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Chlorine in PDB 5m8x: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol, PDB code: 5m8x 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) 47.31 / 1.87
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.766, 73.766, 185.010, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 15.9

Other elements in 5m8x:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol (pdb code 5m8x). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol, PDB code: 5m8x:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5m8x

Go back to Chlorine Binding Sites List in 5m8x
Chlorine binding site 1 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl513

b:33.7
occ:0.74
CL1 A:TC7513 0.0 33.7 0.7
C4 A:TC7513 1.7 25.8 0.7
C5 A:TC7513 2.7 22.3 0.7
C3 A:TC7513 2.7 23.6 0.7
O1 A:TC7513 3.0 29.9 0.7
O A:HOH604 3.4 27.4 1.0
CG2 A:THR242 3.5 15.8 1.0
CE2 A:TYR246 3.5 21.2 1.0
OH A:TYR246 3.7 19.5 1.0
O39 A:BVQ503 3.8 19.7 1.0
NH2 A:ARG305 3.8 16.0 1.0
C6 A:TC7513 4.0 30.3 0.7
C2 A:TC7513 4.0 27.2 0.7
CZ A:TYR246 4.0 18.8 1.0
C38 A:BVQ503 4.0 20.1 1.0
CH2 A:TRP96 4.1 20.4 1.0
CH2 A:TRP376 4.2 17.4 1.0
CB A:TYR382 4.2 15.1 1.0
CG A:TYR382 4.3 19.7 1.0
CZ3 A:TRP376 4.4 23.8 1.0
CZ2 A:TRP96 4.5 18.7 1.0
C1 A:TC7513 4.5 32.2 0.7
CD2 A:TYR382 4.5 18.9 1.0
N40 A:BVQ503 4.5 17.3 1.0
C37 A:BVQ503 4.5 16.9 1.0
CZ A:ARG305 4.5 20.6 1.0
CD2 A:TYR246 4.6 17.9 1.0
CD1 A:TYR382 4.8 22.9 1.0
CB A:THR242 4.9 16.8 1.0
NH1 A:ARG305 5.0 16.7 1.0

Chlorine binding site 2 out of 6 in 5m8x

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Chlorine binding site 2 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl513

b:39.5
occ:0.74
CL3 A:TC7513 0.0 39.5 0.7
C6 A:TC7513 1.7 30.3 0.7
C5 A:TC7513 2.7 22.3 0.7
C1 A:TC7513 2.7 32.2 0.7
CH2 A:TRP56 3.1 34.0 1.0
CL5 A:TC7513 3.2 44.9 0.7
CG A:TYR102 3.4 22.6 1.0
CD1 A:TYR102 3.5 26.1 1.0
CD2 A:TYR102 3.6 21.4 1.0
CZ2 A:TRP56 3.8 38.1 1.0
CE1 A:TYR382 3.8 23.4 1.0
CB A:TYR102 3.8 19.9 1.0
CE1 A:TYR102 3.9 26.3 1.0
C4 A:TC7513 4.0 25.8 0.7
C2 A:TC7513 4.0 27.2 0.7
CZ3 A:TRP56 4.0 29.6 1.0
CE2 A:TYR102 4.1 21.9 1.0
CD1 A:TYR382 4.2 22.9 1.0
CZ A:TYR102 4.2 29.1 1.0
O A:HOH790 4.3 23.7 1.0
O A:HOH931 4.5 34.1 1.0
C3 A:TC7513 4.5 23.6 0.7
CZ3 A:TRP376 4.6 23.8 1.0
CZ A:TYR382 4.6 20.7 1.0
CZ2 A:TRP96 4.7 18.7 1.0
OH A:TYR382 4.9 21.8 1.0
CE3 A:TRP376 4.9 19.0 1.0
CH2 A:TRP96 5.0 20.4 1.0

Chlorine binding site 3 out of 6 in 5m8x

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Chlorine binding site 3 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl513

b:44.9
occ:0.74
CL5 A:TC7513 0.0 44.9 0.7
C1 A:TC7513 1.7 32.2 0.7
C2 A:TC7513 2.7 27.2 0.7
C6 A:TC7513 2.7 30.3 0.7
CB A:TYR102 3.1 19.9 1.0
CL3 A:TC7513 3.2 39.5 0.7
O1 A:GOL505 3.3 70.8 1.0
CZ2 A:TRP56 3.3 38.1 1.0
CH2 A:TRP56 3.8 34.0 1.0
O A:TYR102 3.8 21.8 1.0
CG A:TYR102 3.8 22.6 1.0
CD1 A:PHE38 4.0 20.6 1.0
C3 A:TC7513 4.0 23.6 0.7
C5 A:TC7513 4.0 22.3 0.7
CE1 A:PHE38 4.1 22.4 1.0
CD2 A:TYR102 4.1 21.4 1.0
C1 A:GOL505 4.1 65.4 1.0
CG A:PHE38 4.1 21.1 1.0
CZ A:PHE38 4.3 24.2 1.0
CD2 A:PHE38 4.4 18.5 1.0
CA A:TYR102 4.4 16.0 1.0
O A:HOH949 4.4 29.6 1.0
CE2 A:TRP56 4.5 34.6 1.0
CE2 A:PHE38 4.5 20.0 1.0
C4 A:TC7513 4.5 25.8 0.7
C A:TYR102 4.5 20.7 1.0
O A:HOH738 4.6 25.1 1.0
O A:HOH788 4.7 34.4 1.0
CB A:PHE38 4.7 19.4 1.0
O A:ASN101 4.7 20.9 1.0
CD1 A:TYR102 4.8 26.1 1.0
NE1 A:TRP56 5.0 31.4 1.0

Chlorine binding site 4 out of 6 in 5m8x

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Chlorine binding site 4 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:38.8
occ:0.74
CL1 B:TC7505 0.0 38.8 0.7
C4 B:TC7505 1.7 24.9 0.7
C5 B:TC7505 2.7 19.7 0.7
C3 B:TC7505 2.7 27.6 0.7
O1 B:TC7505 2.9 28.3 0.7
O B:HOH606 3.4 27.5 0.8
CG2 B:THR242 3.5 16.2 1.0
CE2 B:TYR246 3.6 20.1 1.0
OH B:TYR246 3.8 22.2 1.0
O39 B:BVQ503 3.9 21.2 1.0
C6 B:TC7505 4.0 25.5 0.7
C2 B:TC7505 4.0 28.1 0.7
NH2 B:ARG305 4.0 21.6 1.0
CZ B:TYR246 4.1 21.2 1.0
C38 B:BVQ503 4.1 18.9 1.0
CH2 B:TRP376 4.1 19.9 1.0
CH2 B:TRP96 4.2 17.9 1.0
CG B:TYR382 4.2 24.2 1.0
CB B:TYR382 4.2 22.4 1.0
CZ3 B:TRP376 4.3 24.4 1.0
CZ2 B:TRP96 4.4 22.5 1.0
CD2 B:TYR382 4.5 20.7 1.0
N40 B:BVQ503 4.5 20.5 1.0
C1 B:TC7505 4.5 34.5 0.7
C37 B:BVQ503 4.5 19.2 1.0
CD2 B:TYR246 4.6 18.1 1.0
CD1 B:TYR382 4.7 25.8 1.0
CZ B:ARG305 4.7 25.0 1.0
CB B:THR242 4.9 20.4 1.0

Chlorine binding site 5 out of 6 in 5m8x

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Chlorine binding site 5 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:37.2
occ:0.74
CL3 B:TC7505 0.0 37.2 0.7
C6 B:TC7505 1.7 25.5 0.7
C5 B:TC7505 2.7 19.7 0.7
C1 B:TC7505 2.7 34.5 0.7
CH2 B:TRP56 3.1 42.8 1.0
CL5 B:TC7505 3.2 47.3 0.7
CG B:TYR102 3.4 24.3 1.0
CD1 B:TYR102 3.5 25.1 1.0
CD2 B:TYR102 3.7 21.8 1.0
CE1 B:TYR382 3.8 22.0 1.0
CE1 B:TYR102 3.9 24.2 1.0
CZ3 B:TRP56 3.9 40.5 1.0
CB B:TYR102 3.9 22.7 1.0
CZ2 B:TRP56 3.9 42.6 1.0
C4 B:TC7505 4.0 24.9 0.7
C2 B:TC7505 4.0 28.1 0.7
CE2 B:TYR102 4.0 22.2 1.0
CZ B:TYR102 4.1 27.5 1.0
CD1 B:TYR382 4.1 25.8 1.0
O B:HOH879 4.3 32.4 1.0
O B:HOH717 4.3 22.4 1.0
C3 B:TC7505 4.5 27.6 0.7
CZ3 B:TRP376 4.5 24.4 1.0
CZ B:TYR382 4.6 23.7 1.0
CE3 B:TRP376 4.8 21.5 1.0
CZ2 B:TRP96 4.9 22.5 1.0
CB B:PHE57 4.9 28.4 1.0
OH B:TYR382 5.0 24.0 1.0

Chlorine binding site 6 out of 6 in 5m8x

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Chlorine binding site 6 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,5- Trichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:47.3
occ:0.74
CL5 B:TC7505 0.0 47.3 0.7
C1 B:TC7505 1.7 34.5 0.7
C2 B:TC7505 2.7 28.1 0.7
C6 B:TC7505 2.7 25.5 0.7
O1 B:GOL504 2.8 69.1 1.0
CB B:TYR102 3.1 22.7 1.0
CL3 B:TC7505 3.2 37.2 0.7
CZ2 B:TRP56 3.2 42.6 1.0
C1 B:GOL504 3.5 57.6 1.0
CH2 B:TRP56 3.5 42.8 1.0
CG B:TYR102 3.8 24.3 1.0
O B:TYR102 3.9 21.5 1.0
CD1 B:PHE38 4.0 24.1 1.0
C3 B:TC7505 4.0 27.6 0.7
C5 B:TC7505 4.0 19.7 0.7
CD2 B:TYR102 4.0 21.8 1.0
CE1 B:PHE38 4.1 21.7 1.0
CG B:PHE38 4.1 25.0 1.0
CZ B:PHE38 4.4 26.3 1.0
CD2 B:PHE38 4.4 22.2 1.0
O B:HOH894 4.4 28.6 1.0
CA B:TYR102 4.4 24.5 1.0
CE2 B:TRP56 4.4 36.1 1.0
C4 B:TC7505 4.5 24.9 0.7
CE2 B:PHE38 4.5 22.6 1.0
C B:TYR102 4.6 21.4 1.0
O B:HOH660 4.7 25.6 1.0
CB B:PHE38 4.7 23.2 1.0
O B:ASN101 4.7 21.8 1.0
CD1 B:TYR102 4.7 25.1 1.0
O B:HOH676 4.8 33.5 1.0
CZ3 B:TRP56 4.9 40.5 1.0
C2 B:GOL504 4.9 57.6 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: Sat Dec 12 12:05:32 2020

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