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Chlorine in PDB 5m8w: Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Chlorophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Chlorophenol, PDB code: 5m8w 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) 39.63 / 2.28
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.322, 73.322, 184.370, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 19.4

Other elements in 5m8w:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- 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 4- Chlorophenol (pdb code 5m8w). 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 4- Chlorophenol, PDB code: 5m8w:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5m8w

Go back to Chlorine Binding Sites List in 5m8w
Chlorine binding site 1 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- 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 4- Chlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl512

b:37.4
occ:0.96
CL9 A:4CH512 0.0 37.4 1.0
C4 A:4CH512 1.7 31.2 1.0
C5 A:4CH512 2.7 28.8 1.0
C3 A:4CH512 2.7 29.0 1.0
CD1 A:TYR102 3.3 29.2 1.0
CE1 A:TYR382 3.5 19.2 1.0
CH2 A:TRP56 3.5 30.6 1.0
CG A:TYR102 3.5 26.8 1.0
CD1 A:TYR382 3.8 20.1 1.0
CE1 A:TYR102 3.8 28.3 1.0
CB A:TYR102 3.8 19.9 1.0
CZ2 A:TRP96 3.9 14.7 1.0
C6 A:4CH512 4.0 28.8 1.0
C2 A:4CH512 4.0 23.9 1.0
CD2 A:TYR102 4.1 24.5 1.0
CZ A:TYR382 4.1 21.4 1.0
CH2 A:TRP96 4.2 18.6 1.0
CZ3 A:TRP376 4.2 23.8 1.0
CZ3 A:TRP56 4.2 30.6 1.0
CZ A:TYR102 4.4 32.7 1.0
CZ2 A:TRP56 4.4 35.4 1.0
O A:HOH718 4.5 28.5 1.0
C1 A:4CH512 4.5 34.6 1.0
CE2 A:TYR102 4.5 23.4 1.0
OH A:TYR382 4.5 25.4 1.0
O A:HOH849 4.6 49.8 1.0
CG A:TYR382 4.7 26.5 1.0
CE3 A:TRP376 4.7 26.3 1.0
CE2 A:TRP96 4.8 20.4 1.0
CE2 A:TYR382 4.9 22.9 1.0

Chlorine binding site 2 out of 2 in 5m8w

Go back to Chlorine Binding Sites List in 5m8w
Chlorine binding site 2 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- 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 4- Chlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl507

b:31.5
occ:0.91
CL9 B:4CH507 0.0 31.5 0.9
C4 B:4CH507 1.7 24.0 0.9
C5 B:4CH507 2.7 10.6 0.9
C3 B:4CH507 2.7 21.2 0.9
CD1 B:TYR102 3.4 23.9 1.0
CG B:TYR102 3.4 21.5 1.0
CH2 B:TRP56 3.5 35.6 1.0
CB B:TYR102 3.7 23.6 1.0
CE1 B:TYR382 3.8 29.9 1.0
CE1 B:TYR102 3.9 22.0 1.0
CD2 B:TYR102 3.9 22.9 1.0
C6 B:4CH507 4.0 20.0 0.9
C2 B:4CH507 4.0 19.2 0.9
CD1 B:TYR382 4.0 31.7 1.0
CZ2 B:TRP96 4.1 20.6 1.0
CZ3 B:TRP376 4.2 25.6 1.0
CZ3 B:TRP56 4.3 32.7 1.0
CZ B:TYR102 4.4 30.8 1.0
CZ B:TYR382 4.4 23.8 1.0
O B:HOH812 4.4 30.3 1.0
CE2 B:TYR102 4.4 25.9 1.0
CH2 B:TRP96 4.4 14.9 1.0
CZ2 B:TRP56 4.4 37.8 1.0
C1 B:4CH507 4.5 34.0 0.9
O B:HOH640 4.6 22.0 1.0
CE3 B:TRP376 4.7 25.3 1.0
OH B:TYR382 4.8 21.7 1.0
CG B:TYR382 4.8 28.3 1.0
CE2 B:TRP96 5.0 17.4 1.0
CA B:TYR102 5.0 25.4 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 12:05:30 2020

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