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Fluorine in PDB 4whs: 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5

Enzymatic activity of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5

All present enzymatic activity of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5:
1.13.11.3;

Protein crystallography data

The structure of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4whs was solved by C.J.Knoot, V.M.Purpero, J.D.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 1.35
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.013, 140.665, 168.138, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 16.7

Other elements in 4whs:

The structure of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Fluorine atom in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 (pdb code 4whs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 13 binding sites of Fluorine where determined in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5, PDB code: 4whs:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 13 in 4whs

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Fluorine binding site 1 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:30.8
occ:1.00
 F9 A:3N8301 0.0 30.8 1.0
C4 A:3N8301 1.3 24.1 1.0
C5 A:3N8301 2.4 25.5 1.0
C3 A:3N8301 2.4 27.2 1.0
O A:HOH488 3.3 40.2 1.0
CG1 A:ILE171 3.4 15.1 1.0
CA A:GLU168 3.4 14.9 1.0
CG A:GLU168 3.6 21.1 1.0
C6 A:3N8301 3.6 26.0 1.0
N A:GLU168 3.6 14.4 1.0
C2 A:3N8301 3.6 24.0 1.0
C A:ARG167 3.9 14.3 1.0
CB A:GLU168 4.0 16.9 1.0
O A:ARG167 4.0 14.9 1.0
O A:HOH436 4.0 20.1 1.0
CD1 A:ILE171 4.1 15.3 1.0
C1 A:3N8301 4.1 24.3 1.0
CB A:ARG167 4.3 15.9 1.0
CB A:ILE171 4.6 14.9 1.0
C A:GLU168 4.7 14.0 1.0
O A:HOH469 4.7 23.7 1.0
O8 A:3N8301 4.8 31.0 1.0
CA A:ARG167 4.8 14.5 1.0
O A:PRO164 4.9 23.7 1.0
O A:HOH531 4.9 27.4 1.0
O A:GLU168 5.0 14.9 1.0
CD A:GLU168 5.0 28.1 1.0

Fluorine binding site 2 out of 13 in 4whs

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Fluorine binding site 2 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F602

b:39.2
occ:1.00
 F9 F:3N8602 0.0 39.2 1.0
C4 F:3N8602 1.3 30.7 1.0
C5 F:3N8602 2.4 33.9 1.0
C3 F:3N8602 2.4 31.3 1.0
C6 F:3N8602 3.6 31.9 1.0
C2 F:3N8602 3.6 31.6 1.0
NH2 D:ARG450 4.1 41.1 1.0
CG F:PRO340 4.1 19.6 1.0
C1 F:3N8602 4.1 31.8 1.0
CB F:PRO340 4.2 17.7 1.0
CD F:PRO340 4.5 16.8 1.0
NE D:ARG450 4.6 28.8 1.0
CZ D:ARG450 4.7 33.4 1.0
O8 F:3N8602 4.8 49.8 1.0

Fluorine binding site 3 out of 13 in 4whs

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Fluorine binding site 3 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F604

b:41.0
occ:1.00
 F9 F:3N8604 0.0 41.0 1.0
C4 F:3N8604 1.3 30.9 1.0
C5 F:3N8604 2.3 28.1 1.0
C3 F:3N8604 2.4 28.1 1.0
C6 F:3N8604 3.6 26.6 1.0
C2 F:3N8604 3.6 26.1 1.0
C1 F:3N8604 4.1 24.5 1.0
O8 F:3N8604 4.8 35.3 1.0

Fluorine binding site 4 out of 13 in 4whs

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Fluorine binding site 4 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F605

b:21.4
occ:0.35
 F9 F:3N8605 0.0 21.4 0.3
C4 F:3N8605 1.3 17.7 0.3
C5 F:3N8605 1.4 18.2 0.3
C4 F:3N8605 2.2 18.7 0.3
C5 F:3N8605 2.3 16.1 0.3
C3 F:3N8605 2.4 18.2 0.3
F9 F:3N8605 2.4 22.2 0.3
C6 F:3N8605 2.6 17.4 0.3
O E:HOH534 3.0 34.7 1.0
CG E:PRO15 3.0 21.0 1.0
OH E:TYR16 3.5 23.7 1.0
C3 F:3N8605 3.5 18.1 0.3
CZ E:TYR16 3.6 23.5 1.0
C6 F:3N8605 3.6 16.6 0.3
C2 F:3N8605 3.6 17.1 0.3
CE2 E:TYR16 3.7 22.2 1.0
CE2 F:TYR447 3.7 17.1 0.8
CD E:PRO15 3.7 19.9 1.0
C1 F:3N8605 3.8 17.7 0.3
C1 F:3N8605 4.1 15.8 0.3
C2 F:3N8605 4.1 17.0 0.3
OH F:TYR447 4.1 17.9 0.8
CZ F:TYR447 4.3 18.1 0.8
CB E:PRO15 4.4 22.7 1.0
CE1 E:TYR16 4.4 21.8 1.0
CD2 E:TYR16 4.4 21.2 1.0
O F:HOH870 4.5 24.3 1.0
CD2 F:TYR447 4.6 17.7 0.8
O8 F:3N8605 4.8 16.5 0.3
CB F:TRP449 4.9 13.9 1.0
CE1 F:TYR447 4.9 16.0 0.2
O F:HOH871 4.9 23.7 1.0
O7 F:3N8605 5.0 16.2 0.3

Fluorine binding site 5 out of 13 in 4whs

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Fluorine binding site 5 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F605

b:22.2
occ:0.35
 F9 F:3N8605 0.0 22.2 0.3
C5 F:3N8605 1.2 16.1 0.3
C4 F:3N8605 1.3 18.7 0.3
C4 F:3N8605 2.1 17.7 0.3
C6 F:3N8605 2.3 16.6 0.3
C5 F:3N8605 2.4 18.2 0.3
C3 F:3N8605 2.4 18.1 0.3
F9 F:3N8605 2.4 21.4 0.3
CB F:TRP449 3.1 13.9 1.0
CE3 F:TRP449 3.3 13.9 1.0
C3 F:3N8605 3.4 18.2 0.3
CG F:TRP449 3.5 13.6 1.0
CD2 F:TRP449 3.5 13.3 1.0
C1 F:3N8605 3.5 15.8 0.3
C6 F:3N8605 3.6 17.4 0.3
C2 F:3N8605 3.6 17.0 0.3
CE2 F:TYR447 3.7 17.1 0.8
C2 F:3N8605 3.9 17.1 0.3
CD2 F:TYR447 4.1 17.7 0.8
C1 F:3N8605 4.1 17.7 0.3
CE1 F:TYR447 4.2 16.0 0.2
CZ3 F:TRP449 4.3 15.1 1.0
O F:HOH888 4.4 23.2 1.0
O F:HOH870 4.4 24.3 1.0
CA F:TRP449 4.4 13.2 1.0
CD1 F:TRP449 4.6 13.8 1.0
CE2 F:TRP449 4.7 14.2 1.0
O7 F:3N8605 4.7 18.7 0.3
O8 F:3N8605 4.7 18.5 0.3
CG E:PRO15 4.8 21.0 1.0
CD E:PRO15 4.8 19.9 1.0
O E:HOH534 4.9 34.7 1.0
CZ F:TYR447 4.9 18.1 0.8
O F:HOH867 4.9 26.4 1.0
OH F:TYR447 5.0 17.2 0.2

Fluorine binding site 6 out of 13 in 4whs

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Fluorine binding site 6 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:37.7
occ:1.00
 F9 E:3N8301 0.0 37.7 1.0
C4 E:3N8301 1.3 30.0 1.0
C5 E:3N8301 2.4 31.1 1.0
C3 E:3N8301 2.4 30.4 1.0
CA E:GLU168 3.4 18.7 1.0
CG E:GLU168 3.4 24.1 1.0
CG1 E:ILE171 3.5 20.3 1.0
N E:GLU168 3.6 17.7 1.0
C6 E:3N8301 3.6 30.0 1.0
C2 E:3N8301 3.6 29.4 1.0
O E:HOH503 3.7 41.6 1.0
C E:ARG167 3.8 17.7 1.0
O E:ARG167 4.0 18.4 1.0
CB E:GLU168 4.0 19.8 1.0
CD1 E:ILE171 4.1 21.4 1.0
C1 E:3N8301 4.1 29.1 1.0
CB E:ARG167 4.2 18.7 1.0
O E:HOH412 4.3 26.4 1.0
C E:GLU168 4.7 17.6 1.0
CA E:ARG167 4.7 18.2 1.0
CB E:ILE171 4.7 19.6 1.0
CD E:GLU168 4.7 32.4 1.0
O E:PRO164 4.8 26.8 1.0
O8 E:3N8301 4.8 38.0 1.0
O E:HOH499 5.0 30.6 1.0
O E:GLU168 5.0 18.7 1.0

Fluorine binding site 7 out of 13 in 4whs

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Fluorine binding site 7 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:33.0
occ:1.00
 F9 C:3N8301 0.0 33.0 1.0
C4 C:3N8301 1.3 27.8 1.0
C5 C:3N8301 2.4 28.0 1.0
C3 C:3N8301 2.4 32.3 1.0
CA C:GLU168 3.4 16.1 1.0
CG1 C:ILE171 3.4 16.2 1.0
CG C:GLU168 3.5 20.9 1.0
N C:GLU168 3.5 15.3 1.0
C6 C:3N8301 3.6 30.1 1.0
C2 C:3N8301 3.6 28.1 1.0
O C:HOH548 3.7 34.7 1.0
C C:ARG167 3.8 14.9 1.0
CB C:GLU168 3.9 17.8 1.0
O C:ARG167 4.0 15.6 1.0
CD1 C:ILE171 4.1 17.2 1.0
C1 C:3N8301 4.1 28.6 1.0
CB C:ARG167 4.2 16.2 1.0
O C:HOH434 4.3 22.6 1.0
C C:GLU168 4.6 15.7 1.0
CB C:ILE171 4.6 15.3 1.0
CA C:ARG167 4.7 15.6 1.0
O C:PRO164 4.7 23.7 1.0
CD C:GLU168 4.8 29.3 1.0
O8 C:3N8301 4.8 31.9 1.0
O C:HOH506 5.0 27.4 1.0
O C:GLU168 5.0 16.4 1.0

Fluorine binding site 8 out of 13 in 4whs

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Fluorine binding site 8 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:18.9
occ:0.35
 F9 D:3N8602 0.0 18.9 0.3
C4 D:3N8602 1.3 17.3 0.3
C5 D:3N8602 1.4 17.6 0.3
C4 D:3N8602 2.2 18.4 0.3
C5 D:3N8602 2.4 17.0 0.3
C3 D:3N8602 2.4 18.3 0.3
F9 D:3N8602 2.4 20.5 0.3
C6 D:3N8602 2.6 18.0 0.3
O C:HOH554 2.9 34.8 1.0
CG C:PRO15 3.0 19.6 1.0
OH C:TYR16 3.5 22.4 1.0
C3 D:3N8602 3.5 17.8 0.3
CZ C:TYR16 3.6 21.5 1.0
C6 D:3N8602 3.6 17.1 0.3
C2 D:3N8602 3.6 16.7 0.3
CD C:PRO15 3.7 19.8 1.0
CE2 C:TYR16 3.7 20.7 1.0
CE2 D:TYR447 3.7 17.6 0.8
C1 D:3N8602 3.8 16.8 0.3
C1 D:3N8602 4.1 15.8 0.3
OH D:TYR447 4.2 17.1 0.8
C2 D:3N8602 4.2 16.3 0.3
CE1 C:TYR16 4.3 20.3 1.0
CZ D:TYR447 4.4 17.4 0.8
CB C:PRO15 4.4 20.8 1.0
CD2 C:TYR16 4.5 18.6 1.0
O D:HOH887 4.5 23.9 1.0
CD2 D:TYR447 4.6 17.0 0.8
O8 D:3N8602 4.8 15.2 0.3
CE1 D:TYR447 4.9 14.0 0.2
CB D:TRP449 4.9 14.0 1.0
N C:PRO15 5.0 18.4 1.0
O C:HOH552 5.0 37.2 1.0
O7 D:3N8602 5.0 15.3 0.3

Fluorine binding site 9 out of 13 in 4whs

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Fluorine binding site 9 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:20.5
occ:0.35
 F9 D:3N8602 0.0 20.5 0.3
C5 D:3N8602 1.2 17.0 0.3
C4 D:3N8602 1.3 18.4 0.3
C4 D:3N8602 2.1 17.3 0.3
C5 D:3N8602 2.4 17.6 0.3
C3 D:3N8602 2.4 17.8 0.3
F9 D:3N8602 2.4 18.9 0.3
C6 D:3N8602 2.4 17.1 0.3
CB D:TRP449 3.1 14.0 1.0
CE3 D:TRP449 3.3 15.2 1.0
C3 D:3N8602 3.4 18.3 0.3
CG D:TRP449 3.5 14.1 1.0
CD2 D:TRP449 3.6 14.5 1.0
C1 D:3N8602 3.6 15.8 0.3
C6 D:3N8602 3.6 18.0 0.3
C2 D:3N8602 3.6 16.3 0.3
CE2 D:TYR447 3.7 17.6 0.8
C2 D:3N8602 4.0 16.7 0.3
CD2 D:TYR447 4.1 17.0 0.8
C1 D:3N8602 4.1 16.8 0.3
CE1 D:TYR447 4.2 14.0 0.2
CZ3 D:TRP449 4.3 16.5 1.0
O D:HOH887 4.4 23.9 1.0
O D:HOH915 4.4 20.9 1.0
CA D:TRP449 4.5 14.1 1.0
CD1 D:TRP449 4.6 13.9 1.0
CE2 D:TRP449 4.7 15.0 1.0
O8 D:3N8602 4.8 16.9 0.3
O7 D:3N8602 4.8 17.1 0.3
O C:HOH554 4.8 34.8 1.0
OH D:TYR447 4.8 16.0 0.2
CG C:PRO15 4.8 19.6 1.0
CD C:PRO15 4.8 19.8 1.0
CZ D:TYR447 4.9 17.4 0.8
O D:HOH886 4.9 25.6 1.0

Fluorine binding site 10 out of 13 in 4whs

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Fluorine binding site 10 out of 13 in the 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of 4-Fluorocatechol Bound to Protocatechuate 3,4-Dioxygenase (Pseudomonas Putida) at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F603

b:54.3
occ:1.00
 F9 D:3N8603 0.0 54.3 1.0
C4 D:3N8603 1.3 41.3 1.0
C3 D:3N8603 2.4 36.3 1.0
C5 D:3N8603 2.4 38.6 1.0
C2 D:3N8603 3.6 35.5 1.0
C6 D:3N8603 3.7 36.5 1.0
CD2 B:LEU320 3.9 16.1 1.0
O B:HOH883 3.9 39.1 1.0
CD2 D:LEU320 4.0 16.2 1.0
C1 D:3N8603 4.1 33.7 1.0
O8 D:3N8603 4.8 42.2 1.0
O D:HOH893 5.0 40.3 1.0
CG B:LEU320 5.0 14.7 1.0

Reference:

C.J.Knoot, V.M.Purpero, J.D.Lipscomb. Crystal Structures of Alkylperoxo and Anhydride Intermediates in An Intradiol Ring-Cleaving Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 112 388 2015.
ISSN: ESSN 1091-6490
PubMed: 25548185
DOI: 10.1073/PNAS.1419118112
Page generated: Sun Dec 13 12:14:23 2020

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