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Chlorine in PDB 5m8y: Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Chlorophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Chlorophenol, PDB code: 5m8y 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) 47.35 / 1.86
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.783, 73.783, 185.233, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 16

Other elements in 5m8y:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Chlorophenol 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 3- Chlorophenol (pdb code 5m8y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Chlorophenol, PDB code: 5m8y:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5m8y

Go back to Chlorine Binding Sites List in 5m8y
Chlorine binding site 1 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Chlorophenol


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 3- Chlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl510

b:47.1
occ:0.77
CL A:3CH510 0.0 47.1 0.8
C3 A:3CH510 1.7 27.6 0.8
C4 A:3CH510 2.7 27.2 0.8
C2 A:3CH510 2.7 22.9 0.8
CH2 A:TRP56 3.2 34.5 1.0
CG A:TYR102 3.3 22.0 1.0
CB A:TYR102 3.4 19.1 1.0
CD1 A:TYR102 3.4 25.9 1.0
CZ2 A:TRP56 3.7 34.7 1.0
CD2 A:TYR102 3.9 22.8 1.0
C5 A:3CH510 4.0 26.8 0.8
C1 A:3CH510 4.0 24.4 0.8
CE1 A:TYR102 4.1 25.6 1.0
O A:HOH764 4.2 31.2 1.0
CE1 A:TYR382 4.2 24.9 1.0
CZ3 A:TRP56 4.3 34.9 1.0
CZ3 A:TRP376 4.3 24.7 1.0
CZ2 A:TRP96 4.4 21.9 1.0
CD1 A:TYR382 4.4 23.7 1.0
CH2 A:TRP96 4.4 21.6 1.0
C6 A:3CH510 4.5 25.6 0.8
CE2 A:TYR102 4.5 22.9 1.0
CZ A:TYR102 4.6 30.6 1.0
CA A:TYR102 4.6 19.6 1.0
CE1 A:PHE38 4.8 23.4 1.0
CE3 A:TRP376 4.8 21.4 1.0
CZ A:TYR382 4.9 21.2 1.0
CZ A:PHE38 4.9 25.6 1.0

Chlorine binding site 2 out of 2 in 5m8y

Go back to Chlorine Binding Sites List in 5m8y
Chlorine binding site 2 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3- Chlorophenol


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 3- Chlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:44.9
occ:0.79
CL B:3CH506 0.0 44.9 0.8
C3 B:3CH506 1.7 23.4 0.8
C4 B:3CH506 2.7 27.5 0.8
C2 B:3CH506 2.7 24.8 0.8
CH2 B:TRP56 3.2 38.9 1.0
CG B:TYR102 3.2 26.2 1.0
CB B:TYR102 3.4 23.6 1.0
CD1 B:TYR102 3.4 29.1 1.0
CD2 B:TYR102 3.8 22.2 1.0
CZ2 B:TRP56 3.9 44.9 1.0
C5 B:3CH506 4.0 28.2 0.8
C1 B:3CH506 4.0 30.0 0.8
CE1 B:TYR102 4.2 26.3 1.0
CZ3 B:TRP56 4.2 36.4 1.0
O B:HOH615 4.2 35.3 1.0
CZ3 B:TRP376 4.3 28.8 1.0
CE1 B:TYR382 4.4 23.9 1.0
CE2 B:TYR102 4.5 22.5 1.0
C6 B:3CH506 4.5 36.1 0.8
CD1 B:TYR382 4.5 28.6 1.0
CZ2 B:TRP96 4.6 23.5 1.0
CZ B:TYR102 4.6 27.3 1.0
CH2 B:TRP96 4.6 18.1 1.0
CA B:TYR102 4.7 23.0 1.0
CE1 B:PHE38 4.7 24.8 1.0
CE3 B:TRP376 4.8 23.0 1.0
CZ B:PHE38 4.9 26.5 1.0
O B:HOH901 5.0 37.7 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 12:05:33 2020

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