Cobalt in PDB 6zy0: Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant, PDB code: 6zy0 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)	106.66 / 2.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.346, 169.569, 107.799, 90.00, 98.33, 90.00
R / Rfree (%)	18.6 / 22.2

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant also contains other interesting chemical elements:

Iron	(Fe)	24 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	3 atoms

The binding sites of Cobalt atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant (pdb code 6zy0). 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, K488Q Variant, PDB code: 6zy0:
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, K488Q Variant


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, K488Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Co703 b:21.3 occ:1.00 CO A:B12703 0.0 21.3 1.0 N24 A:B12703 1.9 23.4 1.0 N21 A:B12703 1.9 22.5 1.0 N22 A:B12703 1.9 21.3 1.0 N23 A:B12703 1.9 23.9 1.0 O A:HOH886 2.7 21.5 1.0 C19 A:B12703 2.8 27.2 1.0 C1 A:B12703 2.9 21.3 1.0 C4 A:B12703 2.9 26.7 1.0 C9 A:B12703 2.9 21.0 1.0 C14 A:B12703 2.9 27.3 1.0 C11 A:B12703 2.9 23.8 1.0 C6 A:B12703 3.0 27.4 1.0 C16 A:B12703 3.0 23.7 1.0 C10 A:B12703 3.2 20.7 1.0 C5 A:B12703 3.3 28.0 1.0 C15 A:B12703 3.4 26.2 1.0 C20 A:B12703 3.7 26.6 1.0 C2 A:B12703 4.0 22.4 1.0 C18 A:B12703 4.1 26.0 1.0 C3 A:B12703 4.1 23.3 1.0 C13 A:B12703 4.1 26.4 1.0 C8 A:B12703 4.2 19.9 1.0 C7 A:B12703 4.2 22.6 1.0 C17 A:B12703 4.2 23.8 1.0 C12 A:B12703 4.3 23.3 1.0 C26 A:B12703 4.6 21.9 1.0 C35 A:B12703 4.7 25.4 1.0 C37 A:B12703 4.8 25.3 1.0 C41 A:B12703 4.8 20.2 1.0 C53 A:B12703 4.8 26.7 1.0 O39 A:B12703 4.8 35.0 1.0 C54 A:B12703 4.9 23.0 1.0

Cobalt binding site 2 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


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, K488Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Co703 b:27.0 occ:1.00 CO B:B12703 0.0 27.0 1.0 N24 B:B12703 1.9 26.9 1.0 N21 B:B12703 1.9 31.0 1.0 N22 B:B12703 1.9 27.4 1.0 N23 B:B12703 1.9 27.8 1.0 O B:HOH874 2.4 24.4 1.0 C19 B:B12703 2.8 26.6 1.0 C1 B:B12703 2.9 30.3 1.0 C9 B:B12703 2.9 25.8 1.0 C4 B:B12703 2.9 27.9 1.0 C14 B:B12703 2.9 26.0 1.0 C11 B:B12703 2.9 22.3 1.0 C6 B:B12703 2.9 27.5 1.0 C16 B:B12703 3.0 29.6 1.0 C10 B:B12703 3.2 26.9 1.0 C5 B:B12703 3.3 28.4 1.0 C15 B:B12703 3.4 27.8 1.0 C20 B:B12703 3.7 28.4 1.0 C2 B:B12703 4.0 28.8 1.0 C3 B:B12703 4.1 28.0 1.0 C18 B:B12703 4.1 27.8 1.0 C13 B:B12703 4.1 26.2 1.0 C8 B:B12703 4.2 24.6 1.0 C7 B:B12703 4.2 25.8 1.0 C17 B:B12703 4.2 26.2 1.0 C12 B:B12703 4.3 23.6 1.0 C26 B:B12703 4.6 29.2 1.0 O39 B:B12703 4.6 35.3 1.0 C35 B:B12703 4.8 28.9 1.0 C37 B:B12703 4.8 30.6 1.0 C53 B:B12703 4.8 25.5 1.0 C41 B:B12703 4.8 23.6 1.0 C54 B:B12703 4.9 24.0 1.0

Cobalt binding site 3 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged, K488Q Variant


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, K488Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Co703 b:41.6 occ:1.00 CO C:B12703 0.0 41.6 1.0 N24 C:B12703 1.9 46.3 1.0 N21 C:B12703 1.9 43.8 1.0 N22 C:B12703 1.9 45.7 1.0 N23 C:B12703 1.9 46.3 1.0 O C:HOH840 2.5 33.4 1.0 C19 C:B12703 2.8 41.5 1.0 C1 C:B12703 2.9 42.9 1.0 C4 C:B12703 2.9 43.6 1.0 C9 C:B12703 2.9 42.5 1.0 C14 C:B12703 2.9 44.8 1.0 C11 C:B12703 2.9 43.0 1.0 C6 C:B12703 3.0 41.9 1.0 C16 C:B12703 3.0 45.0 1.0 C10 C:B12703 3.3 44.0 1.0 C5 C:B12703 3.3 42.3 1.0 C15 C:B12703 3.4 45.0 1.0 C20 C:B12703 3.7 37.2 1.0 C2 C:B12703 4.0 39.1 1.0 C3 C:B12703 4.1 42.4 1.0 C18 C:B12703 4.1 43.8 1.0 C13 C:B12703 4.1 43.7 1.0 C8 C:B12703 4.2 37.2 1.0 C7 C:B12703 4.2 36.8 1.0 C17 C:B12703 4.2 39.8 1.0 C12 C:B12703 4.3 39.0 1.0 C26 C:B12703 4.5 40.6 1.0 C42 C:B12703 4.7 32.4 1.0 C35 C:B12703 4.8 38.3 1.0 C37 C:B12703 4.8 43.7 1.0 C53 C:B12703 4.8 40.0 1.0 O39 C:B12703 4.9 45.8 1.0 OH C:TYR426 4.9 57.6 1.0 C54 C:B12703 4.9 38.4 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