Chlorine in PDB 5y5r: Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
Protein crystallography data
The structure of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif, PDB code: 5y5r
was solved by
D.Q.Xu,
T.T.Ran,
W.W.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.91 /
1.90
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
168.857,
168.857,
123.864,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
27.3 /
32.2
|
Other elements in 5y5r:
The structure of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
(pdb code 5y5r). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif, PDB code: 5y5r:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 5y5r
Go back to
Chlorine Binding Sites List in 5y5r
Chlorine binding site 1 out
of 6 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl301
b:67.2
occ:1.00
|
CL
|
A:8NL301
|
0.0
|
67.2
|
1.0
|
C21
|
A:8NL301
|
1.8
|
36.4
|
1.0
|
C20
|
A:8NL301
|
2.7
|
29.0
|
1.0
|
F
|
A:8NL301
|
2.8
|
31.9
|
1.0
|
C22
|
A:8NL301
|
2.8
|
35.8
|
1.0
|
OG1
|
A:THR125
|
3.1
|
18.1
|
1.0
|
CG1
|
A:VAL116
|
3.2
|
24.5
|
1.0
|
CB
|
A:ALA128
|
3.3
|
27.1
|
1.0
|
F2
|
A:8NL301
|
3.5
|
35.8
|
1.0
|
F1
|
A:8NL301
|
3.8
|
42.4
|
1.0
|
CG2
|
A:VAL116
|
3.8
|
18.7
|
1.0
|
CD2
|
A:LEU129
|
3.9
|
26.9
|
1.0
|
C16
|
A:8NL301
|
4.1
|
32.6
|
1.0
|
CB
|
A:VAL116
|
4.1
|
19.4
|
1.0
|
CB
|
A:THR125
|
4.1
|
17.1
|
1.0
|
N
|
A:LEU129
|
4.4
|
19.7
|
1.0
|
O
|
A:THR125
|
4.4
|
16.4
|
1.0
|
CG
|
A:LEU129
|
4.4
|
24.2
|
1.0
|
C
|
A:ALA128
|
4.5
|
24.0
|
1.0
|
CE1
|
A:PHE179
|
4.5
|
32.7
|
1.0
|
CA
|
A:ALA128
|
4.5
|
22.9
|
1.0
|
C19
|
A:8NL301
|
4.8
|
27.1
|
1.0
|
CZ
|
A:PHE179
|
4.9
|
31.6
|
1.0
|
CG2
|
A:THR125
|
4.9
|
20.3
|
1.0
|
CA
|
A:VAL116
|
5.0
|
22.5
|
1.0
|
CA
|
A:LEU129
|
5.0
|
22.4
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 5y5r
Go back to
Chlorine Binding Sites List in 5y5r
Chlorine binding site 2 out
of 6 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:73.5
occ:1.00
|
CL
|
B:8NL301
|
0.0
|
73.5
|
1.0
|
C21
|
B:8NL301
|
1.8
|
38.1
|
1.0
|
C20
|
B:8NL301
|
2.7
|
34.9
|
1.0
|
F
|
B:8NL301
|
2.8
|
42.2
|
1.0
|
C22
|
B:8NL301
|
2.8
|
34.7
|
1.0
|
CB
|
B:ALA128
|
3.5
|
26.5
|
1.0
|
F1
|
B:8NL301
|
3.5
|
38.4
|
1.0
|
CG1
|
B:VAL116
|
3.8
|
31.4
|
1.0
|
F2
|
B:8NL301
|
3.8
|
35.5
|
1.0
|
CD2
|
B:LEU129
|
4.1
|
27.7
|
1.0
|
C16
|
B:8NL301
|
4.2
|
31.9
|
1.0
|
OG1
|
B:THR125
|
4.2
|
23.4
|
1.0
|
CE2
|
B:PHE179
|
4.2
|
34.0
|
1.0
|
C
|
B:ALA128
|
4.3
|
24.1
|
1.0
|
CZ
|
B:PHE179
|
4.4
|
27.9
|
1.0
|
N
|
B:LEU129
|
4.4
|
26.2
|
1.0
|
O
|
B:ALA128
|
4.5
|
26.8
|
1.0
|
C18
|
B:8NL301
|
4.5
|
27.4
|
1.0
|
CA
|
B:ALA128
|
4.5
|
27.0
|
1.0
|
CG2
|
B:VAL116
|
4.7
|
34.7
|
1.0
|
CG
|
B:LEU129
|
4.8
|
25.9
|
1.0
|
CA
|
B:LEU129
|
4.8
|
30.0
|
1.0
|
CB
|
B:VAL116
|
4.9
|
30.9
|
1.0
|
C17
|
B:8NL301
|
5.0
|
34.1
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 5y5r
Go back to
Chlorine Binding Sites List in 5y5r
Chlorine binding site 3 out
of 6 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl301
b:47.5
occ:1.00
|
CL
|
C:8NL301
|
0.0
|
47.5
|
1.0
|
C21
|
C:8NL301
|
1.8
|
35.9
|
1.0
|
C20
|
C:8NL301
|
2.6
|
35.3
|
1.0
|
C22
|
C:8NL301
|
2.8
|
36.9
|
1.0
|
F
|
C:8NL301
|
2.9
|
29.9
|
1.0
|
CB
|
C:ALA128
|
3.5
|
22.7
|
1.0
|
F1
|
C:8NL301
|
3.6
|
34.2
|
1.0
|
F2
|
C:8NL301
|
3.8
|
34.2
|
1.0
|
CG1
|
C:VAL116
|
4.0
|
32.6
|
1.0
|
CE2
|
C:PHE179
|
4.1
|
29.1
|
1.0
|
C16
|
C:8NL301
|
4.1
|
31.7
|
1.0
|
OG1
|
C:THR125
|
4.3
|
24.8
|
1.0
|
CZ
|
C:PHE179
|
4.3
|
26.7
|
1.0
|
CD2
|
C:LEU129
|
4.5
|
22.6
|
1.0
|
C19
|
C:8NL301
|
4.5
|
34.4
|
1.0
|
C
|
C:ALA128
|
4.5
|
20.3
|
1.0
|
CA
|
C:ALA128
|
4.6
|
20.9
|
1.0
|
CG2
|
C:VAL116
|
4.7
|
28.2
|
1.0
|
N
|
C:LEU129
|
4.7
|
22.3
|
1.0
|
O
|
C:ALA128
|
4.8
|
23.1
|
1.0
|
C15
|
C:8NL301
|
4.9
|
36.4
|
1.0
|
C17
|
C:8NL301
|
5.0
|
40.1
|
1.0
|
CB
|
C:VAL116
|
5.0
|
25.4
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 5y5r
Go back to
Chlorine Binding Sites List in 5y5r
Chlorine binding site 4 out
of 6 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl301
b:83.7
occ:1.00
|
CL
|
D:8NL301
|
0.0
|
83.7
|
1.0
|
C21
|
D:8NL301
|
1.8
|
36.4
|
1.0
|
OG1
|
D:THR125
|
2.6
|
26.3
|
1.0
|
C20
|
D:8NL301
|
2.7
|
35.8
|
1.0
|
F
|
D:8NL301
|
2.7
|
36.6
|
1.0
|
C22
|
D:8NL301
|
2.8
|
36.9
|
1.0
|
CB
|
D:ALA128
|
3.2
|
30.7
|
1.0
|
CB
|
D:THR125
|
3.4
|
35.3
|
1.0
|
CG1
|
D:VAL116
|
3.5
|
33.7
|
1.0
|
F2
|
D:8NL301
|
3.6
|
30.3
|
1.0
|
F1
|
D:8NL301
|
3.7
|
44.2
|
1.0
|
O
|
D:THR125
|
4.0
|
30.0
|
1.0
|
CG2
|
D:VAL116
|
4.1
|
38.6
|
1.0
|
CG2
|
D:THR125
|
4.1
|
26.4
|
1.0
|
N
|
D:LEU129
|
4.1
|
31.3
|
1.0
|
C16
|
D:8NL301
|
4.1
|
34.2
|
1.0
|
CG
|
D:LEU129
|
4.1
|
28.7
|
1.0
|
CA
|
D:ALA128
|
4.3
|
26.1
|
1.0
|
C
|
D:ALA128
|
4.3
|
23.7
|
1.0
|
CB
|
D:VAL116
|
4.4
|
34.4
|
1.0
|
CA
|
D:THR125
|
4.7
|
30.9
|
1.0
|
CD1
|
D:LEU129
|
4.7
|
35.3
|
1.0
|
CA
|
D:LEU129
|
4.8
|
25.8
|
1.0
|
C
|
D:THR125
|
4.8
|
29.8
|
1.0
|
C19
|
D:8NL301
|
4.8
|
23.7
|
1.0
|
N
|
D:ALA128
|
4.9
|
25.8
|
1.0
|
CD2
|
D:LEU129
|
4.9
|
35.7
|
1.0
|
CB
|
D:LEU129
|
5.0
|
30.8
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 5y5r
Go back to
Chlorine Binding Sites List in 5y5r
Chlorine binding site 5 out
of 6 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl301
b:74.4
occ:1.00
|
CL
|
E:8NL301
|
0.0
|
74.4
|
1.0
|
C21
|
E:8NL301
|
1.8
|
55.3
|
1.0
|
C20
|
E:8NL301
|
2.6
|
53.4
|
1.0
|
C22
|
E:8NL301
|
2.8
|
55.2
|
1.0
|
F
|
E:8NL301
|
2.9
|
54.3
|
1.0
|
CG1
|
E:VAL116
|
3.1
|
44.1
|
1.0
|
CD2
|
E:LEU129
|
3.2
|
49.1
|
1.0
|
OG1
|
E:THR125
|
3.3
|
38.1
|
1.0
|
CB
|
E:ALA128
|
3.5
|
45.2
|
1.0
|
F1
|
E:8NL301
|
3.7
|
58.3
|
1.0
|
F2
|
E:8NL301
|
3.7
|
49.9
|
1.0
|
CG2
|
E:VAL116
|
4.0
|
42.0
|
1.0
|
C16
|
E:8NL301
|
4.0
|
57.1
|
1.0
|
CG
|
E:LEU129
|
4.1
|
41.5
|
1.0
|
CE2
|
E:PHE179
|
4.2
|
55.8
|
1.0
|
CB
|
E:VAL116
|
4.2
|
47.7
|
1.0
|
N
|
E:LEU129
|
4.4
|
40.8
|
1.0
|
CB
|
E:THR125
|
4.4
|
40.8
|
1.0
|
C
|
E:ALA128
|
4.5
|
42.6
|
1.0
|
CA
|
E:ALA128
|
4.6
|
38.5
|
1.0
|
O
|
E:THR125
|
4.7
|
37.9
|
1.0
|
CZ
|
E:PHE179
|
4.8
|
53.5
|
1.0
|
C19
|
E:8NL301
|
4.9
|
49.7
|
1.0
|
CA
|
E:LEU129
|
4.9
|
41.3
|
1.0
|
C15
|
E:8NL301
|
4.9
|
52.5
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 5y5r
Go back to
Chlorine Binding Sites List in 5y5r
Chlorine binding site 6 out
of 6 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl301
b:60.3
occ:1.00
|
CL
|
F:8NL301
|
0.0
|
60.3
|
1.0
|
C21
|
F:8NL301
|
1.8
|
59.4
|
1.0
|
C20
|
F:8NL301
|
2.5
|
61.5
|
1.0
|
OG1
|
F:THR125
|
2.7
|
44.9
|
1.0
|
C22
|
F:8NL301
|
2.9
|
60.9
|
1.0
|
F
|
F:8NL301
|
3.0
|
51.5
|
1.0
|
CG2
|
F:VAL116
|
3.3
|
54.0
|
1.0
|
CB
|
F:THR125
|
3.5
|
42.1
|
1.0
|
CG1
|
F:VAL116
|
3.6
|
48.6
|
1.0
|
CG2
|
F:THR125
|
3.6
|
38.5
|
1.0
|
F2
|
F:8NL301
|
3.6
|
64.1
|
1.0
|
CB
|
F:ALA128
|
3.7
|
44.9
|
1.0
|
CB
|
F:VAL116
|
3.9
|
52.6
|
1.0
|
F1
|
F:8NL301
|
3.9
|
62.8
|
1.0
|
C19
|
F:8NL301
|
4.0
|
59.9
|
1.0
|
C16
|
F:8NL301
|
4.0
|
60.3
|
1.0
|
CA
|
F:VAL116
|
4.2
|
48.4
|
1.0
|
C17
|
F:8NL301
|
4.4
|
60.8
|
1.0
|
CE1
|
F:PHE179
|
4.6
|
60.2
|
1.0
|
C18
|
F:8NL301
|
4.8
|
61.4
|
1.0
|
CA
|
F:THR125
|
4.9
|
35.1
|
1.0
|
O
|
F:VAL116
|
4.9
|
45.6
|
1.0
|
|
Reference:
D.Q.Xu,
T.T.Ran,
J.He,
W.W.Wang.
Structure and Catalytic Mechanism of A Novel Pyrethroid Hydrolase From Sphingobium Faniae Jz-2 To Be Published.
Page generated: Fri Jul 26 21:18:11 2024
|