Chlorine 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:

Cobalt	(Co)	3 atoms
Iron	(Fe)	24 atoms
Sodium	(Na)	3 atoms

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

Chlorine 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 Chlorine with other atoms in the Cl binding site number 1 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl705 b:33.5 occ:1.00 CO A:B12703 2.5 12.7 1.0 N23 A:B12703 3.0 13.1 1.0 O A:HOH1146 3.1 37.9 1.0 N24 A:B12703 3.1 13.4 1.0 N22 A:B12703 3.1 13.9 1.0 N21 A:B12703 3.2 12.4 1.0 OH A:TYR426 3.4 32.1 1.0 NH2 A:ARG552 3.5 26.2 1.0 NZ A:LYS488 3.5 23.6 1.0 O A:HOH1104 3.6 29.3 1.0 C6 A:B12703 3.7 12.1 1.0 C19 A:B12703 3.8 14.1 1.0 C14 A:B12703 3.9 14.1 1.0 C4 A:B12703 3.9 12.4 1.0 C16 A:B12703 3.9 14.6 1.0 C9 A:B12703 3.9 14.1 1.0 CE2 A:PHE291 4.0 22.9 1.0 C11 A:B12703 4.0 14.5 1.0 C5 A:B12703 4.0 11.5 1.0 C1 A:B12703 4.1 13.8 1.0 C15 A:B12703 4.2 13.7 1.0 C37 A:B12703 4.2 14.1 1.0 C10 A:B12703 4.3 13.0 1.0 CZ A:ARG552 4.4 19.5 1.0 CZ A:PHE291 4.5 22.1 1.0 C26 A:B12703 4.6 14.4 1.0 NH1 A:ARG552 4.6 20.0 1.0 C7 A:B12703 4.6 12.9 1.0 O39 A:B12703 4.7 22.4 1.0 CZ A:TYR426 4.7 29.3 1.0 O A:HOH1023 4.7 26.3 1.0 C38 A:B12703 4.7 19.1 1.0 C54 A:B12703 4.8 13.6 1.0 C17 A:B12703 4.8 13.7 1.0 C2 A:B12703 4.9 12.7 1.0 C18 A:B12703 5.0 14.1 1.0 CE A:LYS488 5.0 22.2 1.0 C8 A:B12703 5.0 13.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 2 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl705 b:37.7 occ:1.00 CO B:B12703 2.5 14.6 1.0 N23 B:B12703 3.1 16.4 1.0 O B:HOH1128 3.1 42.9 1.0 N24 B:B12703 3.1 14.7 1.0 N22 B:B12703 3.1 16.5 1.0 N21 B:B12703 3.3 16.6 1.0 NH2 B:ARG552 3.4 22.2 1.0 NZ B:LYS488 3.4 28.7 1.0 O B:HOH1131 3.4 31.8 1.0 OH B:TYR426 3.5 27.5 1.0 C6 B:B12703 3.6 18.2 1.0 C9 B:B12703 3.8 18.4 1.0 C11 B:B12703 3.9 17.8 1.0 C19 B:B12703 3.9 15.3 1.0 C14 B:B12703 4.0 14.9 1.0 C4 B:B12703 4.0 17.0 1.0 CE2 B:PHE291 4.0 20.9 1.0 C5 B:B12703 4.0 15.9 1.0 C16 B:B12703 4.0 13.0 1.0 C37 B:B12703 4.1 20.0 1.0 C10 B:B12703 4.1 18.8 1.0 C1 B:B12703 4.2 14.6 1.0 CZ B:ARG552 4.3 19.1 1.0 C15 B:B12703 4.3 14.0 1.0 NH1 B:ARG552 4.4 18.9 1.0 C7 B:B12703 4.4 19.2 1.0 CZ B:PHE291 4.5 23.2 1.0 C38 B:B12703 4.8 22.1 1.0 O39 B:B12703 4.8 23.1 1.0 C26 B:B12703 4.8 13.8 1.0 CZ B:TYR426 4.8 23.0 1.0 C8 B:B12703 4.8 17.8 1.0 C54 B:B12703 4.9 14.0 1.0 CE B:LYS488 4.9 24.5 1.0 O B:HOH1035 4.9 29.4 1.0 C17 B:B12703 5.0 15.1 1.0 C2 B:B12703 5.0 14.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl binding site number 3 of Catabolic Reductive Dehalogenase Nprdha, N-Terminally Tagged. within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl705 b:46.2 occ:1.00 CO C:B12703 2.4 18.4 1.0 O C:HOH904 2.7 39.8 1.0 N23 C:B12703 3.1 22.0 1.0 N24 C:B12703 3.1 23.6 1.0 N22 C:B12703 3.2 21.1 1.0 N21 C:B12703 3.2 20.9 1.0 NZ C:LYS488 3.4 35.7 1.0 NH2 C:ARG552 3.4 22.4 1.0 OH C:TYR426 3.4 30.4 1.0 C6 C:B12703 3.6 21.1 1.0 O C:HOH1065 3.8 34.5 1.0 C9 C:B12703 3.8 21.1 1.0 C4 C:B12703 3.8 20.6 1.0 C19 C:B12703 3.9 20.9 1.0 C11 C:B12703 3.9 23.7 1.0 C14 C:B12703 3.9 22.1 1.0 C5 C:B12703 4.0 22.4 1.0 C16 C:B12703 4.0 22.0 1.0 CE2 C:PHE291 4.0 27.6 1.0 C37 C:B12703 4.1 21.8 1.0 C1 C:B12703 4.1 18.7 1.0 C10 C:B12703 4.2 22.2 1.0 C15 C:B12703 4.3 25.3 1.0 CZ C:ARG552 4.4 24.2 1.0 C7 C:B12703 4.5 23.7 1.0 CZ C:PHE291 4.5 29.5 1.0 C26 C:B12703 4.5 18.8 1.0 O39 C:B12703 4.6 32.5 1.0 NH1 C:ARG552 4.7 24.7 1.0 C38 C:B12703 4.7 27.0 1.0 CZ C:TYR426 4.8 32.1 1.0 C54 C:B12703 4.8 21.0 1.0 C2 C:B12703 4.8 21.2 1.0 O C:HOH951 4.9 32.5 1.0 CE C:LYS488 4.9 32.3 1.0 C8 C:B12703 4.9 19.1 1.0 C17 C:B12703 5.0 21.9 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