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

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged., PDB code: 6zxx 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)	106.58 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.182, 170.391, 107.957, 90.00, 99.16, 90.00
R / Rfree (%)	18.2 / 21.8

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

Bromine	(Br)	12 atoms
Iron	(Fe)	24 atoms
Sodium	(Na)	3 atoms

The binding sites of Cobalt atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. (pdb code 6zxx). 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: 6zxx:
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:15.7 occ:1.00 CO A:B12703 0.0 15.7 1.0 N21 A:B12703 1.8 16.0 1.0 N23 A:B12703 1.8 15.2 1.0 N24 A:B12703 1.9 16.3 1.0 N22 A:B12703 1.9 15.6 1.0 BR A:BR707 2.4 21.1 0.3 C19 A:B12703 2.7 16.4 1.0 C1 A:B12703 2.7 15.7 1.0 C14 A:B12703 2.8 15.6 1.0 C11 A:B12703 2.8 15.9 1.0 C4 A:B12703 2.9 16.6 1.0 C9 A:B12703 2.9 14.1 1.0 C6 A:B12703 3.0 15.0 1.0 C16 A:B12703 3.0 16.3 1.0 BR2 A:QSH705 3.2 23.1 0.4 C20 A:B12703 3.2 15.2 1.0 C10 A:B12703 3.3 15.2 1.0 C5 A:B12703 3.4 15.9 1.0 C15 A:B12703 3.4 15.3 1.0 C2 A:B12703 4.0 16.3 1.0 C18 A:B12703 4.1 17.3 1.0 C3 A:B12703 4.1 16.3 1.0 C12 A:B12703 4.2 14.9 1.0 C17 A:B12703 4.2 16.4 1.0 C13 A:B12703 4.2 15.3 1.0 C8 A:B12703 4.2 12.8 1.0 C7 A:B12703 4.3 13.4 1.0 C26 A:B12703 4.5 16.4 1.0 C54 A:B12703 4.8 15.8 1.0 C41 A:B12703 4.8 12.3 1.0 C37 A:B12703 4.8 14.3 1.0 C35 A:B12703 4.8 15.7 1.0 C53 A:B12703 4.9 15.6 1.0 NH2 A:ARG552 4.9 17.8 1.0 O A:ASP476 5.0 19.3 1.0 C30 A:B12703 5.0 16.8 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:20.4 occ:1.00 CO B:B12703 0.0 20.4 1.0 N21 B:B12703 1.8 20.1 1.0 N23 B:B12703 1.9 19.3 1.0 N24 B:B12703 1.9 19.1 1.0 N22 B:B12703 1.9 19.6 1.0 BR B:BR707 2.3 23.2 0.3 C19 B:B12703 2.7 18.2 1.0 C1 B:B12703 2.7 18.9 1.0 C14 B:B12703 2.9 18.4 1.0 C4 B:B12703 2.9 19.5 1.0 C11 B:B12703 2.9 18.7 1.0 C6 B:B12703 2.9 20.1 1.0 C9 B:B12703 2.9 19.1 1.0 C16 B:B12703 3.0 18.5 1.0 BR2 B:QSH705 3.2 24.5 0.4 C20 B:B12703 3.2 18.3 1.0 C10 B:B12703 3.3 19.6 1.0 C5 B:B12703 3.3 19.6 1.0 C15 B:B12703 3.4 18.1 1.0 C18 B:B12703 4.0 18.6 1.0 C2 B:B12703 4.1 18.6 1.0 C3 B:B12703 4.1 19.6 1.0 C17 B:B12703 4.2 18.1 1.0 C7 B:B12703 4.2 19.6 1.0 C12 B:B12703 4.2 16.7 1.0 C13 B:B12703 4.2 17.4 1.0 C8 B:B12703 4.2 19.0 1.0 C26 B:B12703 4.5 17.8 1.0 C37 B:B12703 4.6 21.3 1.0 NH1 B:ARG552 4.6 25.9 1.0 C41 B:B12703 4.8 19.0 1.0 C54 B:B12703 4.8 17.4 1.0 C35 B:B12703 4.8 20.7 1.0 C53 B:B12703 4.9 18.7 1.0 C04 B:QSH705 5.0 22.3 0.4

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:Co803 b:26.7 occ:1.00 CO C:B12803 0.0 26.7 1.0 N21 C:B12803 1.8 28.8 1.0 N23 C:B12803 1.9 29.9 1.0 N24 C:B12803 1.9 30.0 1.0 N22 C:B12803 2.0 28.1 1.0 BR C:BR807 2.3 28.9 0.3 C19 C:B12803 2.7 28.9 1.0 C1 C:B12803 2.7 29.1 1.0 C14 C:B12803 2.9 27.9 1.0 C4 C:B12803 2.9 26.0 1.0 C11 C:B12803 2.9 31.0 1.0 C9 C:B12803 3.0 28.1 1.0 C16 C:B12803 3.0 28.9 1.0 C6 C:B12803 3.0 26.6 1.0 BR2 C:QSH805 3.2 29.1 0.4 C20 C:B12803 3.3 27.0 1.0 C15 C:B12803 3.4 28.3 1.0 C10 C:B12803 3.4 31.2 1.0 C5 C:B12803 3.4 24.6 1.0 C2 C:B12803 4.0 28.3 1.0 C18 C:B12803 4.1 28.6 1.0 C3 C:B12803 4.1 28.0 1.0 C13 C:B12803 4.2 26.4 1.0 C17 C:B12803 4.2 29.0 1.0 C12 C:B12803 4.2 30.0 1.0 C8 C:B12803 4.2 26.2 1.0 C7 C:B12803 4.3 25.2 1.0 C26 C:B12803 4.5 27.9 1.0 NH2 C:ARG556 4.6 27.1 1.0 C37 C:B12803 4.7 24.5 1.0 C41 C:B12803 4.8 25.4 1.0 C54 C:B12803 4.9 29.1 1.0 C53 C:B12803 4.9 27.3 1.0 C35 C:B12803 4.9 22.4 1.0 C47 C:B12803 4.9 31.0 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