Bromine in PDB 8i3z: Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom

The structure of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom, PDB code: 8i3z was solved by X.Peng, D.M.J.Lilley, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.59 / 1.67
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.271, 81.271, 61.855, 90, 90, 120
R / Rfree (%)	16.8 / 18.6

The structure of Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Bromine atom in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom (pdb code 8i3z). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total only one binding site of Bromine was determined in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom, PDB code: 8i3z:

Bromine binding site 1 out of 1 in the Crystal Structure of Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom


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 Nad-II Riboswitch (Two Strands) with Nmn at 1.67 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Br21 b:72.2 occ:1.00 BR A:CBV21 0.0 72.2 1.0 C5 A:CBV21 1.9 60.1 1.0 HN42 A:CBV21 2.8 84.5 1.0 C6 A:CBV21 2.9 60.9 1.0 C4 A:CBV21 3.0 66.6 1.0 H6 A:CBV21 3.0 73.1 1.0 N4 A:CBV21 3.3 70.4 1.0 H3' A:U20 3.4 72.8 1.0 O1P A:CBV21 3.7 58.4 1.0 C5 A:U20 3.7 53.4 1.0 C6 A:U20 3.8 52.1 1.0 H2' A:U20 3.8 71.5 1.0 C4 A:U20 3.9 55.2 1.0 H5 A:U20 4.0 64.1 1.0 N1 A:U20 4.0 55.2 1.0 H6 A:U20 4.1 62.6 1.0 N3 A:U20 4.1 55.8 1.0 C2 A:U20 4.3 56.9 1.0 C3' A:U20 4.3 60.6 1.0 N1 A:CBV21 4.3 58.4 1.0 HN41 A:CBV21 4.3 84.5 1.0 N3 A:CBV21 4.3 67.2 1.0 C2' A:U20 4.4 59.5 1.0 O5' A:CBV21 4.5 59.5 1.0 O4 A:U20 4.5 57.9 1.0 H3 A:U20 4.6 66.9 1.0 P A:CBV21 4.7 55.7 1.0 C1' A:U20 4.8 57.4 1.0 C2 A:CBV21 4.9 69.0 1.0 O3' A:U20 5.0 56.2 1.0 O2 A:U20 5.0 59.0 1.0

X.Peng, W.Liao, X.Lin, D.M.J.Lilley, L.Huang. Crystal Structures of the Nad+-II Riboswitch Reveal Two Distinct Ligand-Binding Pockets. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36840714
DOI: 10.1093/NAR/GKAD102