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Chlorine in PDB 5ma0: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol, PDB code: 5ma0 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) 30.99 / 1.90
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.577, 73.577, 184.480, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 16.7

Other elements in 5ma0:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol 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 2,6- Dichlorophenol (pdb code 5ma0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol, PDB code: 5ma0:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5ma0

Go back to Chlorine Binding Sites List in 5ma0
Chlorine binding site 1 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol


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 2,6- Dichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:29.9
occ:0.76
CL1 A:DUB508 0.0 29.9 0.8
C02 A:DUB508 1.6 24.6 0.8
C08 A:DUB508 2.6 30.4 0.8
C03 A:DUB508 2.6 23.9 0.8
O09 A:DUB508 2.9 33.4 0.8
O A:HOH603 3.1 30.0 1.0
O39 A:BVQ503 3.3 22.0 1.0
C38 A:BVQ503 3.5 25.0 1.0
NH2 A:ARG305 3.5 18.2 1.0
CG2 A:THR242 3.6 17.0 1.0
CE2 A:TYR246 3.8 20.6 1.0
C37 A:BVQ503 3.8 18.9 1.0
OH A:TYR246 3.8 18.8 1.0
C06 A:DUB508 3.9 32.9 0.8
CH2 A:TRP376 3.9 18.2 1.0
C04 A:DUB508 3.9 21.9 0.8
N40 A:BVQ503 4.0 18.8 1.0
CB A:TYR382 4.2 17.3 1.0
CZ3 A:TRP376 4.3 23.8 1.0
CZ A:TYR246 4.3 19.8 1.0
CZ A:ARG305 4.3 23.0 1.0
C05 A:DUB508 4.4 31.1 0.8
CG A:TYR382 4.4 24.7 1.0
CD2 A:TYR382 4.7 23.3 1.0
NH1 A:ARG305 4.7 19.3 1.0
CH2 A:TRP96 4.8 21.5 1.0
C6 A:BVQ503 4.9 19.9 1.0
CZ2 A:TRP376 4.9 19.1 1.0
CD2 A:TYR246 4.9 19.5 1.0
CB A:THR242 5.0 20.4 1.0
C7 A:BVQ503 5.0 17.4 1.0

Chlorine binding site 2 out of 4 in 5ma0

Go back to Chlorine Binding Sites List in 5ma0
Chlorine binding site 2 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol


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 2,6- Dichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:48.5
occ:0.76
CL2 A:DUB508 0.0 48.5 0.8
C06 A:DUB508 1.7 32.9 0.8
O A:HOH785 2.4 33.0 1.0
O A:HOH905 2.4 40.1 1.0
C08 A:DUB508 2.6 30.4 0.8
C05 A:DUB508 2.7 31.1 0.8
O09 A:DUB508 2.8 33.4 0.8
O A:TYR102 2.9 26.7 1.0
CE2 A:PHE38 3.3 20.0 1.0
C A:TYR102 3.7 23.6 1.0
CD2 A:PHE38 3.7 20.7 1.0
CZ A:PHE38 3.8 23.4 1.0
ND2 A:ASN272 3.8 18.6 1.0
O A:HOH933 3.8 34.5 1.0
C02 A:DUB508 3.9 24.6 0.8
CB A:TYR102 3.9 21.4 1.0
C04 A:DUB508 4.0 21.9 0.8
CA A:TYR102 4.4 20.7 1.0
CG A:PHE38 4.5 25.7 1.0
C03 A:DUB508 4.5 23.9 0.8
OH A:TYR246 4.5 18.8 1.0
N A:GLY103 4.5 20.6 1.0
CA A:GLY103 4.5 21.3 1.0
CE1 A:PHE38 4.5 27.4 1.0
O A:HOH603 4.7 30.0 1.0
CD1 A:PHE38 4.8 23.9 1.0
CZ A:TYR246 4.9 19.8 1.0
C54 A:BVQ503 5.0 15.9 1.0

Chlorine binding site 3 out of 4 in 5ma0

Go back to Chlorine Binding Sites List in 5ma0
Chlorine binding site 3 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol


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 2,6- Dichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:43.9
occ:0.74
CL1 B:DUB506 0.0 43.9 0.7
C02 B:DUB506 1.7 32.9 0.7
O B:HOH742 2.4 31.4 1.0
C08 B:DUB506 2.6 30.0 0.7
C03 B:DUB506 2.7 32.4 0.7
O09 B:DUB506 2.8 31.5 0.7
O B:TYR102 2.9 24.8 1.0
CE2 B:PHE38 3.3 25.3 1.0
C B:TYR102 3.7 22.2 1.0
CD2 B:PHE38 3.7 26.2 1.0
CB B:TYR102 3.8 23.3 1.0
CZ B:PHE38 3.8 25.8 1.0
C06 B:DUB506 3.9 19.3 0.7
O B:HOH868 3.9 34.7 1.0
C04 B:DUB506 4.0 23.3 0.7
ND2 B:ASN272 4.0 18.2 1.0
CA B:TYR102 4.3 22.9 1.0
C05 B:DUB506 4.4 25.8 0.7
CG B:PHE38 4.4 25.0 1.0
N B:GLY103 4.5 22.4 1.0
CE1 B:PHE38 4.5 22.4 1.0
CA B:GLY103 4.6 19.5 1.0
OH B:TYR246 4.6 23.6 1.0
O1 B:GOL504 4.7 72.5 1.0
O B:HOH603 4.7 28.9 0.7
CD1 B:PHE38 4.8 23.0 1.0
CG B:TYR102 4.9 26.2 1.0
O B:HOH730 5.0 42.7 1.0
CZ B:TYR246 5.0 20.8 1.0

Chlorine binding site 4 out of 4 in 5ma0

Go back to Chlorine Binding Sites List in 5ma0
Chlorine binding site 4 out of 4 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,6- Dichlorophenol


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 2,6- Dichlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:31.9
occ:0.74
CL2 B:DUB506 0.0 31.9 0.7
C06 B:DUB506 1.7 19.3 0.7
C08 B:DUB506 2.6 30.0 0.7
C05 B:DUB506 2.7 25.8 0.7
O09 B:DUB506 2.8 31.5 0.7
O B:HOH603 3.1 28.9 0.7
O39 B:BVQ503 3.3 20.2 1.0
CG2 B:THR242 3.5 19.5 1.0
C38 B:BVQ503 3.5 24.1 1.0
NH2 B:ARG305 3.6 19.7 1.0
OH B:TYR246 3.8 23.6 1.0
CE2 B:TYR246 3.8 19.0 1.0
C02 B:DUB506 3.8 32.9 0.7
CH2 B:TRP376 3.9 23.0 1.0
C37 B:BVQ503 3.9 19.0 1.0
C04 B:DUB506 3.9 23.3 0.7
N40 B:BVQ503 4.0 20.6 1.0
CB B:TYR382 4.2 22.4 1.0
CZ3 B:TRP376 4.3 27.7 1.0
CZ B:TYR246 4.3 20.8 1.0
CZ B:ARG305 4.4 24.3 1.0
C03 B:DUB506 4.4 32.4 0.7
CG B:TYR382 4.5 27.3 1.0
CD2 B:TYR382 4.6 21.7 1.0
NH1 B:ARG305 4.7 19.3 1.0
CH2 B:TRP96 4.8 21.4 1.0
CB B:THR242 4.9 21.8 1.0
CD2 B:TYR246 4.9 18.6 1.0
C6 B:BVQ503 4.9 22.9 1.0
CZ2 B:TRP376 4.9 25.0 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 12:05:36 2020

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