Cobalt in PDB 5m8z: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol, PDB code: 5m8z 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)	47.26 / 1.66
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.579, 73.579, 184.962, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.1

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Iron	(Fe)	16 atoms

The binding sites of Cobalt atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol (pdb code 5m8z). 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 2,3- Difluorophenol, PDB code: 5m8z:
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 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:17.3 occ:1.00 CO A:BVQ503 0.0 17.3 1.0 N21 A:BVQ503 1.9 14.2 1.0 N24 A:BVQ503 1.9 17.2 1.0 N22 A:BVQ503 1.9 18.1 1.0 N23 A:BVQ503 1.9 15.8 1.0 O A:HOH612 2.6 33.7 0.9 C1 A:BVQ503 2.8 14.4 1.0 C19 A:BVQ503 2.8 15.3 1.0 C9 A:BVQ503 2.9 17.4 1.0 C4 A:BVQ503 2.9 15.5 1.0 C11 A:BVQ503 2.9 16.1 1.0 C16 A:BVQ503 3.0 15.1 1.0 C14 A:BVQ503 3.0 16.0 1.0 C6 A:BVQ503 3.0 17.9 1.0 C10 A:BVQ503 3.3 17.6 1.0 C20 A:BVQ503 3.4 16.0 1.0 C5 A:BVQ503 3.4 16.4 1.0 C15 A:BVQ503 3.4 17.5 1.0 O A:HOH702 3.6 19.2 1.0 C18 A:BVQ503 4.1 15.6 1.0 C2 A:BVQ503 4.1 13.8 1.0 C3 A:BVQ503 4.2 14.4 1.0 C8 A:BVQ503 4.2 17.0 1.0 C17 A:BVQ503 4.2 14.4 1.0 C12 A:BVQ503 4.3 17.5 1.0 C7 A:BVQ503 4.3 16.3 1.0 C13 A:BVQ503 4.3 19.2 1.0 C26 A:BVQ503 4.5 14.5 1.0 C41 A:BVQ503 4.7 21.6 1.0 C37 A:BVQ503 4.8 18.6 1.0 CE2 A:PHE38 4.8 17.9 1.0 C35 A:BVQ503 4.9 16.0 1.0 C53 A:BVQ503 4.9 17.7 1.0 O A:ZTN513 4.9 28.6 0.4 F1 A:ZTN513 4.9 26.6 0.4 F A:ZTN513 5.0 27.6 0.6 C54 A:BVQ503 5.0 15.7 1.0

Cobalt binding site 2 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Co503 b:19.7 occ:1.00 CO B:BVQ503 0.0 19.7 1.0 N21 B:BVQ503 1.9 19.1 1.0 N24 B:BVQ503 1.9 20.9 1.0 N22 B:BVQ503 1.9 21.3 1.0 N23 B:BVQ503 1.9 19.3 1.0 C1 B:BVQ503 2.8 14.8 1.0 C19 B:BVQ503 2.8 19.1 1.0 C9 B:BVQ503 2.9 17.4 1.0 C11 B:BVQ503 2.9 19.5 1.0 C4 B:BVQ503 2.9 20.1 1.0 C14 B:BVQ503 3.0 20.4 1.0 C16 B:BVQ503 3.0 18.3 1.0 C6 B:BVQ503 3.0 19.0 1.0 C10 B:BVQ503 3.3 18.1 1.0 C5 B:BVQ503 3.4 18.4 1.0 C15 B:BVQ503 3.4 20.1 1.0 C20 B:BVQ503 3.4 18.9 1.0 O B:HOH639 3.7 23.1 1.0 C18 B:BVQ503 4.1 21.3 1.0 C2 B:BVQ503 4.1 17.9 1.0 C3 B:BVQ503 4.2 17.2 1.0 C8 B:BVQ503 4.2 19.9 1.0 C12 B:BVQ503 4.2 18.4 1.0 C17 B:BVQ503 4.3 20.9 1.0 C7 B:BVQ503 4.3 18.0 1.0 C13 B:BVQ503 4.3 17.5 1.0 C26 B:BVQ503 4.6 16.9 1.0 CE2 B:PHE38 4.8 22.6 1.0 C37 B:BVQ503 4.8 20.5 1.0 C35 B:BVQ503 4.9 20.0 1.0 C41 B:BVQ503 4.9 25.0 1.0 O B:ZTN507 4.9 28.8 0.5 F B:ZTN507 4.9 24.7 0.5 C53 B:BVQ503 4.9 22.4 1.0 C54 B:BVQ503 5.0 17.2 1.0 F1 B:ZTN507 5.0 22.7 0.5

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