Bromine in PDB 6ymm: Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312, PDB code: 6ymm 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)	38.18 / 2.20
Space group	P 3 1 2
Cell size a, b, c (Å), α, β, γ (°)	88.170, 88.170, 76.080, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.1

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Bromine atom in the Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312 (pdb code 6ymm). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312, PDB code: 6ymm:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312


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 From Space Group P312 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br10 b:83.2 occ:1.00 BR A:CBV10 0.0 83.2 1.0 C5 A:CBV10 1.9 69.8 1.0 C6 A:CBV10 2.9 69.5 1.0 C4 A:CBV10 2.9 59.6 1.0 N4 A:CBV10 3.2 55.2 1.0 C5 A:U9 3.7 75.3 1.0 O2P A:CBV10 3.7 73.3 1.0 C4 A:U9 3.8 71.2 1.0 C6 A:U9 3.9 78.5 1.0 N1 A:CBV10 4.1 64.9 1.0 N3 A:U9 4.2 72.6 1.0 N3 A:CBV10 4.2 65.0 1.0 O4 A:U9 4.2 76.2 1.0 N1 A:U9 4.3 72.0 1.0 C2 A:U9 4.4 64.8 1.0 C3' A:U9 4.5 75.1 1.0 O5' A:CBV10 4.6 66.3 1.0 C2 A:CBV10 4.6 63.1 1.0 P A:CBV10 4.7 71.2 1.0 C2' A:U9 5.0 74.5 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312


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 From Space Group P312 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br10 b:0.6 occ:1.00 BR C:CBV10 0.0 0.6 1.0 C5 C:CBV10 1.9 0.1 1.0 C6 C:CBV10 2.9 0.6 1.0 C4 C:CBV10 2.9 96.3 1.0 N4 C:CBV10 3.1 86.0 1.0 C5 C:U9 3.6 0.8 1.0 C6 C:U9 3.6 0.4 1.0 C4 C:U9 3.6 0.3 1.0 O2P C:CBV10 3.7 0.0 1.0 N3 C:U9 3.8 0.7 1.0 N1 C:U9 3.8 0.8 1.0 C2 C:U9 3.9 0.3 1.0 N1 C:CBV10 4.1 0.2 1.0 N3 C:CBV10 4.2 0.7 1.0 C2' C:U9 4.2 0.4 1.0 O4 C:U9 4.2 97.7 1.0 C3' C:U9 4.3 0.3 1.0 O2 C:U9 4.6 0.0 1.0 C1' C:U9 4.6 0.7 1.0 C2 C:CBV10 4.6 0.7 1.0 P C:CBV10 4.7 0.1 1.0 O5' C:CBV10 4.8 0.4 1.0 O3' C:U9 5.0 0.6 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