Bromine in PDB 6tfe: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP), PDB code: 6tfe 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)	47.52 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.350, 59.440, 190.070, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 25.7

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) also contains other interesting chemical elements:

Magnesium	(Mg)	10 atoms
Sodium	(Na)	4 atoms

The binding sites of Bromine atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) (pdb code 6tfe). 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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP), PDB code: 6tfe:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br111 b:0.8 occ:1.00 H5 A:C42 1.2 0.3 1.0 C5 A:C42 2.1 0.5 1.0 H41 A:C42 2.5 87.8 1.0 C4 A:C42 3.0 84.3 1.0 N4 A:C42 3.0 72.7 1.0 C6 A:C42 3.1 94.8 1.0 H6 A:C42 3.2 0.3 1.0 C4 A:U41 3.5 68.4 1.0 N3 A:U41 3.6 68.5 1.0 H2' A:U41 3.7 0.7 1.0 C5 A:U41 3.7 0.1 1.0 C2 A:U41 3.8 81.6 1.0 H3' A:U41 3.8 0.4 1.0 H42 A:C42 3.8 87.8 1.0 OP2 A:C42 3.8 83.0 1.0 H3 A:U41 3.9 82.8 1.0 C6 A:U41 3.9 67.8 1.0 N1 A:U41 3.9 76.6 1.0 O4 A:U41 4.0 80.4 1.0 H5 A:U41 4.2 0.9 1.0 N3 A:C42 4.2 79.8 1.0 N1 A:C42 4.4 0.9 1.0 O2 A:U41 4.4 66.9 1.0 H6 A:U41 4.4 82.0 1.0 C2' A:U41 4.5 91.7 1.0 C3' A:U41 4.6 96.5 1.0 H5 A:U43 4.6 77.1 1.0 O5' A:C42 4.7 70.8 1.0 C2 A:C42 4.8 60.6 1.0 C1' A:U41 4.8 79.3 1.0 P A:C42 4.9 81.5 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br112 b:1.0 occ:1.00 H5 A:C45 1.4 0.3 1.0 C5 A:C45 2.3 0.4 1.0 H41 A:C45 2.8 0.3 1.0 C6 A:C45 3.2 0.4 1.0 H6 A:C45 3.3 0.7 1.0 C4 A:C45 3.3 0.5 1.0 N4 A:C45 3.4 0.4 1.0 H3' A:A44 3.7 92.4 1.0 OP2 A:C45 3.8 0.4 1.0 N7 A:A44 3.9 81.6 1.0 C8 A:A44 4.0 81.3 1.0 H8 A:A44 4.0 98.2 1.0 H42 A:C45 4.2 0.3 1.0 O A:HOH205 4.4 64.5 1.0 C5 A:A44 4.5 73.4 1.0 H2' A:A44 4.5 98.2 1.0 N1 A:C45 4.5 73.3 1.0 N3 A:C45 4.5 76.8 1.0 N9 A:A44 4.5 78.3 1.0 C3' A:A44 4.7 76.5 1.0 O5' A:A44 4.8 93.2 1.0 O5' A:C45 4.8 72.3 1.0 C4 A:A44 4.9 59.0 1.0 H5 A:U46 4.9 0.1 1.0 P A:C45 4.9 80.8 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