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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:

Fluorine (F) 18 atoms

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

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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

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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

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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

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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: Sat Jul 12 10:51:32 2025

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