Cobalt in PDB 5obp: Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor

The structure of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl Norcobamide Cofactor, PDB code: 5obp 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)	36.07 / 1.59
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.565, 73.565, 184.677, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.7

The structure of Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl 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 6- Hydroxybenzimidazolyl Norcobamide Cofactor (pdb code 5obp). 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 6- Hydroxybenzimidazolyl Norcobamide Cofactor, PDB code: 5obp:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl 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 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Co503 b:17.4 occ:1.00 CO A:9QQ503 0.0 17.4 1.0 N21 A:9QQ503 1.9 16.2 1.0 N24 A:9QQ503 1.9 15.8 1.0 N23 A:9QQ503 1.9 15.4 1.0 N22 A:9QQ503 1.9 15.8 1.0 O A:HOH920 2.5 26.5 1.0 C19 A:9QQ503 2.8 15.8 1.0 C1 A:9QQ503 2.9 15.1 1.0 C9 A:9QQ503 2.9 16.8 1.0 C4 A:9QQ503 2.9 13.8 1.0 C11 A:9QQ503 2.9 17.4 1.0 C14 A:9QQ503 3.0 18.9 1.0 C16 A:9QQ503 3.0 16.1 1.0 C6 A:9QQ503 3.0 14.4 1.0 C10 A:9QQ503 3.3 19.4 1.0 C5 A:9QQ503 3.4 15.5 1.0 C15 A:9QQ503 3.4 16.8 1.0 C20 A:9QQ503 3.4 14.4 1.0 O A:HOH680 3.6 20.2 1.0 C18 A:9QQ503 4.1 15.6 1.0 C2 A:9QQ503 4.2 14.8 1.0 C8 A:9QQ503 4.2 18.5 1.0 C3 A:9QQ503 4.2 14.8 1.0 C12 A:9QQ503 4.3 18.5 1.0 C17 A:9QQ503 4.3 18.0 1.0 C7 A:9QQ503 4.3 16.2 1.0 C13 A:9QQ503 4.3 18.5 1.0 C42 A:9QQ503 4.5 26.6 1.0 C26 A:9QQ503 4.6 13.6 1.0 C37 A:9QQ503 4.8 16.8 1.0 C35 A:9QQ503 4.9 15.3 1.0 C53 A:9QQ503 4.9 18.4 1.0 C41 A:9QQ503 4.9 22.4 1.0 CE2 A:PHE38 5.0 18.3 1.0

Cobalt binding site 2 out of 2 in the Pce Reductive Dehalogenase From S. Multivorans with 6- Hydroxybenzimidazolyl 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 6- Hydroxybenzimidazolyl Norcobamide Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Co503 b:18.5 occ:1.00 CO B:9QQ503 0.0 18.5 1.0 N21 B:9QQ503 1.9 17.5 1.0 N24 B:9QQ503 1.9 18.0 1.0 N22 B:9QQ503 1.9 18.7 1.0 N23 B:9QQ503 1.9 16.5 1.0 O B:HOH892 2.5 32.5 1.0 C19 B:9QQ503 2.9 17.2 1.0 C9 B:9QQ503 2.9 18.2 1.0 C1 B:9QQ503 2.9 16.2 1.0 C11 B:9QQ503 2.9 19.7 1.0 C4 B:9QQ503 2.9 18.1 1.0 C16 B:9QQ503 3.0 15.8 1.0 C14 B:9QQ503 3.0 17.9 1.0 C6 B:9QQ503 3.0 19.4 1.0 C10 B:9QQ503 3.3 18.5 1.0 C5 B:9QQ503 3.4 16.7 1.0 C15 B:9QQ503 3.4 16.4 1.0 C20 B:9QQ503 3.5 17.7 1.0 O B:HOH643 3.7 22.5 1.0 C18 B:9QQ503 4.1 16.9 1.0 C2 B:9QQ503 4.2 17.2 1.0 C8 B:9QQ503 4.2 18.7 1.0 C3 B:9QQ503 4.2 18.0 1.0 C7 B:9QQ503 4.2 18.2 1.0 C12 B:9QQ503 4.3 17.2 1.0 C17 B:9QQ503 4.3 16.0 1.0 C13 B:9QQ503 4.3 16.4 1.0 C26 B:9QQ503 4.6 17.6 1.0 C37 B:9QQ503 4.8 17.6 1.0 C41 B:9QQ503 4.8 22.5 1.0 C35 B:9QQ503 4.9 18.4 1.0 CE2 B:PHE38 4.9 21.4 1.0 C53 B:9QQ503 4.9 19.2 1.0 C54 B:9QQ503 5.0 17.0 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