Cobalt in PDB 5ma2: Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol, PDB code: 5ma2 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)	47.27 / 1.88
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.765, 73.765, 184.711, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 16.6

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

Iodine	(I)	11 atoms
Iron	(Fe)	16 atoms

The binding sites of Cobalt atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol (pdb code 5ma2). 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 4- Iodophenol, PDB code: 5ma2:
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 4- Iodophenol


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 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:23.8 occ:1.00 CO A:BVQ503 0.0 23.8 1.0 N21 A:BVQ503 1.9 22.8 1.0 N24 A:BVQ503 1.9 25.5 1.0 N23 A:BVQ503 1.9 20.9 1.0 N22 A:BVQ503 1.9 22.4 1.0 O A:HOH602 2.5 36.2 1.0 C19 A:BVQ503 2.8 18.7 1.0 C9 A:BVQ503 2.9 22.3 1.0 C1 A:BVQ503 2.9 19.7 1.0 C4 A:BVQ503 2.9 20.7 1.0 C11 A:BVQ503 2.9 20.1 1.0 C16 A:BVQ503 3.0 19.0 1.0 C14 A:BVQ503 3.0 19.7 1.0 C6 A:BVQ503 3.0 21.6 1.0 C10 A:BVQ503 3.2 20.1 1.0 C5 A:BVQ503 3.4 21.9 1.0 C15 A:BVQ503 3.4 20.6 1.0 C20 A:BVQ503 3.4 19.0 1.0 O A:HOH734 3.6 22.9 1.0 C18 A:BVQ503 4.1 20.8 1.0 C2 A:BVQ503 4.1 18.4 1.0 C3 A:BVQ503 4.2 17.5 1.0 C8 A:BVQ503 4.2 20.9 1.0 C7 A:BVQ503 4.2 20.1 1.0 C17 A:BVQ503 4.2 19.6 1.0 C12 A:BVQ503 4.3 20.5 1.0 C13 A:BVQ503 4.3 20.8 1.0 O4 A:IOL509 4.5 48.8 0.7 C26 A:BVQ503 4.6 16.8 1.0 C41 A:BVQ503 4.8 22.6 1.0 C37 A:BVQ503 4.8 21.4 1.0 CE2 A:PHE38 4.8 19.5 1.0 C35 A:BVQ503 4.8 21.4 1.0 C53 A:BVQ503 4.9 18.1 1.0 C54 A:BVQ503 5.0 17.5 1.0 CZ A:PHE38 5.0 24.8 1.0

Cobalt binding site 2 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


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 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Co503 b:26.2 occ:1.00 CO B:BVQ503 0.0 26.2 1.0 N21 B:BVQ503 1.9 25.1 1.0 N24 B:BVQ503 1.9 23.4 1.0 N22 B:BVQ503 1.9 24.4 1.0 N23 B:BVQ503 1.9 25.7 1.0 C1 B:BVQ503 2.8 22.1 1.0 C19 B:BVQ503 2.8 21.7 1.0 C9 B:BVQ503 2.9 28.9 1.0 C11 B:BVQ503 2.9 25.8 1.0 C4 B:BVQ503 2.9 24.8 1.0 C16 B:BVQ503 3.0 22.8 1.0 C14 B:BVQ503 3.0 22.5 1.0 C6 B:BVQ503 3.0 22.9 1.0 C10 B:BVQ503 3.2 23.6 1.0 C5 B:BVQ503 3.3 26.2 1.0 C20 B:BVQ503 3.4 22.7 1.0 C15 B:BVQ503 3.4 23.7 1.0 O B:HOH624 3.6 29.4 1.0 C18 B:BVQ503 4.1 24.1 1.0 C2 B:BVQ503 4.1 23.1 1.0 C8 B:BVQ503 4.2 22.5 1.0 C3 B:BVQ503 4.2 20.7 1.0 C7 B:BVQ503 4.3 22.2 1.0 C17 B:BVQ503 4.3 22.9 1.0 C12 B:BVQ503 4.3 22.7 1.0 C13 B:BVQ503 4.3 24.7 1.0 O4 B:IOL509 4.5 46.7 0.7 C26 B:BVQ503 4.6 20.1 1.0 C41 B:BVQ503 4.8 25.8 1.0 C37 B:BVQ503 4.8 22.9 1.0 C35 B:BVQ503 4.8 24.9 1.0 CE2 B:PHE38 4.9 27.2 1.0 C53 B:BVQ503 4.9 23.4 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