 67.0 1.0 H5 M:U9 3.9 72.5 1.0 H3' M:U9 4.0 1.0 1.0 C6 M:U9 4.0 72.0 1.0 O2P M:CBV10 4.0 73.2 1.0 N1 M:CBV10 4.1 85.0 1.0 N3 M:CBV10 4.2 0.9 1.0 HN42 M:CBV10 4.2 0.7 1.0 H2' M:U9 4.3 0.6 1.0 N3 M:U9 4.3 55.6 1.0 O M:HOH222 4.3 47.8 1.0 H6 M:U9 4.3 86.9 1.0 O M:HOH212 4.3 57.5 1.0 O4 M:U9 4.3 85.8 1.0 N1 M:U9 4.4 82.2 1.0 C2 M:U9 4.5 53.9 1.0 O5' M:CBV10 4.6 77.6 1.0 C2 M:CBV10 4.6 0.9 1.0 H3 M:U9 4.7 67.2 1.0 C3' M:U9 4.8 0.9 1.0 C2' M:U9 4.9 0.4 1.0 P M:CBV10 5.0 80.6 1.0

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ O:Br10 b:0.2 occ:1.00 BR O:CBV10 0.0 0.2 1.0 C5 O:CBV10 1.9 1.0 1.0 HN42 O:CBV10 2.7 0.9 1.0 C6 O:CBV10 2.9 0.3 1.0 C4 O:CBV10 2.9 0.8 1.0 H6 O:CBV10 3.0 0.8 1.0 N4 O:CBV10 3.2 0.8 1.0 C5 O:U9 3.4 70.2 1.0 H5 O:U9 3.6 84.1 1.0 H3' O:U9 3.6 0.7 1.0 C6 O:U9 3.6 88.1 1.0 C4 O:U9 3.7 74.2 1.0 O2P O:CBV10 3.8 0.4 1.0 H6 O:U9 3.9 0.2 1.0 N3 O:U9 4.1 82.3 1.0 N1 O:U9 4.1 98.5 1.0 N1 O:CBV10 4.1 0.7 1.0 H2' O:U9 4.1 0.3 1.0 O4 O:U9 4.2 94.1 1.0 N3 O:CBV10 4.2 76.3 1.0 HN41 O:CBV10 4.2 0.9 1.0 C2 O:U9 4.4 0.6 1.0 C3' O:U9 4.5 0.8 1.0 O5' O:CBV10 4.6 0.9 1.0 H3 O:U9 4.6 99.3 1.0 C2 O:CBV10 4.6 79.6 1.0 C2' O:U9 4.7 91.5 1.0 O5' O:U9 4.7 0.9 1.0 OP2 O:U9 4.7 0.2 1.0 P O:CBV10 4.8 0.3 1.0 C1' O:U9 5.0 0.9 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. V. 48 7545 2020.
ISSN: ESSN 1362-4962
PubMed: 32520325
DOI: 10.1093/NAR/GKAA493