Bromine in PDB 5m8u: Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Bromophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Bromophenol, PDB code: 5m8u 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)	36.77 / 1.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.547, 73.547, 184.517, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.2

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- 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 4- Bromophenol (pdb code 5m8u). 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 4- Bromophenol, PDB code: 5m8u:
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 4- 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 4- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br512 b:38.4 occ:0.66 BR4 A:BML512 0.0 38.4 0.7 C4 A:BML512 1.9 19.5 0.7 C3 A:BML512 2.8 18.9 0.7 C5 A:BML512 2.8 17.2 0.7 CH2 A:TRP56 3.4 32.6 1.0 CD1 A:TYR102 3.4 25.8 1.0 CG A:TYR102 3.5 22.4 1.0 CE1 A:TYR382 3.5 19.2 1.0 CD1 A:TYR382 3.8 20.2 1.0 CE1 A:TYR102 3.8 27.0 1.0 CB A:TYR102 3.9 16.9 1.0 CD2 A:TYR102 4.0 27.8 1.0 CZ3 A:TRP56 4.0 33.0 1.0 CZ2 A:TRP96 4.1 16.3 1.0 CZ A:TYR382 4.1 19.8 1.0 C2 A:BML512 4.1 17.6 0.7 C6 A:BML512 4.1 15.8 0.7 O A:HOH791 4.2 22.9 1.0 CZ A:TYR102 4.3 33.9 1.0 CZ3 A:TRP376 4.3 17.5 1.0 CE2 A:TYR102 4.4 22.8 1.0 CZ2 A:TRP56 4.4 30.7 1.0 CH2 A:TRP96 4.4 18.7 1.0 OH A:TYR382 4.5 22.2 1.0 O A:HOH939 4.6 35.2 1.0 C1 A:BML512 4.6 25.9 0.7 CG A:TYR382 4.7 26.2 1.0 CE3 A:TRP376 4.7 16.6 1.0 CE2 A:TRP96 4.9 15.7 1.0 CE2 A:TYR382 4.9 18.4 1.0

Bromine binding site 2 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- 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 4- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br513 b:51.1 occ:0.46 BR4 A:BML513 0.0 51.1 0.5 C4 A:BML513 1.9 41.9 0.5 C3 A:BML513 2.8 46.1 0.5 C5 A:BML513 2.8 43.6 0.5 O A:LEU124 3.2 24.2 1.0 CG A:PRO127 3.8 23.7 1.0 CD A:PRO127 3.9 24.8 1.0 O B:HOH875 3.9 48.3 1.0 C A:LEU124 4.0 24.3 1.0 O A:GLN123 4.0 20.7 1.0 C6 A:BML513 4.1 50.7 0.5 C2 A:BML513 4.1 48.9 0.5 CD2 B:LEU58 4.1 23.8 1.0 CA A:LEU124 4.1 24.6 1.0 CD1 A:LEU124 4.4 16.5 1.0 CD1 B:LEU186 4.4 32.6 1.0 CE2 B:TYR61 4.4 17.9 1.0 CE1 B:PHE57 4.4 32.8 1.0 C1 A:BML513 4.7 49.8 0.5 O A:HOH1017 4.7 56.2 1.0 O A:HOH751 4.7 40.0 1.0 C A:GLN123 4.9 21.5 1.0 OH B:TYR61 5.0 20.6 1.0

Bromine binding site 3 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- 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 4- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br505 b:37.1 occ:0.68 BR4 B:BML505 0.0 37.1 0.7 C4 B:BML505 1.9 19.4 0.7 C5 B:BML505 2.8 25.4 0.7 C3 B:BML505 2.8 27.3 0.7 CD1 B:TYR102 3.4 26.5 1.0 CG B:TYR102 3.4 25.7 1.0 CH2 B:TRP56 3.5 30.4 1.0 CE1 B:TYR382 3.5 22.1 1.0 CE1 B:TYR102 3.8 27.1 1.0 CD2 B:TYR102 3.8 24.3 1.0 CD1 B:TYR382 3.9 27.5 1.0 CB B:TYR102 3.9 17.4 1.0 CZ3 B:TRP56 4.0 34.3 1.0 C6 B:BML505 4.1 25.7 0.7 C2 B:BML505 4.1 22.3 0.7 CZ B:TYR382 4.2 21.6 1.0 CZ B:TYR102 4.2 25.0 1.0 CE2 B:TYR102 4.2 22.9 1.0 CZ2 B:TRP96 4.2 18.4 1.0 O B:HOH893 4.2 30.6 1.0 O B:HOH666 4.3 23.3 1.0 CZ3 B:TRP376 4.4 23.3 1.0 OH B:TYR382 4.5 17.3 1.0 CZ2 B:TRP56 4.6 40.8 1.0 CH2 B:TRP96 4.6 16.4 1.0 C1 B:BML505 4.6 32.1 0.7 CE3 B:TRP376 4.7 16.6 1.0 CG B:TYR382 4.8 25.1 1.0 CE2 B:TRP96 5.0 18.4 1.0 CE2 B:TYR382 5.0 21.7 1.0

Bromine binding site 4 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- 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 4- Bromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br506 b:92.7 occ:0.57 BR4 B:BML506 0.0 92.7 0.6 C4 B:BML506 1.9 82.3 0.6 C5 B:BML506 2.8 76.5 0.6 C3 B:BML506 2.8 81.3 0.6 O B:LEU124 3.3 25.7 1.0 CD B:PRO127 3.8 28.4 1.0 CG B:PRO127 3.9 27.8 1.0 O A:HOH935 3.9 39.4 1.0 O B:GLN123 3.9 24.9 1.0 C B:LEU124 4.0 23.3 1.0 CA B:LEU124 4.1 22.8 1.0 C6 B:BML506 4.1 75.2 0.6 C2 B:BML506 4.1 80.7 0.6 CD1 A:LEU186 4.3 42.9 1.0 CD1 B:LEU124 4.4 20.7 1.0 CD2 A:LEU58 4.5 22.6 1.0 CE2 A:TYR61 4.6 22.4 1.0 C1 B:BML506 4.6 78.1 0.6 CE1 A:PHE57 4.7 30.1 1.0 C B:GLN123 4.8 21.2 1.0 N B:LEU124 5.0 22.1 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