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Bromine in PDB 5m2g: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol, PDB code: 5m2g 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) 47.27 / 1.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.610, 73.610, 184.958, 90.00, 90.00, 90.00
R / Rfree (%) 13.4 / 16.7

Other elements in 5m2g:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol also contains other interesting chemical elements:

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

Bromine Binding Sites:

The binding sites of Bromine atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol (pdb code 5m2g). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol, PDB code: 5m2g:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 5m2g

Go back to Bromine Binding Sites List in 5m2g
Bromine binding site 1 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol


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 2,4,6- Tribromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br510

b:56.3
occ:0.39
 BR2 A:TBP510 0.0 56.3 0.4
C2 A:TBP510 1.9 32.3 0.4
O A:TYR102 2.8 27.4 1.0
C1 A:TBP510 2.8 24.9 0.4
C3 A:TBP510 2.8 25.5 0.4
O A:HOH789 2.9 31.7 1.0
O1 A:TBP510 3.0 27.1 0.4
CE2 A:PHE38 3.3 18.2 1.0
ND2 A:ASN272 3.6 17.3 1.0
C A:TYR102 3.6 25.4 1.0
CD2 A:PHE38 3.7 19.2 1.0
O A:HOH976 3.8 26.8 1.0
CZ A:PHE38 3.8 21.6 1.0
C6 A:TBP510 4.1 20.2 0.4
C4 A:TBP510 4.1 29.3 0.4
CB A:TYR102 4.1 22.1 1.0
CA A:GLY103 4.3 20.3 1.0
OH A:TYR246 4.4 18.5 1.0
N A:GLY103 4.4 19.3 1.0
CA A:TYR102 4.4 20.3 1.0
CG A:PHE38 4.6 23.2 1.0
O A:HOH604 4.6 28.7 1.0
CE1 A:PHE38 4.6 22.7 1.0
C5 A:TBP510 4.7 22.8 0.4
CG A:ASN272 4.7 21.8 1.0
C54 A:BVQ503 4.8 16.2 1.0
CZ A:TYR246 4.8 18.0 1.0
CD1 A:PHE38 5.0 24.0 1.0

Bromine binding site 2 out of 6 in 5m2g

Go back to Bromine Binding Sites List in 5m2g
Bromine binding site 2 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol


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 2,4,6- Tribromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br510

b:46.8
occ:0.39
 BR4 A:TBP510 0.0 46.8 0.4
C4 A:TBP510 1.9 29.3 0.4
C5 A:TBP510 2.8 22.8 0.4
C3 A:TBP510 2.8 25.5 0.4
CH2 A:TRP56 3.2 35.4 1.0
CE1 A:TYR382 3.2 27.2 1.0
CD1 A:TYR102 3.3 29.8 1.0
CG A:TYR102 3.4 24.8 1.0
CE1 A:TYR102 3.6 29.6 1.0
CD1 A:TYR382 3.7 25.0 1.0
CD2 A:TYR102 3.8 22.9 1.0
CZ3 A:TRP56 3.8 30.2 1.0
O A:HOH763 3.9 26.5 1.0
CZ A:TYR102 3.9 33.5 1.0
CZ A:TYR382 4.0 21.1 1.0
CE2 A:TYR102 4.0 22.9 1.0
CB A:TYR102 4.1 22.1 1.0
C6 A:TBP510 4.1 20.2 0.4
C2 A:TBP510 4.1 32.3 0.4
CZ2 A:TRP56 4.2 33.0 1.0
OH A:TYR382 4.2 24.5 1.0
CZ2 A:TRP96 4.2 19.5 1.0
O A:HOH937 4.4 36.5 1.0
CH2 A:TRP96 4.5 20.3 1.0
CZ3 A:TRP376 4.6 22.5 1.0
C1 A:TBP510 4.7 24.9 0.4
OH A:TYR102 4.7 29.2 1.0
CG A:TYR382 4.8 21.4 1.0
CE3 A:TRP376 4.9 21.3 1.0
O A:HOH838 4.9 24.5 1.0
CE2 A:TYR382 5.0 22.8 1.0
CE2 A:TRP96 5.0 18.0 1.0

Bromine binding site 3 out of 6 in 5m2g

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


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 2,4,6- Tribromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br510

b:41.1
occ:0.39
 BR6 A:TBP510 0.0 41.1 0.4
C6 A:TBP510 1.9 20.2 0.4
C5 A:TBP510 2.8 22.8 0.4
C1 A:TBP510 2.8 24.9 0.4
O1 A:TBP510 3.1 27.1 0.4
O39 A:BVQ503 3.1 22.5 1.0
C38 A:BVQ503 3.2 19.7 1.0
CG2 A:THR242 3.4 16.7 1.0
O A:HOH604 3.4 28.7 1.0
N40 A:BVQ503 3.7 19.2 1.0
CB A:TYR382 3.7 17.9 1.0
C37 A:BVQ503 3.7 16.1 1.0
CH2 A:TRP376 3.7 20.5 1.0
NH2 A:ARG305 3.8 16.9 1.0
CG A:TYR382 3.9 21.4 1.0
CE2 A:TYR246 4.0 17.5 1.0
C4 A:TBP510 4.1 29.3 0.4
C2 A:TBP510 4.1 32.3 0.4
CZ3 A:TRP376 4.2 22.5 1.0
OH A:TYR246 4.2 18.5 1.0
CD2 A:TYR382 4.3 18.9 1.0
CZ A:ARG305 4.5 21.7 1.0
CD1 A:TYR382 4.6 25.0 1.0
CZ A:TYR246 4.6 18.0 1.0
C3 A:TBP510 4.6 25.5 0.4
NH1 A:ARG305 4.7 16.2 1.0
CZ2 A:TRP376 4.7 21.7 1.0
CB A:THR242 4.7 15.3 1.0
CH2 A:TRP96 4.8 20.3 1.0
OG1 A:THR242 4.9 19.1 1.0
C6 A:BVQ503 4.9 17.5 1.0
C7 A:BVQ503 4.9 16.6 1.0

Bromine binding site 4 out of 6 in 5m2g

Go back to Bromine Binding Sites List in 5m2g
Bromine binding site 4 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol


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 2,4,6- Tribromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br506

b:41.5
occ:0.43
 BR2 B:TBP506 0.0 41.5 0.4
C2 B:TBP506 1.9 20.0 0.4
C1 B:TBP506 2.8 28.9 0.4
C3 B:TBP506 2.8 25.9 0.4
O1 B:TBP506 3.1 29.7 0.4
O39 B:BVQ503 3.2 23.5 1.0
C38 B:BVQ503 3.2 21.2 1.0
O B:HOH604 3.4 32.8 0.9
CG2 B:THR242 3.4 16.0 1.0
CB B:TYR382 3.6 22.3 1.0
N40 B:BVQ503 3.6 19.7 1.0
C37 B:BVQ503 3.7 18.5 1.0
CH2 B:TRP376 3.7 24.0 1.0
CG B:TYR382 3.9 22.1 1.0
NH2 B:ARG305 3.9 20.3 1.0
C6 B:TBP506 4.1 36.2 0.4
C4 B:TBP506 4.1 27.2 0.4
CZ3 B:TRP376 4.1 25.2 1.0
CE2 B:TYR246 4.1 21.1 1.0
CD2 B:TYR382 4.2 22.0 1.0
OH B:TYR246 4.3 21.0 1.0
CD1 B:TYR382 4.6 26.2 1.0
CZ B:ARG305 4.6 19.3 1.0
C5 B:TBP506 4.6 34.8 0.4
CB B:THR242 4.7 19.7 1.0
CZ2 B:TRP376 4.7 25.5 1.0
CZ B:TYR246 4.7 20.5 1.0
NH1 B:ARG305 4.7 20.0 1.0
OG1 B:THR242 4.8 24.6 1.0
C7 B:BVQ503 5.0 17.4 1.0
CH2 B:TRP96 5.0 19.8 1.0
CA B:TYR382 5.0 20.8 1.0
C6 B:BVQ503 5.0 20.9 1.0

Bromine binding site 5 out of 6 in 5m2g

Go back to Bromine Binding Sites List in 5m2g
Bromine binding site 5 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br506

b:44.4
occ:0.43
 BR4 B:TBP506 0.0 44.4 0.4
C4 B:TBP506 1.9 27.2 0.4
C3 B:TBP506 2.8 25.9 0.4
C5 B:TBP506 2.8 34.8 0.4
CE1 B:TYR382 3.2 25.1 1.0
CD1 B:TYR102 3.3 29.2 1.0
CH2 B:TRP56 3.4 40.3 1.0
CE1 B:TYR102 3.5 27.2 1.0
CG B:TYR102 3.6 28.9 1.0
CD1 B:TYR382 3.7 26.2 1.0
O B:HOH647 3.8 25.8 1.0
CZ B:TYR102 3.9 28.8 1.0
CD2 B:TYR102 3.9 23.1 1.0
CZ3 B:TRP56 3.9 33.5 1.0
CZ B:TYR382 4.0 24.1 1.0
CE2 B:TYR102 4.0 22.3 1.0
C2 B:TBP506 4.1 20.0 0.4
C6 B:TBP506 4.1 36.2 0.4
CB B:TYR102 4.2 23.8 1.0
O B:HOH877 4.2 30.9 1.0
OH B:TYR382 4.3 24.3 1.0
CZ2 B:TRP96 4.4 22.0 1.0
CZ2 B:TRP56 4.4 41.4 1.0
CZ3 B:TRP376 4.6 25.2 1.0
OH B:TYR102 4.7 29.8 1.0
C1 B:TBP506 4.7 28.9 0.4
CH2 B:TRP96 4.8 19.8 1.0
CG B:TYR382 4.8 22.1 1.0
CE3 B:TRP376 4.9 25.5 1.0
O B:HOH789 4.9 27.0 1.0
CE2 B:TYR382 5.0 24.6 1.0

Bromine binding site 6 out of 6 in 5m2g

Go back to Bromine Binding Sites List in 5m2g
Bromine binding site 6 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Tribromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br506

b:51.2
occ:0.43
 BR6 B:TBP506 0.0 51.2 0.4
C6 B:TBP506 1.9 36.2 0.4
O B:TYR102 2.8 30.5 1.0
C1 B:TBP506 2.8 28.9 0.4
C5 B:TBP506 2.8 34.8 0.4
O B:HOH603 2.9 33.5 1.0
O1 B:TBP506 3.0 29.7 0.4
CE2 B:PHE38 3.4 27.0 1.0
C B:TYR102 3.5 24.0 1.0
ND2 B:ASN272 3.6 19.9 1.0
CD2 B:PHE38 3.8 25.7 1.0
O B:HOH884 3.9 29.1 1.0
CB B:TYR102 3.9 23.8 1.0
CZ B:PHE38 4.0 28.4 1.0
C2 B:TBP506 4.1 20.0 0.4
C4 B:TBP506 4.1 27.2 0.4
CA B:GLY103 4.2 18.5 1.0
N B:GLY103 4.2 22.6 1.0
CA B:TYR102 4.3 23.2 1.0
OH B:TYR246 4.3 21.0 1.0
C3 B:TBP506 4.6 25.9 0.4
CG B:PHE38 4.7 24.2 1.0
CZ B:TYR246 4.7 20.5 1.0
O B:HOH604 4.8 32.8 0.9
CG B:ASN272 4.8 21.7 1.0
CE1 B:PHE38 4.8 22.9 1.0
C54 B:BVQ503 5.0 19.6 1.0

Reference:

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
Page generated: Thu Jul 11 00:16:17 2024

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