Bromine in PDB 5m91: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dibromophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dibromophenol, PDB code: 5m91 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)	30.11 / 1.72
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.541, 73.541, 184.613, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.5

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dibromophenol 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 2,6- Dibromophenol (pdb code 5m91). 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 2,6- Dibromophenol, PDB code: 5m91:
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 2,6- Dibromophenol


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 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br510 b:40.9 occ:0.46 BR1 A:94N510 0.0 40.9 0.5 C2 A:94N510 1.9 28.8 0.5 O A:TYR102 2.8 24.9 1.0 C1 A:94N510 2.8 33.7 0.5 C3 A:94N510 2.9 24.4 0.5 ND2 A:ASN272 3.0 14.6 1.0 O A:HOH972 3.0 24.9 1.0 O A:94N510 3.1 41.0 0.5 CE2 A:PHE38 3.6 18.7 1.0 CD2 A:PHE38 3.7 16.5 1.0 C54 A:BVQ503 3.7 15.3 1.0 C A:TYR102 3.9 25.3 1.0 CA A:GLY103 4.0 21.0 1.0 CG A:ASN272 4.0 20.2 1.0 CB A:ASN272 4.1 17.1 1.0 C A:94N510 4.1 30.0 0.5 C4 A:94N510 4.2 31.3 0.5 CG2 A:ILE105 4.3 18.8 1.0 O A:HOH866 4.3 22.2 1.0 N A:GLY103 4.4 20.7 1.0 CZ A:PHE38 4.5 20.6 1.0 C5 A:94N510 4.7 32.6 0.5 O A:HOH811 4.7 28.0 1.0 OH A:TYR246 4.7 17.2 1.0 CG A:PHE38 4.7 20.6 1.0 O A:HOH620 5.0 17.4 1.0

Bromine binding site 2 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dibromophenol


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 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br510 b:45.2 occ:0.46 BR A:94N510 0.0 45.2 0.5 C4 A:94N510 1.9 31.3 0.5 C5 A:94N510 2.8 32.6 0.5 C3 A:94N510 2.9 24.4 0.5 O A:94N510 3.1 41.0 0.5 O A:HOH620 3.1 17.4 1.0 OH A:TYR246 3.5 17.2 1.0 CE2 A:TYR246 3.6 16.9 1.0 CH2 A:TRP376 3.8 16.6 1.0 CG2 A:THR242 3.9 14.7 1.0 NH2 A:ARG305 3.9 15.8 1.0 CZ A:TYR246 3.9 17.0 1.0 O39 A:BVQ503 4.0 18.3 1.0 CZ3 A:TRP376 4.1 20.7 1.0 C A:94N510 4.1 30.0 0.5 C2 A:94N510 4.1 28.8 0.5 C38 A:BVQ503 4.2 17.7 1.0 CH2 A:TRP96 4.3 18.5 1.0 CB A:TYR382 4.3 18.8 1.0 C37 A:BVQ503 4.4 15.6 1.0 CG A:TYR382 4.5 22.7 1.0 C1 A:94N510 4.7 33.7 0.5 CD2 A:TYR246 4.7 15.0 1.0 N40 A:BVQ503 4.7 18.0 1.0 CZ A:ARG305 4.7 19.2 1.0 CZ2 A:TRP96 4.8 17.1 1.0 CD2 A:TYR382 4.8 20.9 1.0 CZ A:PHE38 4.9 20.6 1.0 CD1 A:TYR382 4.9 24.5 1.0 CZ2 A:TRP376 4.9 19.9 1.0

Bromine binding site 3 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dibromophenol


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 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br506 b:45.1 occ:0.47 BR1 B:94N506 0.0 45.1 0.5 C2 B:94N506 1.9 34.6 0.5 C1 B:94N506 2.8 36.1 0.5 C3 B:94N506 2.9 25.4 0.5 O B:TYR102 2.9 24.8 1.0 O B:HOH910 3.0 26.1 1.0 ND2 B:ASN272 3.1 18.7 1.0 O B:94N506 3.1 39.3 0.5 CE2 B:PHE38 3.5 27.6 1.0 CD2 B:PHE38 3.6 26.6 1.0 C54 B:BVQ503 3.8 21.0 1.0 C B:TYR102 3.9 22.1 1.0 CA B:GLY103 4.1 20.5 1.0 CG B:ASN272 4.1 21.0 1.0 CB B:ASN272 4.1 16.1 1.0 C B:94N506 4.1 31.8 0.5 C4 B:94N506 4.1 30.2 0.5 CG2 B:ILE105 4.4 23.2 1.0 O B:HOH843 4.4 21.6 1.0 CZ B:PHE38 4.5 24.9 1.0 N B:GLY103 4.5 23.3 1.0 CG B:PHE38 4.6 21.9 1.0 C5 B:94N506 4.7 31.9 0.5 OH B:TYR246 4.7 20.6 1.0 O B:HOH677 4.7 28.2 1.0 O B:HOH605 5.0 22.1 0.9 CB B:TYR102 5.0 22.1 1.0

Bromine binding site 4 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dibromophenol


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 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br506 b:45.2 occ:0.47 BR B:94N506 0.0 45.2 0.5 C4 B:94N506 1.9 30.2 0.5 C5 B:94N506 2.8 31.9 0.5 C3 B:94N506 2.9 25.4 0.5 O B:94N506 3.1 39.3 0.5 O B:HOH605 3.1 22.1 0.9 OH B:TYR246 3.6 20.6 1.0 CE2 B:TYR246 3.6 18.7 1.0 CH2 B:TRP376 3.9 24.9 1.0 CG2 B:THR242 3.9 15.5 1.0 NH2 B:ARG305 3.9 16.5 1.0 CZ B:TYR246 4.0 20.1 1.0 O39 B:BVQ503 4.0 22.1 1.0 CZ3 B:TRP376 4.1 26.4 1.0 C B:94N506 4.1 31.8 0.5 C2 B:94N506 4.1 34.6 0.5 C38 B:BVQ503 4.2 19.8 1.0 CB B:TYR382 4.4 24.4 1.0 CH2 B:TRP96 4.4 19.3 1.0 C37 B:BVQ503 4.4 18.9 1.0 CG B:TYR382 4.5 23.5 1.0 C1 B:94N506 4.7 36.1 0.5 N40 B:BVQ503 4.7 17.9 1.0 CZ B:ARG305 4.7 18.1 1.0 CD2 B:TYR246 4.7 15.9 1.0 CZ2 B:TRP96 4.8 21.3 1.0 CZ B:PHE38 4.8 24.9 1.0 CD2 B:TYR382 4.8 21.0 1.0 CD1 B:TYR382 4.9 25.2 1.0 CZ2 B:TRP376 5.0 25.4 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