Chlorine 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:

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

Chlorine Binding Sites:

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 6zxu

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

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

Go back to Chlorine Binding Sites List in 6zxu
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

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: Sat Dec 12 14:48:47 2020

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