Fluorine 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 (Cl) 6 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif, PDB code: 5y5r:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 5y5r

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Fluorine binding site 1 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F301

b:35.8
occ:1.00
 F2 A:8NL301 0.0 35.8 1.0
C22 A:8NL301 1.3 35.8 1.0
F A:8NL301 2.2 31.9 1.0
F1 A:8NL301 2.2 42.4 1.0
C21 A:8NL301 2.3 36.4 1.0
C20 A:8NL301 3.0 29.0 1.0
C16 A:8NL301 3.1 32.6 1.0
CB A:ALA128 3.3 27.1 1.0
C15 A:8NL301 3.5 32.2 1.0
CL A:8NL301 3.5 67.2 1.0
CG1 A:ILE132 3.8 23.8 1.0
C14 A:8NL301 4.0 26.4 1.0
CE1 A:PHE155 4.1 21.2 1.0
CZ A:PHE155 4.2 19.3 1.0
O A:8NL301 4.3 26.6 1.0
CA A:ALA128 4.3 22.9 1.0
C17 A:8NL301 4.4 26.8 1.0
CB A:ILE132 4.5 22.0 1.0
O1 A:8NL301 4.7 24.1 1.0
C A:ALA128 4.8 24.0 1.0
O A:ALA128 4.8 26.7 1.0
CG2 A:ILE132 4.8 22.6 1.0
CD1 A:ILE132 4.8 22.3 1.0
C A:8NL301 4.8 19.0 1.0
C19 A:8NL301 5.0 27.1 1.0
CG1 A:VAL204 5.0 23.9 1.0

Fluorine binding site 2 out of 18 in 5y5r

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Fluorine binding site 2 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
A:F301

b:42.4
occ:1.00
 F1 A:8NL301 0.0 42.4 1.0
C22 A:8NL301 1.3 35.8 1.0
F A:8NL301 2.1 31.9 1.0
F2 A:8NL301 2.2 35.8 1.0
C21 A:8NL301 2.4 36.4 1.0
C16 A:8NL301 2.8 32.6 1.0
C20 A:8NL301 2.9 29.0 1.0
CZ A:PHE179 3.2 31.6 1.0
CB A:ALA12 3.6 17.6 1.0
C15 A:8NL301 3.8 32.2 1.0
CL A:8NL301 3.8 67.2 1.0
CE1 A:PHE179 3.9 32.7 1.0
C14 A:8NL301 4.0 26.4 1.0
CE2 A:PHE179 4.1 28.2 1.0
O1 A:8NL301 4.2 24.1 1.0
C17 A:8NL301 4.4 26.8 1.0
C18 A:8NL301 4.6 31.2 1.0
O A:8NL301 4.7 26.6 1.0
CD1 A:LEU141 4.7 22.7 1.0

Fluorine binding site 3 out of 18 in 5y5r

Go back to Fluorine Binding Sites List in 5y5r
Fluorine binding site 3 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
A:F301

b:31.9
occ:1.00
 F A:8NL301 0.0 31.9 1.0
C22 A:8NL301 1.3 35.8 1.0
F1 A:8NL301 2.1 42.4 1.0
F2 A:8NL301 2.2 35.8 1.0
C21 A:8NL301 2.3 36.4 1.0
CL A:8NL301 2.8 67.2 1.0
C20 A:8NL301 3.5 29.0 1.0
CB A:ALA128 3.9 27.1 1.0
CG2 A:ILE132 4.0 22.6 1.0
CB A:ILE132 4.0 22.0 1.0
CZ A:PHE179 4.0 31.6 1.0
CG1 A:ILE132 4.1 23.8 1.0
C16 A:8NL301 4.2 32.6 1.0
CD1 A:LEU141 4.2 22.7 1.0
CE1 A:PHE179 4.4 32.7 1.0
O A:ALA128 4.5 26.7 1.0
C A:ALA128 4.6 24.0 1.0
CA A:ALA128 4.9 22.9 1.0
CD2 A:LEU129 4.9 26.9 1.0
CE2 A:PHE179 5.0 28.2 1.0

Fluorine binding site 4 out of 18 in 5y5r

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Fluorine binding site 4 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F301

b:35.5
occ:1.00
 F2 B:8NL301 0.0 35.5 1.0
C22 B:8NL301 1.3 34.7 1.0
F B:8NL301 2.2 42.2 1.0
F1 B:8NL301 2.2 38.4 1.0
C21 B:8NL301 2.3 38.1 1.0
C20 B:8NL301 2.9 34.9 1.0
C16 B:8NL301 2.9 31.9 1.0
C15 B:8NL301 3.0 32.9 1.0
C14 B:8NL301 3.6 29.1 1.0
C13 B:8NL301 3.6 25.7 1.0
C B:8NL301 3.8 21.4 1.0
CL B:8NL301 3.8 73.5 1.0
CB B:ALA12 3.9 17.7 1.0
O1 B:8NL301 4.1 22.1 1.0
C17 B:8NL301 4.1 34.1 1.0
O B:8NL301 4.1 31.2 1.0
CE1 B:PHE155 4.2 23.0 1.0
CG1 B:ILE132 4.3 23.3 1.0
CB B:ALA128 4.6 26.5 1.0
C18 B:8NL301 4.6 27.4 1.0
CZ B:PHE155 4.7 26.4 1.0
C2 B:8NL301 4.8 20.4 1.0
C1 B:8NL301 4.9 24.1 1.0
CD1 B:ILE132 4.9 23.8 1.0
CB B:ILE132 5.0 23.7 1.0
CG2 B:ILE132 5.0 21.9 1.0

Fluorine binding site 5 out of 18 in 5y5r

Go back to Fluorine Binding Sites List in 5y5r
Fluorine binding site 5 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F301

b:38.4
occ:1.00
 F1 B:8NL301 0.0 38.4 1.0
C22 B:8NL301 1.3 34.7 1.0
F B:8NL301 2.1 42.2 1.0
F2 B:8NL301 2.2 35.5 1.0
C21 B:8NL301 2.3 38.1 1.0
C20 B:8NL301 3.1 34.9 1.0
CZ B:PHE179 3.2 27.9 1.0
CB B:ALA12 3.3 17.7 1.0
C16 B:8NL301 3.5 31.9 1.0
CL B:8NL301 3.5 73.5 1.0
CE1 B:PHE179 4.0 25.8 1.0
CD1 B:LEU141 4.1 23.5 1.0
CE2 B:PHE179 4.2 34.0 1.0
C15 B:8NL301 4.4 32.9 1.0
CG2 B:ILE132 4.7 21.9 1.0
O1 B:8NL301 4.7 22.1 1.0
C14 B:8NL301 4.7 29.1 1.0
CA B:ALA12 4.8 18.2 1.0
C17 B:8NL301 4.9 34.1 1.0

Fluorine binding site 6 out of 18 in 5y5r

Go back to Fluorine Binding Sites List in 5y5r
Fluorine binding site 6 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F301

b:42.2
occ:1.00
 F B:8NL301 0.0 42.2 1.0
C22 B:8NL301 1.3 34.7 1.0
F1 B:8NL301 2.1 38.4 1.0
F2 B:8NL301 2.2 35.5 1.0
C21 B:8NL301 2.3 38.1 1.0
CL B:8NL301 2.8 73.5 1.0
CG1 B:ILE132 3.1 23.3 1.0
CB B:ILE132 3.3 23.7 1.0
CG2 B:ILE132 3.3 21.9 1.0
C20 B:8NL301 3.5 34.9 1.0
CD1 B:ILE132 4.3 23.8 1.0
CB B:ALA128 4.3 26.5 1.0
O B:ALA128 4.3 26.8 1.0
C16 B:8NL301 4.4 31.9 1.0
CD1 B:LEU141 4.6 23.5 1.0
CZ B:PHE179 4.8 27.9 1.0
C B:ALA128 4.8 24.1 1.0
CA B:ILE132 4.8 23.5 1.0
C15 B:8NL301 4.9 32.9 1.0
CA B:ALA128 5.0 27.0 1.0

Fluorine binding site 7 out of 18 in 5y5r

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Fluorine binding site 7 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:34.2
occ:1.00
 F2 C:8NL301 0.0 34.2 1.0
C22 C:8NL301 1.3 36.9 1.0
F C:8NL301 2.1 29.9 1.0
F1 C:8NL301 2.1 34.2 1.0
C21 C:8NL301 2.4 35.9 1.0
C15 C:8NL301 2.8 36.4 1.0
C20 C:8NL301 2.9 35.3 1.0
C16 C:8NL301 3.0 31.7 1.0
C14 C:8NL301 3.1 32.3 1.0
C13 C:8NL301 3.4 31.4 1.0
O1 C:8NL301 3.5 25.9 1.0
O C:8NL301 3.7 29.3 1.0
C C:8NL301 3.8 20.8 1.0
CB C:ALA12 3.8 24.4 1.0
CL C:8NL301 3.8 47.5 1.0
C17 C:8NL301 4.1 40.1 1.0
CE1 C:PHE155 4.4 20.6 1.0
C2 C:8NL301 4.6 25.4 1.0
C19 C:8NL301 4.6 34.4 1.0
C1 C:8NL301 4.7 23.8 1.0
CB C:ALA128 4.7 22.7 1.0
CG1 C:ILE132 4.8 26.5 1.0
CD1 C:ILE132 4.9 23.0 1.0
CA C:ALA12 4.9 24.4 1.0
O C:ALA12 5.0 18.0 1.0
CZ C:PHE179 5.0 26.7 1.0
CZ C:PHE155 5.0 25.8 1.0

Fluorine binding site 8 out of 18 in 5y5r

Go back to Fluorine Binding Sites List in 5y5r
Fluorine binding site 8 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:34.2
occ:1.00
 F1 C:8NL301 0.0 34.2 1.0
C22 C:8NL301 1.3 36.9 1.0
F2 C:8NL301 2.1 34.2 1.0
F C:8NL301 2.2 29.9 1.0
C21 C:8NL301 2.3 35.9 1.0
CB C:ALA12 2.9 24.4 1.0
CZ C:PHE179 2.9 26.7 1.0
C20 C:8NL301 3.0 35.3 1.0
C16 C:8NL301 3.3 31.7 1.0
CL C:8NL301 3.6 47.5 1.0
CE1 C:PHE179 3.8 29.6 1.0
CE2 C:PHE179 3.9 29.1 1.0
O1 C:8NL301 3.9 25.9 1.0
C15 C:8NL301 4.0 36.4 1.0
C14 C:8NL301 4.1 32.3 1.0
CA C:ALA12 4.4 24.4 1.0
CD1 C:LEU141 4.7 29.4 1.0
CB C:LEU79 4.8 26.3 1.0
C17 C:8NL301 4.8 40.1 1.0
N C:ALA12 4.9 19.1 1.0
C13 C:8NL301 4.9 31.4 1.0

Fluorine binding site 9 out of 18 in 5y5r

Go back to Fluorine Binding Sites List in 5y5r
Fluorine binding site 9 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:29.9
occ:1.00
 F C:8NL301 0.0 29.9 1.0
C22 C:8NL301 1.3 36.9 1.0
F2 C:8NL301 2.1 34.2 1.0
F1 C:8NL301 2.2 34.2 1.0
C21 C:8NL301 2.3 35.9 1.0
CL C:8NL301 2.9 47.5 1.0
CG1 C:ILE132 3.5 26.5 1.0
C20 C:8NL301 3.6 35.3 1.0
CG2 C:ILE132 3.8 26.1 1.0
CB C:ILE132 3.9 22.0 1.0
CD1 C:ILE132 4.0 23.0 1.0
C16 C:8NL301 4.4 31.7 1.0
CZ C:PHE179 4.4 26.7 1.0
CD1 C:LEU141 4.4 29.4 1.0
CB C:ALA12 4.5 24.4 1.0
CB C:ALA128 4.5 22.7 1.0
C15 C:8NL301 4.7 36.4 1.0
C C:8NL301 4.8 20.8 1.0

Fluorine binding site 10 out of 18 in 5y5r

Go back to Fluorine Binding Sites List in 5y5r
Fluorine binding site 10 out of 18 in the Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of A Novel Pyrethroid Hydrolase Pyth with Bif within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:30.3
occ:1.00
 F2 D:8NL301 0.0 30.3 1.0
C22 D:8NL301 1.3 36.9 1.0
F1 D:8NL301 2.2 44.2 1.0
F D:8NL301 2.2 36.6 1.0
C21 D:8NL301 2.3 36.4 1.0
C20 D:8NL301 3.0 35.8 1.0
C16 D:8NL301 3.1 34.2 1.0
CL D:8NL301 3.6 83.7 1.0
CG1 D:ILE132 3.7 23.3 1.0
CB D:ALA128 3.7 30.7 1.0
C15 D:8NL301 3.9 34.5 1.0
CB D:ILE132 4.3 26.9 1.0
C14 D:8NL301 4.3 32.1 1.0
CD1 D:ILE132 4.4 25.9 1.0
CG2 D:ILE132 4.5 22.8 1.0
CB D:ALA12 4.5 21.0 1.0
C17 D:8NL301 4.6 37.1 1.0
CE1 D:PHE155 4.6 21.4 1.0
C13 D:8NL301 4.7 26.3 1.0
CZ D:PHE155 4.7 20.9 1.0
O1 D:8NL301 4.8 31.9 1.0
C D:8NL301 4.8 24.4 1.0
CA D:ALA128 4.8 26.1 1.0
CZ D:PHE179 4.9 20.5 1.0
O D:8NL301 5.0 26.6 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: Sun Dec 13 12:43:02 2020

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