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Fluorine in PDB 4whq: Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5

Enzymatic activity of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5

All present enzymatic activity of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5:
1.13.11.3;

Protein crystallography data

The structure of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5, PDB code: 4whq 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) 39.01 / 1.78
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.259, 140.724, 167.824, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.5

Other elements in 4whq:

The structure of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 (pdb code 4whq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5, PDB code: 4whq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 4whq

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Fluorine binding site 1 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:37.0
occ:1.00
 F9 A:3N8302 0.0 37.0 1.0
C4 A:3N8302 1.3 32.0 1.0
C3 A:3N8302 2.4 32.0 1.0
C5 A:3N8302 2.4 30.7 1.0
O A:HOH479 3.3 53.6 1.0
CG A:GLU168 3.4 31.8 1.0
CG1 A:ILE171 3.5 22.8 1.0
CA A:GLU168 3.5 22.4 1.0
C2 A:3N8302 3.6 31.2 1.0
C6 A:3N8302 3.6 29.9 1.0
N A:GLU168 3.7 20.7 1.0
O A:HOH426 3.9 26.9 1.0
C A:ARG167 3.9 20.9 1.0
CB A:GLU168 4.0 25.2 1.0
CD1 A:ILE171 4.1 22.4 1.0
O A:ARG167 4.1 20.3 1.0
C1 A:3N8302 4.1 31.6 1.0
CB A:ARG167 4.4 22.1 1.0
O A:HOH460 4.7 32.8 1.0
CD A:GLU168 4.7 40.9 1.0
O8 A:3N8302 4.7 31.2 1.0
CB A:ILE171 4.7 21.5 1.0
C A:GLU168 4.8 21.3 1.0
CA A:ARG167 4.8 20.3 1.0
O A:PRO164 4.8 28.1 1.0
OE2 A:GLU168 4.9 48.1 1.0

Fluorine binding site 2 out of 18 in 4whq

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Fluorine binding site 2 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:49.9
occ:1.00
 F9 E:3N8301 0.0 49.9 1.0
C4 E:3N8301 1.3 40.8 1.0
C3 E:3N8301 2.4 39.7 1.0
C5 E:3N8301 2.4 39.5 1.0
CG E:GLU168 3.4 39.9 1.0
CA E:GLU168 3.4 28.7 1.0
CG1 E:ILE171 3.6 30.9 1.0
N E:GLU168 3.6 27.1 1.0
C2 E:3N8301 3.6 40.3 1.0
C6 E:3N8301 3.7 39.6 1.0
CB E:GLU168 3.9 34.0 1.0
C E:ARG167 3.9 25.9 1.0
O E:ARG167 4.1 24.8 1.0
C1 E:3N8301 4.1 39.7 1.0
CD1 E:ILE171 4.1 32.1 1.0
CB E:ARG167 4.3 26.6 1.0
O E:HOH412 4.5 33.8 1.0
O E:PRO164 4.6 32.2 1.0
C E:GLU168 4.6 27.6 1.0
CD E:GLU168 4.7 49.3 1.0
O8 E:3N8301 4.7 42.8 1.0
CA E:ARG167 4.7 26.7 1.0
CB E:ILE171 4.8 30.7 1.0
O E:GLU168 5.0 26.5 1.0

Fluorine binding site 3 out of 18 in 4whq

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Fluorine binding site 3 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F602

b:50.0
occ:1.00
 F9 F:3N8602 0.0 50.0 1.0
C4 F:3N8602 1.4 44.2 1.0
C5 F:3N8602 2.4 40.1 1.0
C3 F:3N8602 2.4 43.0 1.0
S2 F:BME606 3.3 62.0 1.0
C6 F:3N8602 3.6 36.1 1.0
C2 F:3N8602 3.7 41.2 1.0
CB F:PRO487 4.0 25.4 1.0
CA F:PRO487 4.1 24.0 1.0
C1 F:3N8602 4.1 38.8 1.0
O F:PRO487 4.6 24.0 1.0
CB F:PRO498 4.7 29.5 1.0
CG F:PRO498 4.8 29.9 1.0
O8 F:3N8602 4.8 39.7 1.0
C F:PRO487 4.9 22.7 1.0
CG F:LYS493 4.9 28.6 1.0
C2 F:BME606 4.9 60.3 1.0
CD F:LYS493 5.0 29.9 1.0

Fluorine binding site 4 out of 18 in 4whq

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Fluorine binding site 4 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F603

b:58.7
occ:1.00
 F9 F:3N8603 0.0 58.7 1.0
C4 F:3N8603 1.3 47.1 1.0
C3 F:3N8603 2.4 46.3 1.0
C5 F:3N8603 2.4 44.8 1.0
CG D:PRO322 3.6 24.3 1.0
C2 F:3N8603 3.6 44.7 1.0
C6 F:3N8603 3.6 42.5 1.0
O D:HOH866 4.0 41.3 1.0
C1 F:3N8603 4.1 42.4 1.0
CD2 F:LEU320 4.2 23.2 1.0
CB D:PRO322 4.3 23.2 1.0
CD D:PRO322 4.7 21.9 1.0
O F:HOH856 4.7 44.4 1.0
O8 F:3N8603 4.7 43.1 1.0
O F:HOH752 4.8 22.1 1.0

Fluorine binding site 5 out of 18 in 4whq

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Fluorine binding site 5 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F604

b:49.8
occ:1.00
 F9 F:3N8604 0.0 49.8 1.0
C4 F:3N8604 1.3 44.2 1.0
C3 F:3N8604 2.3 44.8 1.0
C5 F:3N8604 2.4 40.0 1.0
CB F:SER338 3.1 21.3 1.0
C F:SER338 3.2 21.3 1.0
O F:SER338 3.3 19.9 1.0
N F:ILE339 3.4 19.9 1.0
C2 F:3N8604 3.6 46.3 1.0
C6 F:3N8604 3.6 40.9 1.0
C F:ILE339 3.6 21.9 1.0
CA F:ILE339 3.7 20.4 1.0
CA F:SER338 3.7 19.5 1.0
CA D:PRO453 3.8 20.4 1.0
O F:ILE339 3.9 21.7 1.0
O D:HOH730 4.0 32.3 1.0
C1 F:3N8604 4.1 43.0 1.0
N F:PRO340 4.1 23.0 1.0
CB D:PRO453 4.3 21.7 1.0
OG F:SER338 4.3 20.4 1.0
O D:PRO453 4.3 22.8 1.0
O F:HOH777 4.4 27.4 1.0
O D:GLY452 4.5 21.9 1.0
C D:PRO453 4.5 21.8 1.0
CD F:PRO340 4.5 23.1 1.0
N D:PRO453 4.7 20.5 1.0
O8 F:3N8604 4.7 53.2 1.0
CA F:PRO340 4.8 23.6 1.0
C D:GLY452 4.9 20.7 1.0
N F:SER338 4.9 19.6 1.0
CG D:PRO453 4.9 21.8 1.0

Fluorine binding site 6 out of 18 in 4whq

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Fluorine binding site 6 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F608

b:36.7
occ:1.00
 F9 F:3N8608 0.0 36.7 1.0
C4 F:3N8608 1.4 46.1 1.0
C5 F:3N8608 2.4 45.6 1.0
C3 F:3N8608 2.5 41.7 1.0
N F:GLY425 3.1 25.1 1.0
OD1 F:ASN366 3.2 26.2 1.0
N F:VAL426 3.2 25.7 1.0
CA F:GLY424 3.3 27.8 1.0
O F:HOH767 3.3 26.8 1.0
C F:GLY424 3.4 27.0 1.0
O F:VAL426 3.4 24.9 1.0
C6 F:3N8608 3.7 45.2 1.0
C2 F:3N8608 3.7 44.1 1.0
CG2 F:VAL426 3.8 33.9 1.0
CG F:ASN366 3.9 25.1 1.0
N F:GLY424 3.9 27.0 1.0
CA F:VAL426 4.0 27.0 1.0
CB F:VAL426 4.0 31.6 1.0
ND2 F:ASN366 4.1 26.2 1.0
C F:GLY425 4.1 24.8 1.0
C F:VAL426 4.1 25.3 1.0
CA F:GLY425 4.2 24.5 1.0
C1 F:3N8608 4.2 43.6 1.0
O F:GLY424 4.3 30.2 1.0
CB F:PHE367 4.3 27.7 1.0
CD1 F:PHE367 4.3 30.6 1.0
O F:ASN366 4.7 25.7 1.0
CG F:PHE367 4.7 29.3 1.0
O8 F:3N8608 4.9 42.9 1.0
C F:ASN366 4.9 26.8 1.0

Fluorine binding site 7 out of 18 in 4whq

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Fluorine binding site 7 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:42.9
occ:1.00
 F9 C:3N8301 0.0 42.9 1.0
C4 C:3N8301 1.3 37.6 1.0
C3 C:3N8301 2.4 37.1 1.0
C5 C:3N8301 2.4 36.9 1.0
CG C:GLU168 3.4 30.2 1.0
CA C:GLU168 3.5 23.5 1.0
CG1 C:ILE171 3.6 24.2 1.0
N C:GLU168 3.6 21.8 1.0
C2 C:3N8301 3.6 37.6 1.0
C6 C:3N8301 3.6 37.5 1.0
C C:ARG167 3.9 22.5 1.0
CB C:GLU168 4.0 25.7 1.0
O C:ARG167 4.0 22.7 1.0
C1 C:3N8301 4.1 37.0 1.0
CD1 C:ILE171 4.1 25.3 1.0
CB C:ARG167 4.2 24.4 1.0
O C:HOH420 4.3 31.0 1.0
O C:PRO164 4.7 31.0 1.0
CD C:GLU168 4.7 37.2 1.0
CA C:ARG167 4.7 22.6 1.0
O8 C:3N8301 4.7 34.6 1.0
C C:GLU168 4.7 21.9 1.0
CB C:ILE171 4.8 23.8 1.0
O C:HOH493 4.8 36.3 1.0
OE2 C:GLU168 4.9 47.1 1.0

Fluorine binding site 8 out of 18 in 4whq

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Fluorine binding site 8 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:33.8
occ:1.00
 F9 D:3N8602 0.0 33.8 1.0
C4 D:3N8602 1.4 41.7 1.0
C5 D:3N8602 2.4 39.5 1.0
C3 D:3N8602 2.4 41.6 1.0
N D:VAL426 3.2 21.1 1.0
N D:GLY425 3.2 22.8 1.0
OD1 D:ASN366 3.2 21.7 1.0
O D:HOH751 3.2 27.4 1.0
CG1 D:VAL426 3.3 28.4 1.0
CA D:GLY424 3.3 22.1 1.0
O D:VAL426 3.4 22.0 1.0
C D:GLY424 3.5 24.0 1.0
C6 D:3N8602 3.7 41.7 1.0
C2 D:3N8602 3.7 45.1 1.0
CG D:ASN366 3.9 22.2 1.0
CA D:VAL426 4.0 22.9 1.0
N D:GLY424 4.0 23.4 1.0
ND2 D:ASN366 4.1 23.1 1.0
C D:GLY425 4.1 21.9 1.0
C D:VAL426 4.1 21.8 1.0
CA D:GLY425 4.2 23.5 1.0
C1 D:3N8602 4.2 44.8 1.0
CB D:VAL426 4.3 25.6 1.0
CB D:PHE367 4.3 28.0 1.0
CD1 D:PHE367 4.3 31.1 1.0
O D:GLY424 4.4 28.9 1.0
CG D:PHE367 4.7 27.5 1.0
O D:ASN366 4.7 27.0 1.0
O8 D:3N8602 4.9 46.3 1.0
C D:ASN366 4.9 24.4 1.0

Fluorine binding site 9 out of 18 in 4whq

Go back to Fluorine Binding Sites List in 4whq
Fluorine binding site 9 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F603

b:48.1
occ:1.00
 F9 D:3N8603 0.0 48.1 1.0
C4 D:3N8603 1.3 40.2 1.0
C5 D:3N8603 2.4 36.7 1.0
C3 D:3N8603 2.4 37.5 1.0
C6 D:3N8603 3.6 34.4 1.0
C2 D:3N8603 3.6 35.9 1.0
CB D:PRO487 3.8 24.5 1.0
CA D:PRO487 3.9 24.2 1.0
C1 D:3N8603 4.1 34.4 1.0
O D:PRO487 4.4 25.1 1.0
C D:PRO487 4.7 24.2 1.0
CG D:LYS493 4.7 24.2 1.0
CB D:PRO498 4.8 32.2 1.0
O8 D:3N8603 4.8 34.9 1.0
CD D:LYS493 4.8 27.1 1.0
CG D:PRO498 5.0 32.8 1.0
N D:PRO487 5.0 21.6 1.0

Fluorine binding site 10 out of 18 in 4whq

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Fluorine binding site 10 out of 18 in the Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Alkylperoxo Reaction Intermediate Trapped in Protocatechuate 3,4- Dioxygenase (Pseudomonas Putida) at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F604

b:58.5
occ:1.00
 F9 D:3N8604 0.0 58.5 1.0
C4 D:3N8604 1.3 45.1 1.0
C5 D:3N8604 2.4 44.9 1.0
C3 D:3N8604 2.4 46.2 1.0
C2 D:3N8604 3.6 44.2 1.0
C6 D:3N8604 3.6 45.1 1.0
O B:HOH859 3.8 53.8 1.0
CD2 B:LEU320 3.9 22.3 1.0
C1 D:3N8604 4.1 43.8 1.0
CD2 D:LEU320 4.1 23.6 1.0
CG B:PRO322 4.6 23.1 1.0
O8 D:3N8604 4.8 44.2 1.0
CG B:LEU320 4.8 22.0 1.0
O D:HOH866 4.8 41.3 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: Thu Aug 1 06:24:20 2024

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