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Bromine in PDB 5m92: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol, PDB code: 5m92 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 / 1.79
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.944, 73.944, 185.109, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.8

Other elements in 5m92:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol 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- Dibromophenol (pdb code 5m92). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol, PDB code: 5m92:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 5m92

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Bromine binding site 1 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- 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 2,4- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br512

b:35.9
occ:0.63
 BR1 A:Y8I512 0.0 35.9 0.6
C02 A:Y8I512 1.9 25.7 0.6
C09 A:Y8I512 2.9 29.2 0.6
C03 A:Y8I512 2.9 26.8 0.6
CH2 A:TRP56 3.4 35.0 1.0
CE1 A:TYR382 3.5 22.6 1.0
CD1 A:TYR102 3.6 26.3 1.0
CG A:TYR102 3.7 22.7 1.0
O A:HOH799 3.7 26.6 1.0
CE1 A:TYR102 3.7 25.2 1.0
CD2 A:TYR102 3.9 29.9 1.0
CZ3 A:TRP56 3.9 30.5 1.0
CZ A:TYR102 3.9 30.4 1.0
O A:HOH927 4.0 31.9 1.0
CD1 A:TYR382 4.0 23.2 1.0
CE2 A:TYR102 4.0 22.7 1.0
C04 A:Y8I512 4.2 23.4 0.6
C08 A:Y8I512 4.2 24.9 0.6
CZ A:TYR382 4.2 22.3 1.0
CB A:TYR102 4.4 22.1 1.0
CZ2 A:TRP56 4.4 33.3 1.0
OH A:TYR382 4.5 23.5 1.0
CZ2 A:TRP96 4.6 19.1 1.0
C06 A:Y8I512 4.6 26.3 0.6
OH A:TYR102 4.7 24.1 1.0
CZ3 A:TRP376 4.7 21.5 1.0
O A:HOH723 4.8 21.6 1.0
CE3 A:TRP376 4.9 20.0 1.0
CB A:PHE57 5.0 30.5 1.0

Bromine binding site 2 out of 9 in 5m92

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Bromine binding site 2 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- 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 2,4- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br512

b:32.7
occ:0.63
 BR5 A:Y8I512 0.0 32.7 0.6
C04 A:Y8I512 1.9 23.4 0.6
C03 A:Y8I512 2.9 26.8 0.6
C06 A:Y8I512 2.9 26.3 0.6
O07 A:Y8I512 3.1 26.8 0.6
O A:HOH605 3.3 25.6 1.0
O39 A:BVQ503 3.6 23.4 1.0
CG2 A:THR242 3.6 19.4 1.0
C38 A:BVQ503 3.8 20.1 1.0
CE2 A:TYR246 3.8 17.8 1.0
NH2 A:ARG305 3.9 18.7 1.0
CH2 A:TRP376 3.9 20.4 1.0
OH A:TYR246 3.9 18.6 1.0
CZ3 A:TRP376 4.2 21.5 1.0
C02 A:Y8I512 4.2 25.7 0.6
C37 A:BVQ503 4.2 17.8 1.0
CB A:TYR382 4.2 20.3 1.0
C08 A:Y8I512 4.2 24.9 0.6
N40 A:BVQ503 4.3 18.3 1.0
CZ A:TYR246 4.3 20.3 1.0
CG A:TYR382 4.3 22.9 1.0
CD2 A:TYR382 4.5 18.4 1.0
CH2 A:TRP96 4.5 26.3 1.0
CZ A:ARG305 4.6 22.3 1.0
C09 A:Y8I512 4.7 29.2 0.6
CZ2 A:TRP96 4.8 19.1 1.0
CD2 A:TYR246 4.8 15.5 1.0
CD1 A:TYR382 4.9 23.2 1.0
NH1 A:ARG305 4.9 18.3 1.0
CB A:THR242 5.0 16.5 1.0
CZ2 A:TRP376 5.0 24.9 1.0

Bromine binding site 3 out of 9 in 5m92

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Bromine binding site 3 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- 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 2,4- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br513

b:34.2
occ:0.52
 BR1 A:Y8I513 0.0 34.2 0.5
C02 A:Y8I513 2.0 25.8 0.5
C09 A:Y8I513 3.0 32.1 0.5
C03 A:Y8I513 3.0 27.9 0.5
O B:LEU124 3.2 23.4 1.0
CG B:PRO127 3.9 28.8 1.0
CD B:PRO127 3.9 27.7 1.0
C B:LEU124 4.1 24.7 1.0
CD2 A:LEU58 4.2 24.2 1.0
CE2 A:TYR61 4.2 23.6 1.0
O B:GLN123 4.3 22.8 1.0
C04 A:Y8I513 4.3 33.5 0.5
C08 A:Y8I513 4.3 36.8 0.5
CA B:LEU124 4.3 23.9 1.0
O A:HOH1017 4.3 53.2 1.0
CE1 A:PHE57 4.3 30.4 1.0
CD1 A:LEU186 4.3 35.1 1.0
CD1 B:LEU124 4.3 24.2 1.0
C06 A:Y8I513 4.8 37.3 0.5
OH A:TYR61 4.8 25.9 1.0

Bromine binding site 4 out of 9 in 5m92

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Bromine binding site 4 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- 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 2,4- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br513

b:47.1
occ:0.52
 BR5 A:Y8I513 0.0 47.1 0.5
C04 A:Y8I513 1.9 33.5 0.5
C06 A:Y8I513 2.9 37.3 0.5
C03 A:Y8I513 2.9 27.9 0.5
O07 A:Y8I513 3.0 45.3 0.5
BR A:BR514 3.8 44.9 0.2
CZ A:PHE57 4.1 37.1 1.0
NE2 A:HIS187 4.1 70.6 1.0
C08 A:Y8I513 4.2 36.8 0.5
C02 A:Y8I513 4.2 25.8 0.5
CG A:PRO55 4.3 28.6 1.0
CE1 A:HIS187 4.4 70.7 1.0
CB A:LEU186 4.4 27.6 1.0
CD1 A:LEU58 4.4 31.5 1.0
CD1 A:LEU186 4.6 35.1 1.0
CD2 A:HIS187 4.7 65.7 1.0
CE1 A:PHE57 4.7 30.4 1.0
CB A:PRO55 4.7 29.1 1.0
C09 A:Y8I513 4.8 32.1 0.5
O A:HOH928 4.8 51.1 1.0
CE2 A:PHE57 5.0 33.3 1.0

Bromine binding site 5 out of 9 in 5m92

Go back to Bromine Binding Sites List in 5m92
Bromine binding site 5 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol


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- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br514

b:44.9
occ:0.25
 O A:LEU186 3.0 37.6 1.0
CZ A:PHE44 3.4 34.0 1.0
O A:HOH928 3.5 51.1 1.0
CB A:LEU186 3.8 27.6 1.0
BR5 A:Y8I513 3.8 47.1 0.5
C A:LEU186 3.9 38.0 1.0
C5 A:BEN504 3.9 58.8 1.0
CD2 A:LEU186 4.0 35.4 1.0
CE1 A:PHE44 4.1 32.4 1.0
CA A:LEU186 4.1 26.5 1.0
C4 A:BEN504 4.2 56.2 1.0
C3 A:GOL505 4.2 52.8 1.0
CZ A:PHE57 4.4 37.1 1.0
CE2 A:PHE44 4.4 30.9 1.0
CE2 A:PHE57 4.4 33.3 1.0
CG A:LEU186 4.4 31.2 1.0
C6 A:BEN504 4.5 61.9 1.0
O A:HOH693 4.5 48.6 1.0
OE1 A:GLU189 4.6 28.5 1.0
CD A:GLU189 4.9 31.5 1.0
CD1 A:LEU186 4.9 35.1 1.0
C3 A:BEN504 4.9 56.1 1.0
OE2 A:GLU189 4.9 31.0 1.0
O3 A:GOL505 4.9 49.6 1.0

Bromine binding site 6 out of 9 in 5m92

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Bromine binding site 6 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol


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- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br506

b:31.4
occ:0.63
 BR1 B:Y8I506 0.0 31.4 0.6
C02 B:Y8I506 1.9 19.6 0.6
C03 B:Y8I506 2.8 24.3 0.6
C09 B:Y8I506 2.9 27.6 0.6
CE1 B:TYR382 3.5 25.1 1.0
CH2 B:TRP56 3.6 31.0 1.0
CD1 B:TYR102 3.6 27.7 1.0
CG B:TYR102 3.7 22.9 1.0
O B:HOH668 3.7 22.1 1.0
CE1 B:TYR102 3.8 23.0 1.0
O B:HOH865 3.8 27.2 1.0
CD2 B:TYR102 3.9 21.0 1.0
CZ B:TYR102 4.0 22.1 1.0
CD1 B:TYR382 4.0 28.2 1.0
CZ3 B:TRP56 4.0 31.4 1.0
CE2 B:TYR102 4.0 20.1 1.0
C04 B:Y8I506 4.1 25.8 0.6
C08 B:Y8I506 4.2 19.9 0.6
CZ B:TYR382 4.2 24.5 1.0
CB B:TYR102 4.3 21.4 1.0
OH B:TYR382 4.5 20.4 1.0
CZ2 B:TRP56 4.6 38.2 1.0
C06 B:Y8I506 4.6 21.5 0.6
CZ3 B:TRP376 4.6 25.1 1.0
CZ2 B:TRP96 4.7 22.5 1.0
OH B:TYR102 4.7 27.1 1.0
O B:HOH780 4.8 23.8 1.0
CE3 B:TRP376 4.8 20.8 1.0
CB B:PHE57 5.0 23.6 1.0

Bromine binding site 7 out of 9 in 5m92

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Bromine binding site 7 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br506

b:33.9
occ:0.63
 BR5 B:Y8I506 0.0 33.9 0.6
C04 B:Y8I506 1.9 25.8 0.6
C03 B:Y8I506 2.8 24.3 0.6
C06 B:Y8I506 2.9 21.5 0.6
O07 B:Y8I506 3.1 26.1 0.6
O B:HOH604 3.3 24.5 0.8
CG2 B:THR242 3.5 18.5 1.0
O39 B:BVQ503 3.6 21.6 1.0
CE2 B:TYR246 3.7 20.5 1.0
C38 B:BVQ503 3.8 17.6 1.0
OH B:TYR246 3.9 20.0 1.0
NH2 B:ARG305 3.9 23.9 1.0
CH2 B:TRP376 4.0 26.1 1.0
C02 B:Y8I506 4.1 19.6 0.6
C08 B:Y8I506 4.2 19.9 0.6
CB B:TYR382 4.2 17.5 1.0
C37 B:BVQ503 4.2 21.8 1.0
N40 B:BVQ503 4.2 22.0 1.0
CZ3 B:TRP376 4.2 25.1 1.0
CZ B:TYR246 4.3 25.0 1.0
CG B:TYR382 4.3 26.2 1.0
CD2 B:TYR382 4.4 20.3 1.0
CH2 B:TRP96 4.5 16.7 1.0
CZ B:ARG305 4.6 22.2 1.0
C09 B:Y8I506 4.7 27.6 0.6
CZ2 B:TRP96 4.7 22.5 1.0
CD2 B:TYR246 4.8 17.7 1.0
CB B:THR242 4.9 20.3 1.0
CD1 B:TYR382 4.9 28.2 1.0
NH1 B:ARG305 4.9 20.8 1.0

Bromine binding site 8 out of 9 in 5m92

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Bromine binding site 8 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br507

b:37.1
occ:0.51
 BR1 B:Y8I507 0.0 37.1 0.5
C02 B:Y8I507 2.0 27.9 0.5
C03 B:Y8I507 2.9 29.0 0.5
C09 B:Y8I507 3.0 38.0 0.5
O A:LEU124 3.1 24.5 1.0
CD A:PRO127 3.7 22.6 1.0
CG A:PRO127 3.8 22.8 1.0
C A:LEU124 3.9 23.9 1.0
O A:GLN123 4.0 23.3 1.0
CA A:LEU124 4.1 22.7 1.0
O B:HOH860 4.2 48.4 1.0
CD2 B:LEU58 4.2 24.9 1.0
C04 B:Y8I507 4.2 39.0 0.5
C08 B:Y8I507 4.3 43.0 0.5
CE2 B:TYR61 4.3 18.3 1.0
CD1 A:LEU124 4.3 20.6 1.0
CD1 B:LEU186 4.5 29.1 1.0
CE2 B:PHE57 4.6 34.0 1.0
C06 B:Y8I507 4.7 39.0 0.5
O A:HOH724 4.8 39.9 1.0
O A:HOH1000 4.9 50.5 1.0
C A:GLN123 4.9 22.9 1.0
OH B:TYR61 4.9 23.4 1.0

Bromine binding site 9 out of 9 in 5m92

Go back to Bromine Binding Sites List in 5m92
Bromine binding site 9 out of 9 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4- Dibromophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br507

b:52.1
occ:0.51
 BR5 B:Y8I507 0.0 52.1 0.5
C04 B:Y8I507 1.9 39.0 0.5
C03 B:Y8I507 2.9 29.0 0.5
C06 B:Y8I507 2.9 39.0 0.5
O07 B:Y8I507 3.1 32.5 0.5
CE1 B:HIS187 3.6 57.3 1.0
CZ B:PHE57 4.0 33.4 1.0
NE2 B:HIS187 4.0 61.0 1.0
CD1 B:LEU186 4.1 29.1 1.0
CB B:LEU186 4.1 25.6 1.0
C02 B:Y8I507 4.2 27.9 0.5
ND1 B:HIS187 4.2 55.5 1.0
C08 B:Y8I507 4.2 43.0 0.5
O B:HOH641 4.3 49.4 1.0
CG B:PRO55 4.4 20.4 1.0
CD1 B:LEU58 4.5 23.1 1.0
CE2 B:PHE57 4.6 34.0 1.0
CG B:LEU186 4.7 25.7 1.0
C09 B:Y8I507 4.8 38.0 0.5
CB B:PRO55 4.8 21.4 1.0
CD2 B:HIS187 4.9 56.8 1.0
CE1 B:PHE57 5.0 29.7 1.0
CG B:HIS187 5.0 46.3 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 00:17:22 2024

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