Cobalt in PDB 5obi: Pce Reductive Dehalogenase From S. Multivorans with 5- Methoxybenzimidazolyl-Norcobamide Cofactor

The structure of Pce Reductive Dehalogenase From S. Multivorans with 5- Methoxybenzimidazolyl-Norcobamide Cofactor, PDB code: 5obi was solved by S.Keller, C.Kunze, M.Bommer, C.Paetz, R.C.Menezes, A.Svatos, H.Dobbek, T.Schubert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.79 / 1.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.585, 73.585, 185.284, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.2

The structure of Pce Reductive Dehalogenase From S. Multivorans with 5- Methoxybenzimidazolyl-Norcobamide Cofactor also contains other interesting chemical elements:

Iron

(Fe)

16 atoms

The binding sites of Cobalt atom in the Pce Reductive Dehalogenase From S. Multivorans with 5- Methoxybenzimidazolyl-Norcobamide Cofactor (pdb code 5obi). 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 with 5- Methoxybenzimidazolyl-Norcobamide Cofactor, PDB code: 5obi:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans with 5- Methoxybenzimidazolyl-Norcobamide Cofactor


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 with 5- Methoxybenzimidazolyl-Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:17.3 occ:1.00 CO A:OBL503 0.0 17.3 1.0 N21 A:OBL503 1.9 13.6 1.0 N24 A:OBL503 1.9 16.9 1.0 N22 A:OBL503 1.9 16.9 1.0 N23 A:OBL503 1.9 13.4 1.0 O A:HOH909 2.7 33.4 1.0 C1 A:OBL503 2.8 13.1 1.0 C19 A:OBL503 2.8 14.2 1.0 C9 A:OBL503 2.9 17.7 1.0 C11 A:OBL503 2.9 16.3 1.0 C4 A:OBL503 2.9 14.4 1.0 C14 A:OBL503 3.0 17.5 1.0 C16 A:OBL503 3.0 16.4 1.0 C6 A:OBL503 3.0 18.1 1.0 C10 A:OBL503 3.3 18.7 1.0 C20 A:OBL503 3.4 16.2 1.0 C5 A:OBL503 3.4 15.5 1.0 C15 A:OBL503 3.4 15.1 1.0 O A:HOH695 3.6 17.3 1.0 C18 A:OBL503 4.1 15.2 1.0 C2 A:OBL503 4.1 13.5 1.0 C8 A:OBL503 4.2 17.7 1.0 C3 A:OBL503 4.2 13.9 1.0 C12 A:OBL503 4.3 17.2 1.0 C17 A:OBL503 4.3 14.9 1.0 C7 A:OBL503 4.3 15.9 1.0 C13 A:OBL503 4.3 16.5 1.0 C26 A:OBL503 4.6 13.3 1.0 C41 A:OBL503 4.8 20.1 1.0 C37 A:OBL503 4.8 16.4 1.0 C35 A:OBL503 4.9 15.3 1.0 C53 A:OBL503 4.9 16.0 1.0 CE2 A:PHE38 4.9 18.0 1.0 C54 A:OBL503 5.0 14.8 1.0

Cobalt binding site 2 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans with 5- Methoxybenzimidazolyl-Norcobamide Cofactor


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 with 5- Methoxybenzimidazolyl-Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Co503 b:19.2 occ:1.00 CO B:OBL503 0.0 19.2 1.0 N21 B:OBL503 1.9 17.8 1.0 N24 B:OBL503 1.9 20.3 1.0 N22 B:OBL503 1.9 20.8 1.0 N23 B:OBL503 1.9 17.1 1.0 O B:HOH865 2.8 36.5 1.0 C1 B:OBL503 2.8 17.2 1.0 C19 B:OBL503 2.8 17.0 1.0 C9 B:OBL503 2.9 19.0 1.0 C11 B:OBL503 2.9 18.6 1.0 C4 B:OBL503 2.9 18.0 1.0 C14 B:OBL503 3.0 21.5 1.0 C16 B:OBL503 3.0 17.0 1.0 C6 B:OBL503 3.0 19.9 1.0 C10 B:OBL503 3.3 19.4 1.0 C5 B:OBL503 3.4 18.5 1.0 C15 B:OBL503 3.4 19.7 1.0 C20 B:OBL503 3.4 16.9 1.0 O B:HOH667 3.7 22.5 1.0 C18 B:OBL503 4.1 19.1 1.0 C2 B:OBL503 4.1 17.2 1.0 C3 B:OBL503 4.2 18.2 1.0 C8 B:OBL503 4.2 20.5 1.0 C12 B:OBL503 4.2 16.9 1.0 C7 B:OBL503 4.2 19.3 1.0 C17 B:OBL503 4.3 18.3 1.0 C13 B:OBL503 4.3 19.7 1.0 C26 B:OBL503 4.5 19.3 1.0 C37 B:OBL503 4.8 20.1 1.0 C35 B:OBL503 4.9 19.1 1.0 C41 B:OBL503 4.9 23.5 1.0 CE2 B:PHE38 4.9 20.9 1.0 C53 B:OBL503 4.9 21.4 1.0

S.Keller, C.Kunze, M.Bommer, C.Paetz, R.C.Menezes, A.Svatos, H.Dobbek, T.Schubert. Selective Utilization of Benzimidazolyl-Norcobamides As Cofactors By the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum Multivorans. J. Bacteriol. V. 200 2018.
ISSN: ESSN 1098-5530
PubMed: 29378885
DOI: 10.1128/JB.00584-17