Cobalt 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:

Iron	(Fe)	16 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,4,6- Trichlorophenol, PDB code: 5ma1:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 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 Cobalt with other atoms in the Co 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:Co503 b:37.4 occ:1.00 CO A:BVQ503 0.0 37.4 1.0 N21 A:BVQ503 1.9 32.3 1.0 N24 A:BVQ503 1.9 34.3 1.0 N22 A:BVQ503 1.9 28.9 1.0 N23 A:BVQ503 1.9 33.9 1.0 C19 A:BVQ503 2.8 33.8 1.0 C1 A:BVQ503 2.9 33.4 1.0 C9 A:BVQ503 2.9 31.1 1.0 C4 A:BVQ503 2.9 27.3 1.0 C11 A:BVQ503 2.9 34.5 1.0 C6 A:BVQ503 3.0 29.6 1.0 C16 A:BVQ503 3.0 32.8 1.0 C14 A:BVQ503 3.0 31.9 1.0 C10 A:BVQ503 3.2 33.3 1.0 C5 A:BVQ503 3.3 28.2 1.0 C15 A:BVQ503 3.4 34.5 1.0 C20 A:BVQ503 3.5 29.0 1.0 O A:HOH630 3.8 30.8 1.0 C2 A:BVQ503 4.1 35.8 1.0 C18 A:BVQ503 4.1 34.0 1.0 C3 A:BVQ503 4.2 31.8 1.0 C8 A:BVQ503 4.2 32.1 1.0 C7 A:BVQ503 4.2 34.0 1.0 C12 A:BVQ503 4.3 38.2 1.0 C17 A:BVQ503 4.3 32.8 1.0 C13 A:BVQ503 4.3 36.9 1.0 C26 A:BVQ503 4.5 34.2 1.0 O1 A:T6C505 4.6 55.3 0.9 C37 A:BVQ503 4.6 32.7 1.0 C35 A:BVQ503 4.8 30.3 1.0 C41 A:BVQ503 4.9 32.4 1.0 CE2 A:PHE38 4.9 41.9 1.0 C53 A:BVQ503 4.9 32.9 1.0

Cobalt binding site 2 out of 2 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 Cobalt with other atoms in the Co 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 B:Co503 b:41.7 occ:1.00 CO B:BVQ503 0.0 41.7 1.0 N21 B:BVQ503 1.9 40.2 1.0 N24 B:BVQ503 1.9 38.6 1.0 N23 B:BVQ503 1.9 37.2 1.0 N22 B:BVQ503 1.9 39.8 1.0 C19 B:BVQ503 2.8 38.1 1.0 C1 B:BVQ503 2.9 35.6 1.0 C9 B:BVQ503 2.9 37.4 1.0 C11 B:BVQ503 2.9 36.6 1.0 C4 B:BVQ503 2.9 29.1 1.0 C16 B:BVQ503 3.0 39.8 1.0 C14 B:BVQ503 3.0 33.6 1.0 C6 B:BVQ503 3.0 31.7 1.0 C10 B:BVQ503 3.3 33.4 1.0 C5 B:BVQ503 3.4 28.8 1.0 C20 B:BVQ503 3.4 25.7 1.0 C15 B:BVQ503 3.4 37.1 1.0 O B:HOH636 3.7 38.1 1.0 C18 B:BVQ503 4.1 42.4 1.0 C2 B:BVQ503 4.1 34.9 1.0 C3 B:BVQ503 4.2 34.3 1.0 C8 B:BVQ503 4.2 35.9 1.0 C17 B:BVQ503 4.2 34.7 1.0 C12 B:BVQ503 4.3 35.3 1.0 C7 B:BVQ503 4.3 34.0 1.0 O1 B:T6C505 4.3 49.9 0.9 C13 B:BVQ503 4.3 36.0 1.0 C26 B:BVQ503 4.6 31.6 1.0 C37 B:BVQ503 4.7 34.7 1.0 C35 B:BVQ503 4.9 32.2 1.0 C41 B:BVQ503 4.9 37.6 1.0 C53 B:BVQ503 4.9 29.3 1.0 C54 B:BVQ503 5.0 19.3 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