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Fluorine in PDB 3pcf: Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate

Enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate

All present enzymatic activity of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate:
1.13.11.3;

Protein crystallography data

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate, PDB code: 3pcf was solved by A.M.Orville, N.Elango, J.D.Lipscomb, D.H.Ohlendorf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.15
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.030, 127.220, 133.700, 90.00, 97.70, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3pcf:

The structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate also contains other interesting chemical elements:

Iron (Fe) 6 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate (pdb code 3pcf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate, PDB code: 3pcf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 3pcf

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Fluorine binding site 1 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:F550

b:18.8
occ:1.00
 F3 M:FHB550 0.0 18.8 1.0
C3 M:FHB550 1.4 19.1 1.0
C2 M:FHB550 2.4 18.6 1.0
C4 M:FHB550 2.4 18.8 1.0
O4 M:FHB550 2.7 18.1 1.0
NE2 M:GLN477 2.9 8.6 1.0
NH1 M:ARG457 3.2 9.9 1.0
CG2 A:THR12 3.4 11.2 1.0
CE1 M:HIS462 3.6 12.3 1.0
C5 M:FHB550 3.7 19.0 1.0
C1 M:FHB550 3.7 18.9 1.0
CD1 M:ILE491 3.7 16.8 1.0
CD M:GLN477 3.8 10.6 1.0
CA A:GLY14 3.8 15.9 1.0
OE1 M:GLN477 3.8 10.2 1.0
O M:HOH747 4.0 17.3 1.0
C6 M:FHB550 4.2 18.6 1.0
CZ M:ARG457 4.2 11.3 1.0
FE M:FE600 4.2 21.6 1.0
N A:GLY14 4.3 14.4 1.0
NE2 M:HIS462 4.3 13.2 1.0
O A:THR12 4.3 11.9 1.0
ND1 M:HIS462 4.6 12.9 1.0
CG2 M:ILE491 4.7 14.7 1.0
CD A:PRO15 4.8 17.8 1.0
CB A:THR12 4.8 11.7 1.0
C A:ALA13 4.8 14.0 1.0
NE M:ARG457 4.9 11.5 1.0
C7 M:FHB550 4.9 18.9 1.0
NH2 M:ARG457 4.9 10.8 1.0
CD M:ARG457 4.9 11.5 1.0
NE2 M:HIS460 4.9 12.7 1.0
OH M:TYR447 4.9 21.1 1.0
C A:THR12 5.0 12.3 1.0

Fluorine binding site 2 out of 12 in 3pcf

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Fluorine binding site 2 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:F551

b:25.9
occ:1.00
 F3 M:FHB551 0.0 25.9 1.0
C3 M:FHB551 1.4 24.1 1.0
C2 M:FHB551 2.4 23.4 1.0
C4 M:FHB551 2.4 23.6 1.0
O4 M:FHB551 2.8 23.9 1.0
C1 M:FHB551 3.7 23.8 1.0
C5 M:FHB551 3.7 23.3 1.0
CD2 O:LEU320 4.0 15.5 1.0
NH2 O:ARG333 4.0 15.1 1.0
CD M:ARG333 4.1 16.6 1.0
C6 M:FHB551 4.2 23.5 1.0
CD1 O:LEU320 4.2 15.5 1.0
CZ O:ARG333 4.6 16.0 1.0
NE O:ARG333 4.6 16.6 1.0
NE M:ARG333 4.7 16.1 1.0
CG O:LEU320 4.7 15.8 1.0
C7 M:FHB551 4.9 24.8 1.0

Fluorine binding site 3 out of 12 in 3pcf

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Fluorine binding site 3 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:F550

b:19.0
occ:1.00
 F3 N:FHB550 0.0 19.0 1.0
C3 N:FHB550 1.4 19.2 1.0
C2 N:FHB550 2.4 18.8 1.0
C4 N:FHB550 2.4 18.9 1.0
O4 N:FHB550 2.7 18.0 1.0
NE2 N:GLN477 2.9 8.7 1.0
NH1 N:ARG457 3.3 9.0 1.0
CG2 B:THR12 3.5 9.6 1.0
CE1 N:HIS462 3.5 11.8 1.0
CD1 N:ILE491 3.6 15.8 1.0
C1 N:FHB550 3.7 18.9 1.0
C5 N:FHB550 3.7 19.4 1.0
CD N:GLN477 3.8 9.8 1.0
CA B:GLY14 3.8 16.0 1.0
OE1 N:GLN477 4.0 7.0 1.0
O N:HOH861 4.1 16.9 0.8
C6 N:FHB550 4.1 18.6 1.0
O B:THR12 4.2 11.2 1.0
NE2 N:HIS462 4.2 12.8 1.0
FE N:FE600 4.2 21.2 1.0
CZ N:ARG457 4.2 10.8 1.0
N B:GLY14 4.3 14.2 1.0
ND1 N:HIS462 4.5 11.5 1.0
CD N:ARG457 4.8 11.7 1.0
CB B:THR12 4.8 11.7 1.0
NE2 N:HIS460 4.8 12.8 1.0
OH N:TYR447 4.8 21.4 1.0
C B:ALA13 4.8 13.9 1.0
O B:ALA13 4.9 14.1 1.0
CD B:PRO15 4.9 18.2 1.0
CG1 N:ILE491 4.9 16.4 1.0
CG2 N:ILE491 4.9 15.5 1.0
C7 N:FHB550 4.9 19.1 1.0
C B:THR12 4.9 11.8 1.0
NE N:ARG457 4.9 11.2 1.0
O B:HOH606 5.0 15.1 1.0

Fluorine binding site 4 out of 12 in 3pcf

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Fluorine binding site 4 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
N:F551

b:26.3
occ:1.00
 F3 N:FHB551 0.0 26.3 1.0
C3 N:FHB551 1.4 24.2 1.0
C2 N:FHB551 2.4 23.4 1.0
C4 N:FHB551 2.4 23.5 1.0
O4 N:FHB551 2.7 24.0 1.0
C1 N:FHB551 3.7 23.9 1.0
C5 N:FHB551 3.7 23.2 1.0
CD2 M:LEU320 3.9 15.4 1.0
NH2 M:ARG333 4.0 16.3 1.0
C6 N:FHB551 4.2 23.4 1.0
CD N:ARG333 4.2 16.8 1.0
NE M:ARG333 4.3 16.1 1.0
CZ M:ARG333 4.5 16.5 1.0
NE N:ARG333 4.6 16.7 1.0
CD1 M:LEU320 4.8 15.5 1.0
CG M:LEU320 4.8 15.5 1.0
C7 N:FHB551 4.9 24.7 1.0

Fluorine binding site 5 out of 12 in 3pcf

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Fluorine binding site 5 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F550

b:19.1
occ:1.00
 F3 O:FHB550 0.0 19.1 1.0
C3 O:FHB550 1.4 19.1 1.0
C2 O:FHB550 2.4 18.7 1.0
C4 O:FHB550 2.4 18.7 1.0
O4 O:FHB550 2.8 18.2 1.0
NE2 O:GLN477 3.0 7.1 1.0
CE1 O:HIS462 3.3 13.6 1.0
NH1 O:ARG457 3.5 10.8 1.0
CG2 C:THR12 3.5 11.0 1.0
C1 O:FHB550 3.7 18.9 1.0
C5 O:FHB550 3.7 18.9 1.0
CA C:GLY14 3.7 15.9 1.0
CD O:GLN477 3.8 9.8 1.0
CD1 O:ILE491 3.8 16.4 1.0
OE1 O:GLN477 4.0 8.7 1.0
O O:HOH851 4.0 17.3 1.0
NE2 O:HIS462 4.0 13.8 1.0
FE O:FE600 4.1 21.3 1.0
O C:THR12 4.2 11.6 1.0
C6 O:FHB550 4.2 18.8 1.0
N C:GLY14 4.2 14.0 1.0
ND1 O:HIS462 4.3 12.4 1.0
CZ O:ARG457 4.4 10.9 1.0
CD C:PRO15 4.6 17.9 1.0
C C:ALA13 4.7 13.8 1.0
CB C:THR12 4.8 11.5 1.0
C C:THR12 4.8 12.2 1.0
OH O:TYR324 4.8 11.7 1.0
O C:ALA13 4.8 14.3 1.0
OH O:TYR447 4.9 21.4 1.0
CG2 O:ILE491 4.9 15.8 1.0
C7 O:FHB550 4.9 19.2 1.0
NE2 O:HIS460 4.9 12.8 1.0
CD O:ARG457 5.0 11.6 1.0
NE O:ARG457 5.0 10.4 1.0

Fluorine binding site 6 out of 12 in 3pcf

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Fluorine binding site 6 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F551

b:26.4
occ:1.00
 F3 O:FHB551 0.0 26.4 1.0
C3 O:FHB551 1.4 24.1 1.0
C2 O:FHB551 2.4 23.1 1.0
C4 O:FHB551 2.4 23.3 1.0
O4 O:FHB551 2.7 24.0 1.0
C1 O:FHB551 3.7 23.6 1.0
C5 O:FHB551 3.7 23.1 1.0
NH2 N:ARG333 3.7 15.0 1.0
CD2 N:LEU320 4.0 15.3 1.0
CD O:ARG333 4.1 16.0 1.0
C6 O:FHB551 4.2 23.1 1.0
CZ N:ARG333 4.3 15.8 1.0
NE N:ARG333 4.4 16.7 1.0
CD1 N:LEU320 4.6 14.7 1.0
NE O:ARG333 4.7 16.6 1.0
CG N:LEU320 4.8 15.4 1.0
C7 O:FHB551 4.9 24.6 1.0

Fluorine binding site 7 out of 12 in 3pcf

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Fluorine binding site 7 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F550

b:19.2
occ:1.00
 F3 P:FHB550 0.0 19.2 1.0
C3 P:FHB550 1.4 19.0 1.0
C2 P:FHB550 2.4 18.6 1.0
C4 P:FHB550 2.4 18.8 1.0
O4 P:FHB550 2.7 18.1 1.0
NE2 P:GLN477 3.0 8.1 1.0
NH1 P:ARG457 3.1 10.7 1.0
CG2 D:THR12 3.6 9.8 1.0
CE1 P:HIS462 3.6 12.4 1.0
C5 P:FHB550 3.7 19.0 1.0
CD1 P:ILE491 3.7 15.8 1.0
C1 P:FHB550 3.7 18.8 1.0
CD P:GLN477 3.7 10.6 1.0
OE1 P:GLN477 3.7 9.8 1.0
CA D:GLY14 3.8 15.7 1.0
CZ P:ARG457 4.0 11.3 1.0
C6 P:FHB550 4.2 18.5 1.0
O P:HOH785 4.2 17.2 0.8
FE P:FE600 4.3 21.5 1.0
N D:GLY14 4.3 14.4 1.0
O D:THR12 4.3 11.4 1.0
NE2 P:HIS462 4.4 12.4 1.0
ND1 P:HIS462 4.5 12.1 1.0
CG2 P:ILE491 4.7 15.2 1.0
NE P:ARG457 4.8 11.1 1.0
NH2 P:ARG457 4.8 10.6 1.0
C D:ALA13 4.8 13.8 1.0
NE2 P:HIS460 4.8 13.2 1.0
CD D:PRO15 4.9 18.3 1.0
OH P:TYR447 4.9 21.9 1.0
CB D:THR12 4.9 11.3 1.0
C7 P:FHB550 4.9 19.1 1.0
CD P:ARG457 4.9 11.9 1.0
C D:THR12 4.9 12.3 1.0
CG1 P:ILE491 5.0 16.2 1.0

Fluorine binding site 8 out of 12 in 3pcf

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Fluorine binding site 8 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F551

b:26.3
occ:1.00
 F3 P:FHB551 0.0 26.3 1.0
C3 P:FHB551 1.4 24.4 1.0
C4 P:FHB551 2.4 23.7 1.0
C2 P:FHB551 2.4 23.3 1.0
O4 P:FHB551 2.7 23.7 1.0
NH2 R:ARG333 3.6 15.6 1.0
C1 P:FHB551 3.7 23.8 1.0
C5 P:FHB551 3.7 23.3 1.0
CD P:ARG333 4.1 16.0 1.0
CD2 R:LEU320 4.1 16.0 1.0
C6 P:FHB551 4.2 23.5 1.0
NE R:ARG333 4.2 16.5 1.0
CZ R:ARG333 4.2 16.2 1.0
CD1 R:LEU320 4.4 15.6 1.0
NE P:ARG333 4.6 16.1 1.0
CG R:LEU320 4.9 15.6 1.0
C7 P:FHB551 4.9 24.8 1.0

Fluorine binding site 9 out of 12 in 3pcf

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Fluorine binding site 9 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:F550

b:18.9
occ:1.00
 F3 Q:FHB550 0.0 18.9 1.0
C3 Q:FHB550 1.3 19.0 1.0
C2 Q:FHB550 2.4 18.7 1.0
C4 Q:FHB550 2.4 18.8 1.0
O4 Q:FHB550 2.7 18.4 1.0
NE2 Q:GLN477 3.1 9.4 1.0
CG2 E:THR12 3.3 10.4 1.0
NH1 Q:ARG457 3.3 10.4 1.0
CE1 Q:HIS462 3.4 12.4 1.0
CA E:GLY14 3.6 15.8 1.0
C5 Q:FHB550 3.7 19.1 1.0
C1 Q:FHB550 3.7 18.9 1.0
CD1 Q:ILE491 3.7 16.6 1.0
CD Q:GLN477 3.9 10.6 1.0
OE1 Q:GLN477 3.9 10.3 1.0
O E:THR12 4.1 11.6 1.0
N E:GLY14 4.1 14.2 1.0
O Q:HOH776 4.1 17.4 1.0
C6 Q:FHB550 4.2 18.5 1.0
FE Q:FE600 4.2 22.9 1.0
NE2 Q:HIS462 4.2 13.4 1.0
CZ Q:ARG457 4.3 11.8 1.0
ND1 Q:HIS462 4.4 12.1 1.0
CD E:PRO15 4.5 17.8 1.0
C E:ALA13 4.7 13.9 1.0
CB E:THR12 4.8 12.2 1.0
OH Q:TYR447 4.8 21.1 1.0
O E:ALA13 4.8 14.5 1.0
C E:THR12 4.9 12.1 1.0
C7 Q:FHB550 4.9 19.4 1.0
CG2 Q:ILE491 4.9 15.2 1.0
C E:GLY14 4.9 17.1 1.0
NE2 Q:HIS460 5.0 13.3 1.0
NH2 Q:ARG457 5.0 10.5 1.0

Fluorine binding site 10 out of 12 in 3pcf

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Fluorine binding site 10 out of 12 in the Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of Protocatechuate 3,4-Dioxygenase Complexed with 3-Fluro-4- Hydroxybenzoate within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:F551

b:26.3
occ:1.00
 F3 Q:FHB551 0.0 26.3 1.0
C3 Q:FHB551 1.4 24.2 1.0
C4 Q:FHB551 2.4 23.4 1.0
C2 Q:FHB551 2.4 23.3 1.0
O4 Q:FHB551 2.7 24.1 1.0
C5 Q:FHB551 3.7 23.3 1.0
C1 Q:FHB551 3.7 23.8 1.0
NH2 P:ARG333 3.7 15.4 1.0
CD2 P:LEU320 3.9 15.4 1.0
CD Q:ARG333 4.1 16.1 1.0
C6 Q:FHB551 4.2 23.3 1.0
NE P:ARG333 4.4 16.1 1.0
CZ P:ARG333 4.4 16.0 1.0
CD1 P:LEU320 4.6 15.6 1.0
NE Q:ARG333 4.7 16.4 1.0
CG P:LEU320 4.8 15.6 1.0
CG2 P:ILE328 4.8 15.4 1.0
C7 Q:FHB551 4.9 24.8 1.0

Reference:

A.M.Orville, N.Elango, J.D.Lipscomb, D.H.Ohlendorf. Structures of Competitive Inhibitor Complexes of Protocatechuate 3,4-Dioxygenase: Multiple Exogenous Ligand Binding Orientations Within the Active Site. Biochemistry V. 36 10039 1997.
ISSN: ISSN 0006-2960
PubMed: 9254599
DOI: 10.1021/BI970468N
Page generated: Wed Jul 31 21:39:04 2024

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