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Cobalt in PDB 6zy1: Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid

Protein crystallography data

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid, PDB code: 6zy1 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) 106.00 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.871, 170.104, 107.651, 90.00, 98.35, 90.00
R / Rfree (%) 17.7 / 21.1

Other elements in 6zy1:

The structure of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid also contains other interesting chemical elements:

Bromine (Br) 9 atoms
Iron (Fe) 24 atoms
Sodium (Na) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid (pdb code 6zy1). 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 in Complex with 3-Bromo-4-Hydroxybenzoic Acid, PDB code: 6zy1:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 6zy1

Go back to Cobalt Binding Sites List in 6zy1
Cobalt binding site 1 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid


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 in Complex with 3-Bromo-4-Hydroxybenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co703

b:12.9
occ:1.00
CO A:B12703 0.0 12.9 1.0
N24 A:B12703 1.9 16.3 1.0
N21 A:B12703 1.9 20.9 1.0
N22 A:B12703 1.9 13.1 1.0
N23 A:B12703 1.9 14.3 1.0
C19 A:B12703 2.7 17.5 1.0
C4 A:B12703 2.9 15.7 1.0
C14 A:B12703 2.9 15.1 1.0
C11 A:B12703 2.9 16.6 1.0
C1 A:B12703 2.9 14.1 1.0
C9 A:B12703 2.9 11.3 1.0
BR1 A:QSB705 2.9 16.1 0.3
C6 A:B12703 2.9 15.3 1.0
C16 A:B12703 3.0 14.5 1.0
C10 A:B12703 3.2 12.3 1.0
C5 A:B12703 3.3 16.4 1.0
C15 A:B12703 3.3 14.6 1.0
C20 A:B12703 3.8 16.0 1.0
C2 A:B12703 4.0 16.3 1.0
C18 A:B12703 4.1 18.5 1.0
C3 A:B12703 4.1 14.2 1.0
C13 A:B12703 4.1 15.6 1.0
C7 A:B12703 4.2 11.0 1.0
C8 A:B12703 4.2 9.6 1.0
C17 A:B12703 4.2 16.1 1.0
C12 A:B12703 4.3 12.1 1.0
C26 A:B12703 4.5 15.7 1.0
NH2 A:ARG552 4.6 17.3 1.0
C37 A:B12703 4.7 14.4 1.0
C35 A:B12703 4.7 13.9 1.0
H041 A:QSB705 4.8 25.1 0.3
C02 A:QSB705 4.8 20.5 0.3
C53 A:B12703 4.8 15.8 1.0
NZ A:LYS488 4.9 14.4 1.0
C54 A:B12703 4.9 18.6 1.0
H101 A:QSB705 4.9 25.3 0.4
C49 A:B12703 4.9 15.0 1.0
C41 A:B12703 4.9 7.0 1.0
C47 A:B12703 5.0 16.9 1.0
C42 A:B12703 5.0 7.1 1.0

Cobalt binding site 2 out of 3 in 6zy1

Go back to Cobalt Binding Sites List in 6zy1
Cobalt binding site 2 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid


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 in Complex with 3-Bromo-4-Hydroxybenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co703

b:16.1
occ:1.00
CO B:B12703 0.0 16.1 1.0
N24 B:B12703 1.9 22.5 1.0
N22 B:B12703 1.9 19.9 1.0
N21 B:B12703 1.9 20.7 1.0
N23 B:B12703 1.9 18.1 1.0
C19 B:B12703 2.7 18.6 1.0
BR1 B:QSB705 2.8 19.7 0.3
C4 B:B12703 2.9 14.6 1.0
C1 B:B12703 2.9 18.1 1.0
C9 B:B12703 2.9 18.3 1.0
C14 B:B12703 2.9 13.8 1.0
C11 B:B12703 2.9 16.6 1.0
C6 B:B12703 2.9 16.2 1.0
C16 B:B12703 3.0 19.0 1.0
C10 B:B12703 3.2 15.7 1.0
C5 B:B12703 3.3 17.1 1.0
C15 B:B12703 3.4 16.4 1.0
C20 B:B12703 3.8 15.7 1.0
C2 B:B12703 4.0 17.2 1.0
C18 B:B12703 4.1 15.9 1.0
C3 B:B12703 4.1 16.4 1.0
C13 B:B12703 4.1 19.2 1.0
C7 B:B12703 4.1 18.1 1.0
C17 B:B12703 4.2 15.4 1.0
C8 B:B12703 4.2 15.3 1.0
C12 B:B12703 4.3 14.8 1.0
C26 B:B12703 4.5 17.8 1.0
H041 B:QSB705 4.6 26.4 0.3
C37 B:B12703 4.6 20.4 1.0
NH2 B:ARG552 4.7 19.2 1.0
H101 B:QSB705 4.7 23.1 0.3
C35 B:B12703 4.7 16.8 1.0
C02 B:QSB705 4.7 22.1 0.3
C53 B:B12703 4.8 16.8 1.0
C54 B:B12703 4.8 11.4 1.0
NZ B:LYS488 4.9 14.4 1.0
C41 B:B12703 4.9 14.1 1.0
C49 B:B12703 5.0 17.5 1.0
C30 B:B12703 5.0 16.1 1.0

Cobalt binding site 3 out of 3 in 6zy1

Go back to Cobalt Binding Sites List in 6zy1
Cobalt binding site 3 out of 3 in the Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged in Complex with 3-Bromo-4-Hydroxybenzoic Acid


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 in Complex with 3-Bromo-4-Hydroxybenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co703

b:21.9
occ:1.00
CO C:B12703 0.0 21.9 1.0
N24 C:B12703 1.9 29.4 1.0
N22 C:B12703 1.9 29.9 1.0
N21 C:B12703 1.9 26.2 1.0
N23 C:B12703 1.9 25.3 1.0
C19 C:B12703 2.7 27.4 1.0
BR1 C:QSB705 2.8 28.7 0.3
C4 C:B12703 2.9 24.1 1.0
C14 C:B12703 2.9 25.1 1.0
C1 C:B12703 2.9 24.6 1.0
C9 C:B12703 2.9 21.8 1.0
C11 C:B12703 2.9 23.5 1.0
C6 C:B12703 2.9 23.0 1.0
C16 C:B12703 3.0 25.9 1.0
C10 C:B12703 3.2 22.9 1.0
C5 C:B12703 3.3 25.7 1.0
C15 C:B12703 3.3 25.9 1.0
C20 C:B12703 3.8 25.9 1.0
C2 C:B12703 4.0 23.2 1.0
C18 C:B12703 4.1 26.0 1.0
C3 C:B12703 4.1 25.3 1.0
C13 C:B12703 4.1 24.6 1.0
C7 C:B12703 4.1 19.8 1.0
C8 C:B12703 4.2 18.3 1.0
C17 C:B12703 4.2 21.8 1.0
C12 C:B12703 4.3 21.3 1.0
H041 C:QSB705 4.4 34.2 0.3
C26 C:B12703 4.4 25.4 1.0
H101 C:QSB705 4.5 34.6 0.4
C37 C:B12703 4.6 26.9 1.0
C02 C:QSB705 4.7 28.6 0.3
C35 C:B12703 4.7 22.6 1.0
C53 C:B12703 4.8 24.4 1.0
NZ C:LYS488 4.8 23.4 1.0
C54 C:B12703 4.9 22.2 1.0
C41 C:B12703 4.9 16.1 1.0
NH2 C:ARG552 4.9 19.9 1.0
C49 C:B12703 4.9 23.6 1.0
C47 C:B12703 5.0 19.3 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 Dec 13 10:54:38 2020

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