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

The structure of Crystal Structure of the Sam-Sah Riboswitch with Amp, PDB code: 6ymi 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)	74.59 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.506, 147.359, 74.844, 90.00, 91.36, 90.00
R / Rfree (%)	21.4 / 24.2

The binding sites of Bromine atom in the Crystal Structure of the Sam-Sah Riboswitch with Amp (pdb code 6ymi). 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: 6ymi:
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:Br101 b:72.5 occ:1.00 BR A:CBV101 0.0 72.5 1.0 C5 A:CBV101 1.9 59.8 1.0 C6 A:CBV101 2.9 58.8 1.0 C4 A:CBV101 2.9 49.0 1.0 N4 A:CBV101 3.2 46.7 1.0 O2P A:CBV101 3.6 61.6 1.0 C5 A:U9 3.7 63.7 1.0 C4 A:U9 3.8 64.3 1.0 C6 A:U9 4.0 62.4 1.0 N1 A:CBV101 4.1 51.9 1.0 N3 A:U9 4.2 58.5 1.0 O4 A:U9 4.2 60.7 1.0 N3 A:CBV101 4.2 49.5 1.0 O5' A:CBV101 4.3 64.3 1.0 N1 A:U9 4.3 62.1 1.0 C2 A:U9 4.5 57.9 1.0 P A:CBV101 4.5 63.3 1.0 C2 A:CBV101 4.6 52.5 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:Br101 b:0.8 occ:1.00 BR C:CBV101 0.0 0.8 1.0 C5 C:CBV101 1.9 95.4 1.0 C6 C:CBV101 2.9 90.3 1.0 C4 C:CBV101 2.9 79.0 1.0 N4 C:CBV101 3.2 64.4 1.0 C5 C:U9 3.5 95.1 1.0 C4 C:U9 3.6 94.1 1.0 O1P C:CBV101 3.7 0.2 1.0 C6 C:U9 3.7 98.6 1.0 N3 C:U9 3.9 0.1 1.0 N1 C:U9 4.0 0.8 1.0 O4 C:U9 4.1 91.0 1.0 N1 C:CBV101 4.1 80.5 1.0 C2 C:U9 4.2 0.5 1.0 N3 C:CBV101 4.2 84.5 1.0 O5' C:CBV101 4.4 90.1 1.0 P C:CBV101 4.6 98.6 1.0 C2 C:CBV101 4.6 82.0 1.0 C2' C:U9 4.8 0.8 1.0 C3' C:U9 4.8 0.8 1.0 C1' C:U9 4.9 0.6 1.0 O2 C:U9 4.9 0.2 1.0 O5' C:U9 5.0 0.8 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:Br101 b:80.0 occ:1.00 BR F:CBV101 0.0 80.0 1.0 C5 F:CBV101 1.9 61.1 1.0 C6 F:CBV101 2.9 56.5 1.0 C4 F:CBV101 2.9 51.4 1.0 N4 F:CBV101 3.2 45.5 1.0 C5 F:U9 3.7 57.7 1.0 C4 F:U9 3.8 54.7 1.0 C6 F:U9 4.0 54.0 1.0 O2P F:CBV101 4.1 82.6 1.0 N1 F:CBV101 4.1 53.6 1.0 N3 F:U9 4.2 54.4 1.0 O4 F:U9 4.2 53.9 1.0 O5' F:CBV101 4.2 64.3 1.0 N3 F:CBV101 4.2 47.4 1.0 P F:CBV101 4.3 66.8 1.0 N1 F:U9 4.4 59.0 1.0 C2 F:U9 4.5 56.2 1.0 C2 F:CBV101 4.6 44.5 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:Br101 b:1.0 occ:1.00 BR I:CBV101 0.0 1.0 1.0 C5 I:CBV101 1.9 90.7 1.0 C6 I:CBV101 2.9 93.3 1.0 C4 I:CBV101 2.9 72.8 1.0 N4 I:CBV101 3.2 73.9 1.0 C5 I:U9 3.6 89.4 1.0 C4 I:U9 3.7 90.0 1.0 O2P I:CBV101 3.7 84.3 1.0 C6 I:U9 3.8 94.4 1.0 N3 I:U9 4.0 93.7 1.0 N1 I:U9 4.1 97.9 1.0 N1 I:CBV101 4.1 86.9 1.0 O4 I:U9 4.2 79.5 1.0 N3 I:CBV101 4.2 71.4 1.0 C2 I:U9 4.2 95.4 1.0 O5' I:CBV101 4.3 86.7 1.0 P I:CBV101 4.5 94.3 1.0 C2 I:CBV101 4.6 77.2 1.0 C2' I:U9 4.8 98.6 1.0 C3' I:U9 4.8 0.2 1.0 O2 I:U9 5.0 93.1 1.0 C1' I:U9 5.0 0.0 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:Br101 b:73.8 occ:1.00 BR M:CBV101 0.0 73.8 1.0 C5 M:CBV101 1.9 54.4 1.0 C6 M:CBV101 2.9 46.9 1.0 C4 M:CBV101 3.0 48.8 1.0 N4 M:CBV101 3.2 53.8 1.0 O2P M:CBV101 3.6 77.9 1.0 C5 M:U9 3.7 55.5 1.0 C4 M:U9 3.8 55.4 1.0 C6 M:U9 4.0 55.5 1.0 N1 M:CBV101 4.1 44.2 1.0 N3 M:U9 4.2 62.9 1.0 N3 M:CBV101 4.2 42.5 1.0 O5' M:CBV101 4.2 58.8 1.0 O4 M:U9 4.2 54.5 1.0 N1 M:U9 4.3 62.6 1.0 P M:CBV101 4.4 70.9 1.0 C2 M:U9 4.5 65.8 1.0 C2 M:CBV101 4.6 41.9 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:Br101 b:0.3 occ:1.00 BR O:CBV101 0.0 0.3 1.0 C5 O:CBV101 1.9 89.9 1.0 C6 O:CBV101 2.9 85.1 1.0 C4 O:CBV101 2.9 77.0 1.0 N4 O:CBV101 3.2 81.7 1.0 C5 O:U9 3.4 89.1 1.0 C6 O:U9 3.6 96.2 1.0 C4 O:U9 3.6 88.5 1.0 O O:HOH202 3.8 57.4 1.0 O2P O:CBV101 3.9 90.7 1.0 N3 O:U9 3.9 97.6 1.0 N1 O:U9 3.9 0.5 1.0 C2 O:U9 4.1 0.4 1.0 N1 O:CBV101 4.1 79.2 1.0 O4 O:U9 4.1 87.0 1.0 N3 O:CBV101 4.2 67.4 1.0 O5' O:CBV101 4.4 86.1 1.0 C3' O:U9 4.5 0.7 1.0 C2' O:U9 4.6 0.9 1.0 P O:CBV101 4.6 84.3 1.0 C2 O:CBV101 4.6 73.0 1.0 C1' O:U9 4.8 0.7 1.0 O5' O:U9 4.9 0.5 1.0 O2 O:U9 4.9 0.8 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