Cobalt in PDB 5m90: Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol, PDB code: 5m90 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)	47.30 / 1.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.631, 73.631, 185.137, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 16.7

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol 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 3,4,5- Trifluorophenol (pdb code 5m90). 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 3,4,5- Trifluorophenol, PDB code: 5m90:
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 3,4,5- Trifluorophenol


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 3,4,5- Trifluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:16.1 occ:1.00 CO A:BVQ503 0.0 16.1 1.0 N21 A:BVQ503 1.9 13.9 1.0 N24 A:BVQ503 1.9 15.9 1.0 N22 A:BVQ503 1.9 17.2 1.0 N23 A:BVQ503 1.9 14.0 1.0 O A:HOH817 2.7 30.3 1.0 C1 A:BVQ503 2.8 14.0 1.0 C19 A:BVQ503 2.8 15.5 1.0 C9 A:BVQ503 2.9 17.9 1.0 C4 A:BVQ503 2.9 16.2 1.0 C11 A:BVQ503 2.9 15.0 1.0 C16 A:BVQ503 3.0 15.3 1.0 C14 A:BVQ503 3.0 15.1 1.0 C6 A:BVQ503 3.0 18.6 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 16.6 1.0 C15 A:BVQ503 3.4 14.8 1.0 O A:HOH717 3.6 18.6 1.0 C18 A:BVQ503 4.1 16.4 1.0 C2 A:BVQ503 4.1 13.5 1.0 C8 A:BVQ503 4.2 18.1 1.0 O A:HOH644 4.2 45.4 1.0 C3 A:BVQ503 4.2 13.2 1.0 C17 A:BVQ503 4.2 14.9 1.0 C12 A:BVQ503 4.3 15.1 1.0 C7 A:BVQ503 4.3 15.6 1.0 C13 A:BVQ503 4.3 17.1 1.0 C26 A:BVQ503 4.6 13.9 1.0 C37 A:BVQ503 4.8 17.1 1.0 C41 A:BVQ503 4.8 21.6 1.0 CE2 A:PHE38 4.8 18.0 1.0 C35 A:BVQ503 4.9 15.5 1.0 C53 A:BVQ503 4.9 15.7 1.0 O A:JIF509 5.0 24.1 0.7

Cobalt binding site 2 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


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 3,4,5- Trifluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Co503 b:18.9 occ:1.00 CO B:BVQ503 0.0 18.9 1.0 N21 B:BVQ503 1.9 16.9 1.0 N24 B:BVQ503 1.9 21.1 1.0 N22 B:BVQ503 1.9 22.8 1.0 N23 B:BVQ503 1.9 15.3 1.0 O B:HOH671 2.8 32.2 1.0 C1 B:BVQ503 2.8 14.0 1.0 C19 B:BVQ503 2.8 18.2 1.0 C9 B:BVQ503 2.9 18.0 1.0 C11 B:BVQ503 2.9 17.5 1.0 C4 B:BVQ503 2.9 19.9 1.0 C14 B:BVQ503 3.0 20.7 1.0 C16 B:BVQ503 3.0 17.2 1.0 C6 B:BVQ503 3.0 19.2 1.0 C10 B:BVQ503 3.3 18.6 1.0 C5 B:BVQ503 3.4 18.4 1.0 C20 B:BVQ503 3.4 17.0 1.0 C15 B:BVQ503 3.4 19.0 1.0 O B:HOH694 3.7 22.7 1.0 C18 B:BVQ503 4.1 19.1 1.0 C2 B:BVQ503 4.1 17.7 1.0 C3 B:BVQ503 4.2 16.4 1.0 C8 B:BVQ503 4.2 20.7 1.0 C12 B:BVQ503 4.2 18.6 1.0 C7 B:BVQ503 4.3 18.2 1.0 C17 B:BVQ503 4.3 18.5 1.0 C13 B:BVQ503 4.3 17.4 1.0 C26 B:BVQ503 4.6 17.1 1.0 CE2 B:PHE38 4.7 20.5 1.0 C37 B:BVQ503 4.7 17.7 1.0 CZ B:PHE38 4.8 23.6 1.0 C41 B:BVQ503 4.8 23.1 1.0 C35 B:BVQ503 4.9 18.3 1.0 C53 B:BVQ503 4.9 20.9 1.0 O B:JIF507 4.9 25.1 0.8 C54 B:BVQ503 5.0 17.4 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