Bromine in PDB 6yl5: Crystal Structure of the Sam-Sah Riboswitch with Sah

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sah, PDB code: 6yl5 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)	74.61 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.750, 147.610, 74.660, 90.00, 92.07, 90.00
R / Rfree (%)	17.2 / 20

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

Magnesium	(Mg)	5 atoms
Sodium	(Na)	14 atoms

The binding sites of Bromine atom in the Crystal Structure of the Sam-Sah Riboswitch with Sah (pdb code 6yl5). 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 Sah, PDB code: 6yl5:
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 Sah


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Br10 b:49.7 occ:1.00 BR A:CBV10 0.0 49.7 1.0 C5 A:CBV10 1.9 42.8 1.0 HN42 A:CBV10 2.6 51.1 1.0 C6 A:CBV10 2.9 39.4 1.0 C4 A:CBV10 2.9 40.5 1.0 H6 A:CBV10 3.0 47.3 1.0 N4 A:CBV10 3.1 42.5 1.0 O A:HOH378 3.4 63.7 1.0 O A:HOH308 3.5 51.8 1.0 H3' A:U9 3.5 62.3 1.0 O2P A:CBV10 3.6 53.1 1.0 C5 A:U9 3.7 44.4 1.0 C4 A:U9 3.8 47.3 1.0 C6 A:U9 3.9 46.8 1.0 H5 A:U9 3.9 53.3 1.0 HN41 A:CBV10 4.1 51.1 1.0 N1 A:CBV10 4.1 38.2 1.0 O A:HOH347 4.2 43.6 1.0 H6 A:U9 4.2 56.1 1.0 O A:HOH361 4.2 39.3 1.0 N3 A:CBV10 4.2 40.0 1.0 N3 A:U9 4.2 41.1 1.0 N1 A:U9 4.3 39.4 1.0 O4 A:U9 4.3 43.4 1.0 C2 A:U9 4.4 42.1 1.0 H2' A:U9 4.4 53.9 1.0 H5'' A:U9 4.5 65.1 1.0 C3' A:U9 4.5 51.9 1.0 O5' A:CBV10 4.5 45.3 1.0 C2 A:CBV10 4.7 32.8 1.0 H3 A:U9 4.7 49.4 1.0 P A:CBV10 4.7 48.4 1.0 C2' A:U9 4.9 44.9 1.0

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


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ C:Br10 b:70.5 occ:1.00 BR C:CBV10 0.0 70.5 1.0 C5 C:CBV10 1.9 63.1 1.0 HN41 C:CBV10 2.7 69.1 1.0 C6 C:CBV10 2.8 65.5 1.0 C4 C:CBV10 2.9 63.0 1.0 H6 C:CBV10 2.9 78.7 1.0 N4 C:CBV10 3.2 57.5 1.0 O C:HOH207 3.4 62.9 1.0 C5 C:U9 3.5 60.7 1.0 H3' C:U9 3.5 82.6 1.0 H5 C:U9 3.6 72.9 1.0 C6 C:U9 3.7 63.7 1.0 O2P C:CBV10 3.8 83.3 1.0 C4 C:U9 3.8 68.0 1.0 H6 C:U9 3.9 76.4 1.0 H2' C:U9 4.0 87.7 1.0 N1 C:CBV10 4.1 67.4 1.0 N1 C:U9 4.1 71.2 1.0 N3 C:CBV10 4.1 81.8 1.0 HN42 C:CBV10 4.2 69.1 1.0 N3 C:U9 4.2 82.5 1.0 O4 C:U9 4.3 65.9 1.0 C2 C:U9 4.4 82.7 1.0 C3' C:U9 4.4 68.8 1.0 O5' C:CBV10 4.5 73.3 1.0 C2 C:CBV10 4.6 81.3 1.0 C2' C:U9 4.6 73.0 1.0 P C:CBV10 4.7 79.5 1.0 H3 C:U9 4.7 99.0 1.0 H3' C:CBV10 4.7 0.8 1.0 O5' C:U9 4.8 71.3 1.0 H61 C:A11 4.8 67.6 1.0 N7 C:A11 4.8 65.7 1.0 OP2 C:U9 4.9 64.1 1.0 C1' C:U9 5.0 71.2 1.0

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


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ E:Br10 b:54.2 occ:1.00 BR E:CBV10 0.0 54.2 1.0 C5 E:CBV10 1.9 43.4 1.0 HN41 E:CBV10 2.6 45.1 1.0 C6 E:CBV10 2.9 40.0 1.0 C4 E:CBV10 2.9 36.8 1.0 H6 E:CBV10 3.0 48.0 1.0 N4 E:CBV10 3.1 37.5 1.0 O E:HOH258 3.4 53.3 1.0 O E:HOH280 3.5 59.1 1.0 C5 E:U9 3.6 43.1 1.0 O2P E:CBV10 3.7 52.9 1.0 C4 E:U9 3.8 40.3 1.0 H5 E:U9 3.8 51.8 1.0 C6 E:U9 3.9 50.5 1.0 H3' E:U9 3.9 1.0 1.0 HN42 E:CBV10 4.1 45.1 1.0 N1 E:CBV10 4.1 41.7 1.0 O E:HOH275 4.1 42.7 1.0 O E:HOH256 4.1 49.5 1.0 N3 E:CBV10 4.2 34.8 1.0 N3 E:U9 4.2 39.7 1.0 H6 E:U9 4.2 60.7 1.0 H2' E:U9 4.2 86.2 1.0 N1 E:U9 4.3 46.6 1.0 O4 E:U9 4.3 43.7 1.0 C2 E:U9 4.4 46.5 1.0 O5' E:CBV10 4.5 49.9 1.0 H3 E:U9 4.6 47.7 1.0 C2 E:CBV10 4.6 33.8 1.0 C3' E:U9 4.7 89.9 1.0 P E:CBV10 4.8 55.2 1.0 C2' E:U9 4.8 71.8 1.0

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


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ G:Br10 b:73.8 occ:1.00 BR G:CBV10 0.0 73.8 1.0 C5 G:CBV10 1.9 77.6 1.0 HN41 G:CBV10 2.6 70.4 1.0 C6 G:CBV10 2.8 80.5 1.0 C4 G:CBV10 2.9 63.2 1.0 H6 G:CBV10 2.9 96.6 1.0 N4 G:CBV10 3.1 58.6 1.0 O G:HOH202 3.2 62.5 1.0 C5 G:U9 3.5 60.8 1.0 C4 G:U9 3.6 59.6 1.0 H3' G:U9 3.6 0.8 1.0 C6 G:U9 3.6 71.4 1.0 H2' G:U9 3.7 0.0 1.0 N3 G:U9 3.8 62.2 1.0 H5 G:U9 3.8 73.0 1.0 N1 G:U9 3.8 79.5 1.0 O G:HOH253 3.9 62.3 1.0 O2P G:CBV10 3.9 66.0 1.0 C2 G:U9 3.9 72.1 1.0 H6 G:U9 4.0 85.7 1.0 N1 G:CBV10 4.0 64.9 1.0 HN42 G:CBV10 4.1 70.4 1.0 N3 G:CBV10 4.1 71.6 1.0 O4 G:U9 4.1 58.9 1.0 H3 G:U9 4.2 74.7 1.0 C3' G:U9 4.4 0.6 1.0 C2' G:U9 4.4 95.0 1.0 O5' G:CBV10 4.4 90.0 1.0 C2 G:CBV10 4.6 70.5 1.0 O2 G:U9 4.7 74.6 1.0 C1' G:U9 4.7 95.2 1.0 H3' G:CBV10 4.7 0.7 1.0 P G:CBV10 4.8 86.0 1.0 N7 G:A11 5.0 51.8 1.0

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


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ I:Br10 b:50.2 occ:1.00 BR I:CBV10 0.0 50.2 1.0 C5 I:CBV10 1.9 38.5 1.0 HN41 I:CBV10 2.5 46.4 1.0 C6 I:CBV10 2.9 39.0 1.0 C4 I:CBV10 2.9 35.5 1.0 H6 I:CBV10 3.0 46.9 1.0 N4 I:CBV10 3.0 38.6 1.0 O I:HOH283 3.1 63.9 1.0 O I:HOH263 3.6 51.2 1.0 O2P I:CBV10 3.7 52.5 1.0 C5 I:U9 3.7 43.1 1.0 O I:HOH290 3.7 73.7 1.0 NA I:NA104 3.8 0.2 1.0 C4 I:U9 3.8 42.0 1.0 H3' I:U9 3.9 65.4 1.0 C6 I:U9 3.9 43.5 1.0 H5 I:U9 3.9 51.8 1.0 HN42 I:CBV10 4.0 46.4 1.0 N1 I:CBV10 4.1 39.7 1.0 N3 I:U9 4.1 39.5 1.0 O I:HOH281 4.2 42.6 1.0 N3 I:CBV10 4.2 40.5 1.0 H2' I:U9 4.2 62.0 1.0 N1 I:U9 4.3 43.4 1.0 O4 I:U9 4.3 44.8 1.0 H6 I:U9 4.3 52.3 1.0 C2 I:U9 4.4 41.8 1.0 H3 I:U9 4.5 47.4 1.0 O5' I:CBV10 4.6 45.2 1.0 C2 I:CBV10 4.6 34.8 1.0 C3' I:U9 4.7 54.5 1.0 P I:CBV10 4.8 49.8 1.0 C2' I:U9 4.8 51.7 1.0

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


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ K:Br10 b:66.2 occ:1.00 BR K:CBV10 0.0 66.2 1.0 C5 K:CBV10 1.9 53.2 1.0 HN42 K:CBV10 2.7 60.9 1.0 C6 K:CBV10 2.8 54.4 1.0 C4 K:CBV10 2.9 58.1 1.0 H6 K:CBV10 2.9 65.3 1.0 N4 K:CBV10 3.1 50.7 1.0 C5 K:U9 3.6 59.1 1.0 H3' K:U9 3.6 0.7 1.0 O K:HOH216 3.6 58.1 1.0 C4 K:U9 3.7 58.7 1.0 C6 K:U9 3.7 71.0 1.0 H2' K:U9 3.8 0.5 1.0 H5 K:U9 3.8 71.0 1.0 O2P K:CBV10 3.8 68.9 1.0 N3 K:U9 3.9 53.9 1.0 N1 K:U9 3.9 70.6 1.0 N1 K:CBV10 4.0 63.2 1.0 H6 K:U9 4.0 85.3 1.0 C2 K:U9 4.1 66.9 1.0 HN41 K:CBV10 4.1 60.9 1.0 N3 K:CBV10 4.1 58.8 1.0 O4 K:U9 4.2 54.5 1.0 H3 K:U9 4.3 64.7 1.0 C3' K:U9 4.4 0.3 1.0 O5' K:CBV10 4.4 84.6 1.0 C2' K:U9 4.4 0.6 1.0 C2 K:CBV10 4.6 62.5 1.0 P K:CBV10 4.7 70.4 1.0 H3' K:CBV10 4.8 0.6 1.0 C1' K:U9 4.8 95.0 1.0 O2 K:U9 4.8 83.9 1.0 H62 K:A11 4.8 64.8 1.0 N7 K:A11 4.8 49.9 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. 2020.
ISSN: ESSN 1362-4962
PubMed: 32520325
DOI: 10.1093/NAR/GKAA493