Atomistry » Fluorine » PDB 5xd5-5y5r » 5y5r
Atomistry »
  Fluorine »
    PDB 5xd5-5y5r »
      5y5r »

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

Go back to Fluorine Binding Sites List in 5y5r
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

Go back to Fluorine Binding Sites List in 5y5r
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

Go back to Fluorine Binding Sites List in 5y5r
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

Go back to Fluorine Binding Sites List in 5y5r
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: Thu Aug 1 17:07:26 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy