Cobalt in PDB 6zxu: Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged., PDB code: 6zxu was solved by D.Leys, T.Halliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	121.69 / 1.73
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.110, 170.958, 107.873, 90.00, 98.37, 90.00
R / Rfree (%)	16.3 / 19.4

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. also contains other interesting chemical elements:

Iron	(Fe)	24 atoms
Chlorine	(Cl)	3 atoms
Sodium	(Na)	3 atoms

The binding sites of Cobalt atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. (pdb code 6zxu). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged., PDB code: 6zxu:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co703 b:12.7 occ:1.00 CO A:B12703 0.0 12.7 1.0 N23 A:B12703 1.8 13.1 1.0 N21 A:B12703 1.9 12.4 1.0 N24 A:B12703 1.9 13.4 1.0 N22 A:B12703 1.9 13.9 1.0 CL A:CL705 2.5 33.5 1.0 C19 A:B12703 2.7 14.1 1.0 C1 A:B12703 2.8 13.8 1.0 C11 A:B12703 2.8 14.5 1.0 C14 A:B12703 2.9 14.1 1.0 C4 A:B12703 2.9 12.4 1.0 C9 A:B12703 3.0 14.1 1.0 C6 A:B12703 3.0 12.1 1.0 C16 A:B12703 3.0 14.6 1.0 C10 A:B12703 3.2 13.0 1.0 C5 A:B12703 3.4 11.5 1.0 C15 A:B12703 3.4 13.7 1.0 C20 A:B12703 3.4 11.1 1.0 C2 A:B12703 4.1 12.7 1.0 C18 A:B12703 4.1 14.1 1.0 C13 A:B12703 4.2 15.1 1.0 C12 A:B12703 4.2 14.8 1.0 C3 A:B12703 4.2 13.1 1.0 C8 A:B12703 4.2 13.9 1.0 C17 A:B12703 4.2 13.7 1.0 C7 A:B12703 4.3 12.9 1.0 C26 A:B12703 4.6 14.4 1.0 C37 A:B12703 4.7 14.1 1.0 C41 A:B12703 4.8 14.1 1.0 NH2 A:ARG552 4.8 26.2 1.0 C35 A:B12703 4.9 11.4 1.0 C53 A:B12703 4.9 13.2 1.0 C54 A:B12703 5.0 13.6 1.0

Cobalt binding site 2 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. within 5.0Å range: probe atom residue distance (Å) B Occ B:Co703 b:14.6 occ:1.00 CO B:B12703 0.0 14.6 1.0 N24 B:B12703 1.8 14.7 1.0 N23 B:B12703 1.9 16.4 1.0 N22 B:B12703 1.9 16.5 1.0 N21 B:B12703 1.9 16.6 1.0 CL B:CL705 2.5 37.7 1.0 C19 B:B12703 2.7 15.3 1.0 C1 B:B12703 2.8 14.6 1.0 C11 B:B12703 2.8 17.8 1.0 C9 B:B12703 2.9 18.4 1.0 C4 B:B12703 2.9 17.0 1.0 C14 B:B12703 2.9 14.9 1.0 C6 B:B12703 3.0 18.2 1.0 C16 B:B12703 3.0 13.0 1.0 C10 B:B12703 3.2 18.8 1.0 C5 B:B12703 3.4 15.9 1.0 C20 B:B12703 3.4 13.4 1.0 C15 B:B12703 3.4 14.0 1.0 C2 B:B12703 4.1 14.9 1.0 C18 B:B12703 4.1 14.7 1.0 C3 B:B12703 4.2 16.2 1.0 C17 B:B12703 4.2 15.1 1.0 C8 B:B12703 4.2 17.8 1.0 C12 B:B12703 4.2 16.2 1.0 C13 B:B12703 4.2 17.0 1.0 C7 B:B12703 4.2 19.2 1.0 C26 B:B12703 4.6 13.8 1.0 C37 B:B12703 4.7 20.0 1.0 NH2 B:ARG552 4.8 22.2 1.0 C41 B:B12703 4.9 16.4 1.0 C35 B:B12703 4.9 17.4 1.0 C54 B:B12703 4.9 14.0 1.0 C53 B:B12703 4.9 16.1 1.0

Cobalt binding site 3 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co703 b:18.4 occ:1.00 CO C:B12703 0.0 18.4 1.0 N21 C:B12703 1.9 20.9 1.0 N23 C:B12703 1.9 22.0 1.0 N24 C:B12703 1.9 23.6 1.0 N22 C:B12703 2.0 21.1 1.0 CL C:CL705 2.4 46.2 1.0 C19 C:B12703 2.7 20.9 1.0 C1 C:B12703 2.8 18.7 1.0 C11 C:B12703 2.9 23.7 1.0 C4 C:B12703 2.9 20.6 1.0 C14 C:B12703 2.9 22.1 1.0 C9 C:B12703 3.0 21.1 1.0 C6 C:B12703 3.0 21.1 1.0 C16 C:B12703 3.0 22.0 1.0 C10 C:B12703 3.3 22.2 1.0 C5 C:B12703 3.4 22.4 1.0 C15 C:B12703 3.4 25.3 1.0 C20 C:B12703 3.5 18.3 1.0 C2 C:B12703 4.1 21.2 1.0 C18 C:B12703 4.1 22.3 1.0 C3 C:B12703 4.2 20.4 1.0 C17 C:B12703 4.3 21.9 1.0 C8 C:B12703 4.3 19.1 1.0 C13 C:B12703 4.3 22.9 1.0 C12 C:B12703 4.3 20.8 1.0 C7 C:B12703 4.3 23.7 1.0 C26 C:B12703 4.6 18.8 1.0 C37 C:B12703 4.7 21.8 1.0 C41 C:B12703 4.7 20.0 1.0 O C:HOH904 4.8 39.8 1.0 NH2 C:ARG552 4.9 22.4 1.0 C54 C:B12703 4.9 21.0 1.0 C35 C:B12703 4.9 19.4 1.0 NZ C:LYS488 5.0 35.7 1.0 C53 C:B12703 5.0 22.0 1.0

T.Halliwell, K.Fisher, K.A.P.Payne, S.E.J.Rigby, D.Leys. Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope. Microorganisms V. 8 2020.
ISSN: ISSN 2076-2607
PubMed: 32887524
DOI: 10.3390/MICROORGANISMS8091344