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

The structure of Crystal Structure of the Sam-Sah Riboswitch with Adenosine, PDB code: 6ymj 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)	37.34 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.599, 147.570, 75.013, 90.00, 91.36, 90.00
R / Rfree (%)	19.8 / 23.3

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

Magnesium	(Mg)	1 atom
Sodium	(Na)	3 atoms

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Br101 b:73.7 occ:1.00 BR A:CBV101 0.0 73.7 1.0 C5 A:CBV101 1.9 60.5 1.0 C6 A:CBV101 2.9 58.7 1.0 C4 A:CBV101 2.9 58.2 1.0 N4 A:CBV101 3.2 56.0 1.0 O2P A:CBV101 3.6 66.4 1.0 C5 A:U9 3.7 66.4 1.0 C4 A:U9 3.8 64.3 1.0 C6 A:U9 3.9 62.9 1.0 N1 A:CBV101 4.1 59.6 1.0 N3 A:U9 4.2 53.8 1.0 N3 A:CBV101 4.2 65.2 1.0 N1 A:U9 4.3 64.2 1.0 O4 A:U9 4.3 67.3 1.0 NA A:NA104 4.3 81.8 1.0 C2 A:U9 4.4 60.9 1.0 O5' A:CBV101 4.4 70.1 1.0 C3' A:U9 4.6 71.0 1.0 C2 A:CBV101 4.6 62.6 1.0 P A:CBV101 4.7 61.7 1.0 C2' A:U9 4.8 64.8 1.0

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ C:Br101 b:0.5 occ:1.00 BR C:CBV101 0.0 0.5 1.0 C5 C:CBV101 1.9 81.3 1.0 C6 C:CBV101 2.9 83.4 1.0 C4 C:CBV101 2.9 80.7 1.0 N4 C:CBV101 3.2 76.4 1.0 C5 C:U9 3.5 90.7 1.0 C4 C:U9 3.6 88.3 1.0 C6 C:U9 3.8 93.4 1.0 O2P C:CBV101 4.0 98.6 1.0 O4 C:U9 4.0 86.6 1.0 N3 C:U9 4.1 93.8 1.0 N1 C:CBV101 4.1 79.3 1.0 N3 C:CBV101 4.2 81.9 1.0 N1 C:U9 4.2 94.5 1.0 C2 C:U9 4.4 96.8 1.0 C2 C:CBV101 4.6 80.0 1.0 O5' C:CBV101 4.7 91.4 1.0 N7 C:A11 4.9 85.9 1.0 C3' C:U9 4.9 96.2 1.0 P C:CBV101 5.0 97.5 1.0 C2' 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 Adenosine


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ F:Br101 b:70.9 occ:1.00 BR F:CBV101 0.0 70.9 1.0 C5 F:CBV101 1.9 63.0 1.0 C6 F:CBV101 2.9 62.7 1.0 C4 F:CBV101 2.9 59.0 1.0 N4 F:CBV101 3.2 56.0 1.0 C5 F:U9 3.8 60.9 1.0 O F:HOH201 3.8 63.4 1.0 C4 F:U9 3.8 60.4 1.0 O F:HOH210 3.9 63.2 1.0 O2P F:CBV101 4.0 73.1 1.0 C6 F:U9 4.0 60.0 1.0 N1 F:CBV101 4.1 62.3 1.0 N3 F:U9 4.1 54.4 1.0 N3 F:CBV101 4.2 63.1 1.0 O4 F:U9 4.2 59.9 1.0 N1 F:U9 4.3 64.7 1.0 O5' F:CBV101 4.3 69.1 1.0 C2 F:U9 4.4 59.4 1.0 P F:CBV101 4.6 66.5 1.0 C2 F:CBV101 4.6 59.5 1.0 C3' F:U9 4.7 78.2 1.0 C2' F:U9 4.9 69.6 1.0

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ I:Br101 b:0.8 occ:1.00 BR I:CBV101 0.0 0.8 1.0 C5 I:CBV101 1.9 82.3 1.0 C6 I:CBV101 2.9 81.8 1.0 C4 I:CBV101 2.9 74.3 1.0 N4 I:CBV101 3.2 75.3 1.0 C5 I:U9 3.4 98.3 1.0 C4 I:U9 3.6 91.4 1.0 C6 I:U9 3.6 0.8 1.0 N3 I:U9 3.8 95.5 1.0 N1 I:U9 3.9 0.7 1.0 C2 I:U9 4.0 0.0 1.0 O4 I:U9 4.1 86.7 1.0 N1 I:CBV101 4.1 77.3 1.0 N3 I:CBV101 4.2 76.4 1.0 O2P I:CBV101 4.2 81.7 1.0 O5' I:CBV101 4.4 87.8 1.0 C3' I:U9 4.4 0.5 1.0 C2' I:U9 4.5 0.5 1.0 P I:CBV101 4.6 88.7 1.0 C2 I:CBV101 4.6 77.3 1.0 O2 I:U9 4.8 88.8 1.0 C1' I:U9 4.8 0.4 1.0 N7 I:A11 5.0 81.9 1.0

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ M:Br101 b:75.8 occ:1.00 BR M:CBV101 0.0 75.8 1.0 C5 M:CBV101 1.9 59.0 1.0 C6 M:CBV101 2.9 60.0 1.0 C4 M:CBV101 2.9 59.8 1.0 N4 M:CBV101 3.2 56.1 1.0 C5 M:U9 3.7 61.2 1.0 C4 M:U9 3.9 61.1 1.0 C6 M:U9 3.9 61.9 1.0 O2P M:CBV101 4.0 75.9 1.0 N1 M:CBV101 4.1 61.8 1.0 N3 M:CBV101 4.2 60.2 1.0 N3 M:U9 4.2 57.0 1.0 N1 M:U9 4.3 63.1 1.0 O4 M:U9 4.3 62.0 1.0 O5' M:CBV101 4.4 71.4 1.0 C2 M:U9 4.5 57.5 1.0 P M:CBV101 4.6 70.6 1.0 C2 M:CBV101 4.6 58.2 1.0 C3' M:U9 4.7 76.2 1.0 C2' M:U9 4.8 71.8 1.0

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ O:Br101 b:0.2 occ:1.00 BR O:CBV101 0.0 0.2 1.0 C5 O:CBV101 1.9 83.5 1.0 C6 O:CBV101 2.8 80.4 1.0 C4 O:CBV101 2.9 76.2 1.0 N4 O:CBV101 3.2 74.3 1.0 C5 O:U9 3.5 80.7 1.0 C4 O:U9 3.5 78.9 1.0 O2P O:CBV101 3.6 92.2 1.0 N3 O:U9 3.7 79.2 1.0 C6 O:U9 3.7 91.1 1.0 O4 O:U9 3.9 82.1 1.0 N1 O:U9 4.0 95.4 1.0 C2 O:U9 4.1 88.3 1.0 N1 O:CBV101 4.1 75.0 1.0 N3 O:CBV101 4.2 77.1 1.0 O5' O:CBV101 4.5 96.1 1.0 C2 O:CBV101 4.6 74.2 1.0 P O:CBV101 4.7 94.0 1.0 C2' O:U9 4.8 0.9 1.0 C3' O:U9 4.8 0.0 1.0 O2 O:U9 4.8 92.0 1.0 N7 O:A11 4.9 84.1 1.0 C1' O:U9 5.0 0.0 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