Chlorine in PDB 5ma1: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Trichlorophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Trichlorophenol, PDB code: 5ma1 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)	36.73 / 2.50
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.461, 73.461, 179.365, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 22

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Trichlorophenol also contains other interesting chemical elements:

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

The binding sites of Chlorine atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Trichlorophenol (pdb code 5ma1). 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 2,4,6- Trichlorophenol, PDB code: 5ma1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- 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 2,4,6- Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:51.7 occ:0.88 CL2 A:T6C505 0.0 51.7 0.9 C2 A:T6C505 1.7 38.4 0.9 C3 A:T6C505 2.7 39.4 0.9 C1 A:T6C505 2.7 37.6 0.9 O1 A:T6C505 3.0 55.3 0.9 O39 A:BVQ503 3.3 44.1 1.0 C38 A:BVQ503 3.3 41.5 1.0 CG2 A:THR242 3.4 26.7 1.0 NH2 A:ARG305 3.7 31.9 1.0 N40 A:BVQ503 3.8 40.3 1.0 C37 A:BVQ503 3.8 32.7 1.0 CB A:TYR382 3.9 31.5 1.0 CE2 A:TYR246 3.9 35.6 1.0 C4 A:T6C505 4.0 42.6 0.9 C6 A:T6C505 4.0 41.0 0.9 CH2 A:TRP376 4.0 40.9 1.0 CG A:TYR382 4.1 41.5 1.0 OH A:TYR246 4.1 28.4 1.0 CD2 A:TYR382 4.2 38.1 1.0 CZ3 A:TRP376 4.2 43.3 1.0 CZ A:ARG305 4.3 37.6 1.0 C5 A:T6C505 4.5 39.3 0.9 NH1 A:ARG305 4.5 27.7 1.0 CZ A:TYR246 4.5 32.9 1.0 CB A:THR242 4.7 31.3 1.0 CH2 A:TRP96 4.8 36.1 1.0 CD1 A:TYR382 4.9 41.9 1.0 OG1 A:THR242 4.9 31.6 1.0 CZ2 A:TRP96 5.0 39.4 1.0 CD2 A:TYR246 5.0 33.4 1.0

Chlorine binding site 2 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- 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 2,4,6- Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:59.2 occ:0.88 CL6 A:T6C505 0.0 59.2 0.9 C6 A:T6C505 1.7 41.0 0.9 C1 A:T6C505 2.7 37.6 0.9 C5 A:T6C505 2.7 39.3 0.9 O1 A:T6C505 2.9 55.3 0.9 O A:TYR102 3.2 51.5 1.0 O A:HOH699 3.3 44.2 1.0 CE2 A:PHE38 3.4 41.9 1.0 OD1 A:ASN272 3.7 42.8 1.0 C A:TYR102 3.8 48.3 1.0 CD2 A:PHE38 3.9 37.4 1.0 CZ A:PHE38 3.9 43.7 1.0 C4 A:T6C505 4.0 42.6 0.9 C2 A:T6C505 4.0 38.4 0.9 CB A:TYR102 4.2 54.0 1.0 OH A:TYR246 4.3 28.4 1.0 CA A:GLY103 4.3 39.9 1.0 N A:GLY103 4.3 42.3 1.0 C3 A:T6C505 4.5 39.4 0.9 CA A:TYR102 4.5 53.2 1.0 CE1 A:PHE38 4.7 45.6 1.0 CG A:PHE38 4.7 38.3 1.0 CZ A:TYR246 4.8 32.9 1.0 CG A:ASN272 4.8 38.6 1.0

Chlorine binding site 3 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- 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 2,4,6- Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:46.0 occ:0.88 CL4 A:T6C505 0.0 46.0 0.9 C4 A:T6C505 1.7 42.6 0.9 C3 A:T6C505 2.7 39.4 0.9 C5 A:T6C505 2.7 39.3 0.9 CE1 A:TYR382 3.4 42.8 1.0 CD1 A:TYR102 3.4 47.6 1.0 CH2 A:TRP56 3.5 53.8 1.0 CE1 A:TYR102 3.7 42.1 1.0 CG A:TYR102 3.7 52.3 1.0 CD1 A:TYR382 3.8 41.9 1.0 CZ A:TYR382 3.9 45.4 1.0 C2 A:T6C505 4.0 38.4 0.9 C6 A:T6C505 4.0 41.0 0.9 CZ2 A:TRP96 4.0 39.4 1.0 CZ3 A:TRP56 4.0 51.2 1.0 CZ A:TYR102 4.2 43.9 1.0 CD2 A:TYR102 4.2 47.2 1.0 OH A:TYR382 4.2 49.1 1.0 CB A:TYR102 4.3 54.0 1.0 CH2 A:TRP96 4.4 36.1 1.0 CE2 A:TYR102 4.5 36.2 1.0 C1 A:T6C505 4.5 37.6 0.9 CZ2 A:TRP56 4.5 54.1 1.0 CG A:TYR382 4.6 41.5 1.0 CZ3 A:TRP376 4.8 43.3 1.0 CE2 A:TYR382 4.8 40.1 1.0 CE2 A:TRP96 4.8 39.9 1.0 CE3 A:TRP376 5.0 51.5 1.0

Chlorine binding site 4 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- 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 2,4,6- Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:69.5 occ:0.86 CL2 B:T6C505 0.0 69.5 0.9 C2 B:T6C505 1.7 50.9 0.9 C1 B:T6C505 2.7 47.8 0.9 C3 B:T6C505 2.7 44.4 0.9 O B:HOH642 2.7 25.4 1.0 O1 B:T6C505 3.0 49.9 0.9 CE2 B:PHE38 3.2 30.8 1.0 O B:TYR102 3.3 39.7 1.0 O B:HOH669 3.4 62.6 1.0 ND2 B:ASN272 3.4 29.8 1.0 CZ B:PHE38 3.5 32.5 1.0 OH B:TYR246 4.0 24.6 1.0 C6 B:T6C505 4.0 44.5 0.9 C4 B:T6C505 4.0 46.9 0.9 CD2 B:PHE38 4.0 33.0 1.0 O B:HOH703 4.2 37.2 1.0 C B:TYR102 4.3 41.1 1.0 C54 B:BVQ503 4.4 19.3 1.0 C5 B:T6C505 4.5 42.4 0.9 CE1 B:PHE38 4.5 30.9 1.0 CZ B:TYR246 4.6 27.4 1.0 CB B:TYR102 4.6 32.4 1.0 CG B:ASN272 4.7 32.7 1.0 CA B:GLY103 4.9 40.0 1.0 CG B:PHE38 4.9 33.5 1.0 N B:GLY103 5.0 36.5 1.0

Chlorine binding site 5 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- 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 2,4,6- Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:56.8 occ:0.86 CL6 B:T6C505 0.0 56.8 0.9 C6 B:T6C505 1.7 44.5 0.9 C1 B:T6C505 2.7 47.8 0.9 C5 B:T6C505 2.7 42.4 0.9 O1 B:T6C505 2.9 49.9 0.9 CG2 B:THR242 3.1 26.5 1.0 O39 B:BVQ503 3.2 30.1 1.0 C38 B:BVQ503 3.4 31.4 1.0 CB B:TYR382 3.6 32.7 1.0 NH2 B:ARG305 3.7 37.0 1.0 N40 B:BVQ503 3.8 28.4 1.0 CG B:TYR382 3.9 31.6 1.0 CE2 B:TYR246 3.9 31.6 1.0 C37 B:BVQ503 3.9 34.7 1.0 C4 B:T6C505 4.0 46.9 0.9 C2 B:T6C505 4.0 50.9 0.9 CH2 B:TRP376 4.0 26.9 1.0 CD2 B:TYR382 4.0 26.1 1.0 CZ B:ARG305 4.2 38.0 1.0 NH1 B:ARG305 4.3 37.9 1.0 OH B:TYR246 4.3 24.6 1.0 CB B:THR242 4.3 32.0 1.0 OG1 B:THR242 4.4 34.8 1.0 CZ3 B:TRP376 4.4 26.1 1.0 C3 B:T6C505 4.5 44.4 0.9 CZ B:TYR246 4.6 27.4 1.0 CD1 B:TYR382 4.7 28.2 1.0 CZ2 B:TRP376 4.8 36.1 1.0 CD2 B:TYR246 4.9 30.8 1.0 CE2 B:TYR382 4.9 34.3 1.0 CH2 B:TRP96 5.0 37.1 1.0

Chlorine binding site 6 out of 6 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- 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 2,4,6- Trichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:51.1 occ:0.86 CL4 B:T6C505 0.0 51.1 0.9 C4 B:T6C505 1.7 46.9 0.9 C5 B:T6C505 2.7 42.4 0.9 C3 B:T6C505 2.7 44.4 0.9 CE1 B:TYR382 3.3 30.4 1.0 CG B:TYR102 3.4 36.3 1.0 CD1 B:TYR102 3.4 32.6 1.0 CH2 B:TRP56 3.5 45.9 1.0 CD1 B:TYR382 3.7 28.2 1.0 CE1 B:TYR102 3.8 36.1 1.0 CD2 B:TYR102 3.8 38.4 1.0 CB B:TYR102 3.9 32.4 1.0 C6 B:T6C505 4.0 44.5 0.9 C2 B:T6C505 4.0 50.9 0.9 CZ B:TYR382 4.0 36.3 1.0 CZ3 B:TRP56 4.0 42.5 1.0 O B:HOH646 4.0 42.3 1.0 CZ B:TYR102 4.1 38.2 1.0 CE2 B:TYR102 4.2 35.2 1.0 CZ2 B:TRP96 4.2 36.0 1.0 CZ3 B:TRP376 4.3 26.1 1.0 OH B:TYR382 4.4 39.9 1.0 CZ2 B:TRP56 4.5 49.1 1.0 C1 B:T6C505 4.5 47.8 0.9 CH2 B:TRP96 4.5 37.1 1.0 CG B:TYR382 4.6 31.6 1.0 CE3 B:TRP376 4.7 28.7 1.0 CE2 B:TYR382 4.9 34.3 1.0 CE2 B:TRP96 5.0 34.4 1.0

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