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Fluorine in PDB 4fp1: P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

Enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

All present enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid:
5.1.2.2;

Protein crystallography data

The structure of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid, PDB code: 4fp1 was solved by A.D.Lietzan, M.St.Maurice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.68
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 148.870, 148.870, 169.640, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.3

Other elements in 4fp1:

The structure of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid (pdb code 4fp1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid, PDB code: 4fp1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4fp1

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Fluorine binding site 1 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:24.1
occ:0.50
 F07 A:BFM402 0.0 24.1 0.5
C06 A:BFM402 1.4 26.0 0.5
F09 A:BFM402 2.2 25.7 0.5
F08 A:BFM402 2.2 23.6 0.5
F12 A:BFM402 2.3 31.1 0.5
C02 A:BFM402 2.3 26.3 0.5
C10 A:BFM402 2.6 28.1 0.5
O04 A:BFM402 2.6 26.4 0.5
C03 A:BFM402 2.9 26.0 0.5
F13 A:BFM402 3.0 27.9 0.5
O01 A:BFM402 3.5 24.3 0.5
CG2 A:THR24 3.6 22.3 1.0
CG2 A:VAL29 3.7 26.9 1.0
F11 A:BFM402 3.7 30.3 0.5
CG1 A:VAL22 3.8 23.2 1.0
CD1 B:LEU93 3.9 21.6 1.0
O05 A:BFM402 4.1 25.5 0.5
ND2 A:ASN197 4.5 15.2 1.0
CE A:LYS166 4.6 19.0 1.0
CB A:VAL22 4.6 23.8 1.0
O A:HOH732 4.6 24.9 1.0
CB A:VAL29 4.7 25.4 1.0
CD2 B:LEU93 4.8 21.2 1.0
CG B:LEU93 4.9 19.8 1.0
O A:VAL22 5.0 23.8 1.0
CB A:THR24 5.0 21.8 0.5

Fluorine binding site 2 out of 12 in 4fp1

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Fluorine binding site 2 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:23.6
occ:0.50
 F08 A:BFM402 0.0 23.6 0.5
C06 A:BFM402 1.4 26.0 0.5
F09 A:BFM402 2.2 25.7 0.5
F07 A:BFM402 2.2 24.1 0.5
C02 A:BFM402 2.3 26.3 0.5
F12 A:BFM402 2.5 31.1 0.5
O01 A:BFM402 2.5 24.3 0.5
C10 A:BFM402 2.8 28.1 0.5
F11 A:BFM402 3.4 30.3 0.5
CG2 A:VAL29 3.6 26.9 1.0
C03 A:BFM402 3.7 26.0 0.5
CD1 B:LEU93 3.7 21.6 1.0
CE2 A:PHE52 3.8 12.5 1.0
CD1 A:TYR54 3.8 15.3 1.0
F13 A:BFM402 3.9 27.9 0.5
CZ A:PHE52 4.0 12.5 1.0
O04 A:BFM402 4.0 26.4 0.5
CB B:LEU93 4.3 18.9 1.0
CE1 A:TYR54 4.3 15.9 1.0
O05 A:BFM402 4.5 25.5 0.5
CG B:LEU93 4.5 19.8 1.0
CB A:VAL29 4.7 25.4 1.0
CG1 A:VAL29 4.9 26.6 1.0
CG A:TYR54 4.9 14.1 1.0
CD2 B:LEU93 4.9 21.2 1.0
O A:HOH751 5.0 31.9 1.0

Fluorine binding site 3 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 3 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:25.7
occ:0.50
 F09 A:BFM402 0.0 25.7 0.5
C06 A:BFM402 1.3 26.0 0.5
F07 A:BFM402 2.2 24.1 0.5
F08 A:BFM402 2.2 23.6 0.5
C02 A:BFM402 2.2 26.3 0.5
C03 A:BFM402 2.7 26.0 0.5
O01 A:BFM402 2.7 24.3 0.5
O04 A:BFM402 2.7 26.4 0.5
CD1 B:LEU93 3.5 21.6 1.0
CD2 B:LEU93 3.5 21.2 1.0
O05 A:BFM402 3.5 25.5 0.5
C10 A:BFM402 3.5 28.1 0.5
O A:HOH751 3.6 31.9 1.0
O A:HOH732 3.6 24.9 1.0
ND2 A:ASN197 3.8 15.2 1.0
F12 A:BFM402 3.8 31.1 0.5
CG B:LEU93 3.8 19.8 1.0
CB B:LEU93 3.9 18.9 1.0
OE1 A:GLU247 4.0 10.9 0.5
F13 A:BFM402 4.2 27.9 0.5
O A:HOH729 4.5 19.0 1.0
F11 A:BFM402 4.5 30.3 0.5
OE1 A:GLU247 4.8 13.8 0.5
CG2 A:THR24 4.8 22.3 1.0
CD1 A:TYR54 4.8 15.3 1.0
CG A:ASN197 4.9 14.8 1.0
CA B:LEU93 4.9 18.6 1.0
CE1 A:TYR54 5.0 15.9 1.0

Fluorine binding site 4 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 4 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:30.3
occ:0.50
 F11 A:BFM402 0.0 30.3 0.5
C10 A:BFM402 1.3 28.1 0.5
F12 A:BFM402 2.0 31.1 0.5
F13 A:BFM402 2.1 27.9 0.5
C02 A:BFM402 2.4 26.3 0.5
O01 A:BFM402 2.7 24.3 0.5
C06 A:BFM402 3.3 26.0 0.5
F08 A:BFM402 3.4 23.6 0.5
C03 A:BFM402 3.5 26.0 0.5
CD2 A:LEU298 3.6 15.9 1.0
CE2 A:PHE52 3.6 12.5 1.0
CD1 A:LEU298 3.7 13.4 1.0
F07 A:BFM402 3.7 24.1 0.5
O05 A:BFM402 3.8 25.5 0.5
CZ A:PHE52 3.9 12.5 1.0
CG A:LEU298 4.1 13.0 1.0
CD1 A:LEU319 4.3 19.7 1.0
O04 A:BFM402 4.3 26.4 0.5
CD1 A:LEU321 4.4 24.9 1.0
F09 A:BFM402 4.5 25.7 0.5
CD2 A:LEU321 4.6 23.1 1.0
CD2 A:PHE52 4.6 13.0 1.0
NE2 A:HIS297 4.7 11.0 1.0
CG A:LEU321 4.8 21.9 1.0
O A:HOH750 4.8 21.0 1.0
CD2 A:LEU319 4.9 21.0 1.0
CG1 A:VAL22 5.0 23.2 1.0
CE1 A:PHE52 5.0 13.3 1.0

Fluorine binding site 5 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 5 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:31.1
occ:0.50
 F12 A:BFM402 0.0 31.1 0.5
C10 A:BFM402 1.3 28.1 0.5
F11 A:BFM402 2.0 30.3 0.5
F13 A:BFM402 2.1 27.9 0.5
F07 A:BFM402 2.3 24.1 0.5
C06 A:BFM402 2.5 26.0 0.5
F08 A:BFM402 2.5 23.6 0.5
C02 A:BFM402 2.5 26.3 0.5
O01 A:BFM402 3.4 24.3 0.5
CG1 A:VAL22 3.6 23.2 1.0
C03 A:BFM402 3.6 26.0 0.5
CG2 A:VAL29 3.7 26.9 1.0
F09 A:BFM402 3.8 25.7 0.5
CB A:VAL22 3.9 23.8 1.0
O04 A:BFM402 3.9 26.4 0.5
CB A:VAL29 4.0 25.4 1.0
CG2 A:VAL22 4.1 23.3 1.0
CZ A:PHE52 4.1 12.5 1.0
CG1 A:VAL29 4.1 26.6 1.0
CE2 A:PHE52 4.3 12.5 1.0
O05 A:BFM402 4.5 25.5 0.5

Fluorine binding site 6 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 6 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:27.9
occ:0.50
 F13 A:BFM402 0.0 27.9 0.5
C10 A:BFM402 1.3 28.1 0.5
F12 A:BFM402 2.1 31.1 0.5
F11 A:BFM402 2.1 30.3 0.5
C02 A:BFM402 2.4 26.3 0.5
C03 A:BFM402 2.6 26.0 0.5
O04 A:BFM402 2.9 26.4 0.5
F07 A:BFM402 3.0 24.1 0.5
C06 A:BFM402 3.2 26.0 0.5
O05 A:BFM402 3.3 25.5 0.5
CG1 A:VAL22 3.4 23.2 1.0
CD1 A:LEU319 3.5 19.7 1.0
O01 A:BFM402 3.5 24.3 0.5
O A:HOH750 3.7 21.0 1.0
CE A:LYS166 3.8 19.0 1.0
F08 A:BFM402 3.9 23.6 0.5
F09 A:BFM402 4.2 25.7 0.5
CB A:VAL22 4.2 23.8 1.0
CG2 A:VAL22 4.2 23.3 1.0
NZ A:LYS166 4.3 14.9 1.0
CD2 A:LEU298 4.6 15.9 1.0
O A:HOH732 4.8 24.9 1.0
CG A:LEU319 4.8 18.6 1.0
CD2 A:LEU319 5.0 21.0 1.0
O A:HOH733 5.0 20.1 1.0

Fluorine binding site 7 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 7 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:33.5
occ:0.50
 F07 B:BFM402 0.0 33.5 0.5
C06 B:BFM402 1.3 34.9 0.5
F08 B:BFM402 2.2 32.3 0.5
F09 B:BFM402 2.2 32.0 0.5
C02 B:BFM402 2.3 36.2 1.0
O01 B:BFM402 2.7 34.4 1.0
C03 B:BFM402 2.9 38.2 1.0
O05 B:BFM402 2.9 43.0 1.0
CD1 A:LEU93 3.3 25.8 1.0
CD2 A:LEU93 3.5 26.8 1.0
C10 B:BFM402 3.6 38.7 1.0
O B:HOH686 3.7 29.6 1.0
CG A:LEU93 3.7 26.3 1.0
O B:HOH690 3.7 41.4 1.0
CB A:LEU93 3.8 22.4 1.0
O04 B:BFM402 3.8 39.0 1.0
ND2 B:ASN197 3.9 20.7 1.0
O B:HOH682 4.0 29.8 1.0
F12 B:BFM402 4.0 38.9 0.5
F11 B:BFM402 4.2 36.8 0.5
OE2 B:GLU247 4.2 13.9 0.5
O B:HOH548 4.6 22.7 1.0
CG2 B:THR24 4.6 26.3 1.0
F13 B:BFM402 4.6 38.1 0.5
CD1 B:TYR54 4.8 21.0 1.0
CA A:LEU93 4.8 22.3 1.0
CG2 B:VAL29 5.0 32.4 1.0
CE1 B:TYR54 5.0 20.5 1.0

Fluorine binding site 8 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 8 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:32.3
occ:0.50
 F08 B:BFM402 0.0 32.3 0.5
C06 B:BFM402 1.4 34.9 0.5
F07 B:BFM402 2.2 33.5 0.5
F09 B:BFM402 2.2 32.0 0.5
C02 B:BFM402 2.4 36.2 1.0
F12 B:BFM402 2.5 38.9 0.5
O05 B:BFM402 2.6 43.0 1.0
C10 B:BFM402 2.9 38.7 1.0
C03 B:BFM402 3.0 38.2 1.0
CG2 B:THR24 3.6 26.3 1.0
O01 B:BFM402 3.6 34.4 1.0
F11 B:BFM402 3.6 36.8 0.5
CG1 B:VAL22 3.8 30.9 1.0
CG2 B:VAL29 3.8 32.4 1.0
CD1 A:LEU93 3.9 25.8 1.0
F13 B:BFM402 4.0 38.1 0.5
O04 B:BFM402 4.2 39.0 1.0
CE B:LYS166 4.5 25.5 1.0
ND2 B:ASN197 4.5 20.7 1.0
CB B:VAL22 4.6 30.3 1.0
CB B:VAL29 4.6 32.2 1.0
O B:HOH682 4.8 29.8 1.0
CG A:LEU93 4.9 26.3 1.0
CD2 A:LEU93 4.9 26.8 1.0
CB B:THR24 5.0 26.8 1.0

Fluorine binding site 9 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 9 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:32.0
occ:0.50
 F09 B:BFM402 0.0 32.0 0.5
C06 B:BFM402 1.4 34.9 0.5
F07 B:BFM402 2.2 33.5 0.5
F08 B:BFM402 2.2 32.3 0.5
C02 B:BFM402 2.3 36.2 1.0
O01 B:BFM402 2.6 34.4 1.0
F11 B:BFM402 2.7 36.8 0.5
C10 B:BFM402 2.8 38.7 1.0
F12 B:BFM402 3.2 38.9 0.5
CG2 B:VAL29 3.6 32.4 1.0
C03 B:BFM402 3.7 38.2 1.0
CE2 B:PHE52 3.7 17.2 1.0
CD1 A:LEU93 3.9 25.8 1.0
CD1 B:TYR54 3.9 21.0 1.0
CZ B:PHE52 3.9 16.5 1.0
O05 B:BFM402 4.1 43.0 1.0
F13 B:BFM402 4.1 38.1 0.5
CE1 B:TYR54 4.4 20.5 1.0
CB A:LEU93 4.4 22.4 1.0
CB B:VAL29 4.6 32.2 1.0
O04 B:BFM402 4.6 39.0 1.0
O B:HOH690 4.7 41.4 1.0
CG A:LEU93 4.7 26.3 1.0
CG1 B:VAL29 4.9 30.0 1.0
CG B:TYR54 5.0 18.2 1.0

Fluorine binding site 10 out of 12 in 4fp1

Go back to Fluorine Binding Sites List in 4fp1
Fluorine binding site 10 out of 12 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:36.8
occ:0.50
 F11 B:BFM402 0.0 36.8 0.5
C10 B:BFM402 1.3 38.7 1.0
F12 B:BFM402 2.1 38.9 0.5
F13 B:BFM402 2.2 38.1 0.5
C02 B:BFM402 2.4 36.2 1.0
F09 B:BFM402 2.7 32.0 0.5
O01 B:BFM402 2.8 34.4 1.0
C06 B:BFM402 3.0 34.9 0.5
CE2 B:PHE52 3.1 17.2 1.0
CZ B:PHE52 3.3 16.5 1.0
F08 B:BFM402 3.6 32.3 0.5
CD1 B:LEU298 3.7 17.3 1.0
C03 B:BFM402 3.8 38.2 1.0
CD2 B:PHE52 4.1 15.5 1.0
O04 B:BFM402 4.2 39.0 1.0
CD2 B:LEU298 4.2 17.1 1.0
F07 B:BFM402 4.2 33.5 0.5
CD1 B:LEU321 4.3 26.3 1.0
O05 B:BFM402 4.5 43.0 1.0
CG B:LEU298 4.5 14.9 1.0
CE1 B:PHE52 4.5 16.0 1.0
CD2 B:LEU321 4.6 27.0 1.0
CG B:LEU321 4.9 26.1 1.0
NE2 B:HIS297 5.0 15.6 1.0

Reference:

M.Nagar, A.D.Lietzan, M.St Maurice, S.L.Bearne. Potent Inhibition of Mandelate Racemase By A Fluorinated Substrate-Product Analogue with A Novel Binding Mode. Biochemistry V. 53 1169 2014.
ISSN: ISSN 0006-2960
PubMed: 24472022
DOI: 10.1021/BI401703H
Page generated: Thu Aug 1 01:40:02 2024

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