Bromine in PDB 5maa: Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol, PDB code: 5maa was solved by C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.38 / 1.69
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.835, 73.835, 185.360, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 16.7

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Iron	(Fe)	16 atoms

The binding sites of Bromine atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol (pdb code 5maa). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol, PDB code: 5maa:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br509 b:58.1 occ:0.60 BR8 A:B3R509 0.0 58.1 0.6 C3 A:B3R509 1.9 29.8 0.6 C2 A:B3R509 2.8 25.0 0.6 C6 A:B3R509 2.8 22.5 0.6 CG A:TYR102 3.3 28.4 1.0 CH2 A:TRP56 3.3 32.3 1.0 CD1 A:TYR102 3.4 32.5 1.0 CB A:TYR102 3.5 22.8 1.0 CD2 A:TYR102 3.8 26.3 1.0 CE1 A:TYR382 4.0 25.4 1.0 CE1 A:TYR102 4.1 34.0 1.0 CZ3 A:TRP56 4.1 28.4 1.0 C5 A:B3R509 4.1 21.2 0.6 C1 A:B3R509 4.1 22.7 0.6 CD1 A:TYR382 4.1 23.9 1.0 CZ3 A:TRP376 4.2 21.5 1.0 CZ2 A:TRP56 4.2 36.1 1.0 CZ2 A:TRP96 4.3 19.9 1.0 CH2 A:TRP96 4.4 18.5 1.0 CE2 A:TYR102 4.4 27.8 1.0 CZ A:TYR102 4.5 36.5 1.0 C4 A:B3R509 4.6 25.1 0.6 CZ A:TYR382 4.6 22.9 1.0 O A:HOH923 4.7 44.0 1.0 CA A:TYR102 4.7 23.3 1.0 CE3 A:TRP376 4.8 19.8 1.0 O A:HOH712 4.9 28.8 1.0 CE1 A:PHE38 4.9 22.8 1.0 CG A:TYR382 5.0 21.2 1.0

Bromine binding site 2 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br510 b:46.1 occ:0.56 BR8 A:B3R510 0.0 46.1 0.6 C3 A:B3R510 1.9 41.5 0.6 C2 A:B3R510 2.8 43.1 0.6 C6 A:B3R510 2.8 42.2 0.6 O A:LEU124 3.1 23.8 1.0 CG A:PRO127 3.8 28.2 1.0 CD A:PRO127 3.8 25.4 1.0 C A:LEU124 3.9 21.9 1.0 O A:GLN123 4.0 23.1 1.0 CD2 B:LEU58 4.1 26.0 1.0 CA A:LEU124 4.1 21.9 1.0 C5 A:B3R510 4.1 44.2 0.6 C1 A:B3R510 4.1 38.8 0.6 CE2 B:PHE57 4.2 31.3 1.0 CE2 B:TYR61 4.3 22.3 1.0 CD1 A:LEU124 4.4 23.5 1.0 CD1 B:LEU186 4.5 48.8 1.0 C4 A:B3R510 4.7 40.0 0.6 OH B:TYR61 4.9 26.4 1.0 C A:GLN123 4.9 21.0 1.0

Bromine binding site 3 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br504 b:52.0 occ:0.60 BR8 B:B3R504 0.0 52.0 0.6 C3 B:B3R504 1.9 29.1 0.6 C6 B:B3R504 2.8 26.8 0.6 C2 B:B3R504 2.8 27.5 0.6 CG B:TYR102 3.3 25.3 1.0 CH2 B:TRP56 3.4 39.2 1.0 CD1 B:TYR102 3.4 29.8 1.0 CB B:TYR102 3.5 26.0 1.0 CD2 B:TYR102 3.9 22.7 1.0 CE1 B:TYR102 4.1 29.6 1.0 C5 B:B3R504 4.1 25.2 0.6 C1 B:B3R504 4.1 26.9 0.6 CE1 B:TYR382 4.2 28.6 1.0 CZ3 B:TRP376 4.2 25.5 1.0 CZ2 B:TRP56 4.2 42.1 1.0 CZ3 B:TRP56 4.3 35.5 1.0 O B:HOH893 4.3 40.0 1.0 CD1 B:TYR382 4.4 28.1 1.0 CE2 B:TYR102 4.4 25.0 1.0 CZ2 B:TRP96 4.5 22.8 1.0 CZ B:TYR102 4.5 30.3 1.0 C4 B:B3R504 4.6 26.7 0.6 CH2 B:TRP96 4.7 20.8 1.0 CE3 B:TRP376 4.8 22.2 1.0 CZ B:TYR382 4.8 24.8 1.0 CA B:TYR102 4.8 21.6 1.0 O B:HOH682 4.8 27.6 1.0 O B:HOH902 4.9 35.1 1.0 CE1 B:PHE38 4.9 23.1 1.0 CZ B:PHE38 5.0 27.1 1.0

Bromine binding site 4 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br505 b:49.2 occ:0.58 BR8 B:B3R505 0.0 49.2 0.6 C3 B:B3R505 1.9 44.4 0.6 C6 B:B3R505 2.8 45.9 0.6 C2 B:B3R505 2.8 40.8 0.6 O B:LEU124 3.2 23.1 1.0 CD B:PRO127 3.9 25.5 1.0 CG B:PRO127 3.9 28.3 1.0 C B:LEU124 3.9 24.0 1.0 O B:GLN123 4.0 25.3 1.0 CA B:LEU124 4.1 20.6 1.0 C5 B:B3R505 4.1 46.6 0.6 C1 B:B3R505 4.1 44.7 0.6 CE2 A:PHE57 4.2 36.0 1.0 CD2 A:LEU58 4.2 29.0 1.0 CD1 B:LEU124 4.3 25.9 1.0 CE2 A:TYR61 4.4 23.1 1.0 C4 B:B3R505 4.7 44.0 0.6 C B:GLN123 4.9 23.0 1.0 CD1 A:LEU186 4.9 30.6 1.0 OH A:TYR61 5.0 26.1 1.0 N B:LEU124 5.0 20.4 1.0

C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert. Cobamide-Mediated Enzymatic Reductive Dehalogenation Via Long-Range Electron Transfer. Nat Commun V. 8 15858 2017.
ISSN: ESSN 2041-1723
PubMed: 28671181
DOI: 10.1038/NCOMMS15858