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

Protein crystallography data

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

Other elements in 6zxu:

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

Cobalt Binding Sites:

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 6zxu

Go back to Cobalt Binding Sites List in 6zxu
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 6zxu

Go back to Cobalt Binding Sites List in 6zxu
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 6zxu

Go back to Cobalt Binding Sites List in 6zxu
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

Reference:

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
Page generated: Sun Jul 13 21:23:15 2025

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