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:
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.
![](/pictures/CL/pdb/zx/6zxu-CL-sphere_01.jpg) Mono view
![](/pictures/CL/pdb/zx/6zxu-CL-sphere_01_stereo.jpg) 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.
![](/pictures/CL/pdb/zx/6zxu-CL-sphere_02.jpg) Mono view
![](/pictures/CL/pdb/zx/6zxu-CL-sphere_02_stereo.jpg) 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.
![](/pictures/CL/pdb/zx/6zxu-CL-sphere_03.jpg) Mono view
![](/pictures/CL/pdb/zx/6zxu-CL-sphere_03_stereo.jpg) 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: Mon Jul 29 18:15:12 2024
|