Bromine in PDB 6tfh: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+), PDB code: 6tfh 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)	48.49 / 2.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.935, 58.360, 193.968, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.6

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) also contains other interesting chemical elements:

Manganese	(Mn)	9 atoms
Sodium	(Na)	1 atom

The binding sites of Bromine atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) (pdb code 6tfh). 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 the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+), PDB code: 6tfh:

Bromine binding site 1 out of 1 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+)


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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3 b:0.6 occ:1.00 BR A:CBV3 0.0 0.6 1.0 C5 A:CBV3 1.9 0.0 1.0 HN42 A:CBV3 2.8 0.6 1.0 C6 A:CBV3 2.8 0.5 1.0 H6 A:CBV3 2.9 0.4 1.0 C4 A:CBV3 3.0 0.5 1.0 N4 A:CBV3 3.2 0.8 1.0 N7 A:G2 3.5 0.9 1.0 C8 A:G2 3.5 0.2 1.0 O2P A:CBV3 3.7 0.3 1.0 C5 A:G2 3.7 0.8 1.0 N9 A:G2 3.8 0.4 1.0 C4 A:G2 3.9 0.6 1.0 C3' A:G2 4.0 0.1 1.0 N1 A:CBV3 4.0 0.3 1.0 C2' A:G2 4.2 0.1 1.0 N3 A:CBV3 4.2 0.8 1.0 HN41 A:CBV3 4.2 0.6 1.0 O5' A:CBV3 4.3 0.5 1.0 C6 A:G2 4.4 0.0 1.0 O5' A:G2 4.5 0.9 1.0 P A:CBV3 4.5 0.0 1.0 C1' A:G2 4.6 0.7 1.0 C2 A:CBV3 4.6 0.8 1.0 N3 A:G2 4.7 0.6 1.0 O3' A:G2 4.8 0.5 1.0 O6 A:G2 4.8 0.5 1.0 O4' A:CBV3 5.0 0.4 1.0

L.Huang, J.Wang, D.M.J.Lilley. Structure and Ligand Binding of the Adp-Binding Domain of the Nad+ Riboswitch. Rna V. 26 878 2020.
ISSN: ESSN 1469-9001
PubMed: 32295864
DOI: 10.1261/RNA.074898.120