Fluorine in PDB 7m2l: The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring

Enzymatic activity of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring

All present enzymatic activity of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring:
4.2.1.20;

Protein crystallography data

The structure of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring, PDB code: 7m2l was solved by E.Hilario, M.F.Dunn, L.J.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.41 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.518, 58.598, 67.098, 90, 95.18, 90
R / Rfree (%) 17.4 / 20.2

Other elements in 7m2l:

The structure of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring (pdb code 7m2l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring, PDB code: 7m2l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7m2l

Go back to Fluorine Binding Sites List in 7m2l
Fluorine binding site 1 out of 6 in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:35.7
occ:1.00
 F9 A:F6F301 0.0 35.7 1.0
C8 A:F6F301 1.3 37.6 1.0
F10 A:F6F301 2.1 35.5 1.0
F11 A:F6F301 2.1 38.3 1.0
O7 A:F6F301 2.2 34.4 1.0
O A:ALA129 3.1 21.4 1.0
O B:HOH769 3.2 24.2 1.0
CB B:PRO18 3.3 22.8 1.0
O B:HOH830 3.4 27.6 1.0
C1 A:F6F301 3.5 31.7 1.0
O A:HOH540 3.5 36.0 1.0
CB A:ALA59 3.7 33.0 1.0
CG B:PRO18 3.8 23.0 1.0
CB A:ALA129 3.9 22.0 1.0
C A:ALA129 3.9 20.4 1.0
CA A:ALA129 3.9 20.6 1.0
CA B:PRO18 4.0 20.7 1.0
C6 A:F6F301 4.1 32.0 1.0
C2 A:F6F301 4.5 33.7 1.0
CG1 A:ILE153 4.5 36.0 1.0
N B:GLN19 4.8 21.3 1.0
C B:PRO18 4.9 19.9 1.0

Fluorine binding site 2 out of 6 in 7m2l

Go back to Fluorine Binding Sites List in 7m2l
Fluorine binding site 2 out of 6 in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:35.5
occ:1.00
 F10 A:F6F301 0.0 35.5 1.0
C8 A:F6F301 1.3 37.6 1.0
F9 A:F6F301 2.1 35.7 1.0
F11 A:F6F301 2.1 38.3 1.0
O7 A:F6F301 2.2 34.4 1.0
C6 A:F6F301 2.8 32.0 1.0
C1 A:F6F301 2.9 31.7 1.0
CG1 A:ILE153 3.2 36.0 1.0
O B:HOH769 3.3 24.2 1.0
CA A:ALA129 3.5 20.6 1.0
CD2 A:LEU127 3.5 25.7 1.0
CD1 A:ILE153 3.6 38.4 1.0
O A:ALA129 3.7 21.4 1.0
CB A:ALA129 3.8 22.0 1.0
C A:ALA129 4.1 20.4 1.0
C5 A:F6F301 4.2 33.5 1.0
C2 A:F6F301 4.3 33.7 1.0
O B:HOH830 4.4 27.6 1.0
CB A:ILE153 4.5 31.1 1.0
CD1 A:LEU127 4.6 24.9 1.0
O A:HOH486 4.6 28.0 1.0
N A:ALA129 4.6 18.4 1.0
CG A:LEU127 4.7 25.9 1.0
O A:HOH540 4.8 36.0 1.0
CD2 A:LEU100 4.8 28.1 1.0
O A:VAL128 5.0 18.0 1.0

Fluorine binding site 3 out of 6 in 7m2l

Go back to Fluorine Binding Sites List in 7m2l
Fluorine binding site 3 out of 6 in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:38.3
occ:1.00
 F11 A:F6F301 0.0 38.3 1.0
C8 A:F6F301 1.3 37.6 1.0
F10 A:F6F301 2.1 35.5 1.0
F9 A:F6F301 2.1 35.7 1.0
O7 A:F6F301 2.2 34.4 1.0
C1 A:F6F301 2.6 31.7 1.0
C6 A:F6F301 2.8 32.0 1.0
O A:HOH540 3.0 36.0 1.0
CZ A:PHE212 3.5 43.1 1.0
CD1 A:ILE153 3.6 38.4 1.0
O B:HOH830 3.6 27.6 1.0
CG1 A:ILE153 3.7 36.0 1.0
C2 A:F6F301 3.8 33.7 1.0
C5 A:F6F301 4.0 33.5 1.0
CE1 A:PHE212 4.1 37.6 1.0
O B:HOH769 4.2 24.2 1.0
CE2 A:PHE212 4.4 48.8 1.0
CD1 A:LEU177 4.6 45.0 1.0
CB A:ALA59 4.7 33.0 1.0
CG2 A:ILE153 4.7 34.8 1.0
C3 A:F6F301 4.7 32.8 1.0
CB A:ILE153 4.7 31.1 1.0
C4 A:F6F301 4.8 33.3 1.0
CD2 A:LEU177 4.9 43.2 1.0
CB B:PRO18 5.0 22.8 1.0

Fluorine binding site 4 out of 6 in 7m2l

Go back to Fluorine Binding Sites List in 7m2l
Fluorine binding site 4 out of 6 in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:33.0
occ:1.00
 F9 B:F6F502 0.0 33.0 1.0
C8 B:F6F502 1.3 29.1 1.0
F10 B:F6F502 2.1 27.1 1.0
F11 B:F6F502 2.1 32.2 1.0
O7 B:F6F502 2.2 26.1 1.0
C2 B:F6F502 2.8 23.4 1.0
C1 B:F6F502 2.9 23.4 1.0
OH B:TYR186 3.1 22.5 1.0
CE2 B:TYR186 3.5 21.3 1.0
CD1 B:LEU188 3.6 17.1 1.0
CZ B:TYR186 3.8 21.3 1.0
CD1 B:LEU174 4.0 29.4 1.0
CG B:LEU188 4.0 17.9 1.0
C3 B:F6F502 4.1 22.8 1.0
CG B:LEU174 4.2 23.5 1.0
C6 B:F6F502 4.2 24.4 1.0
CD2 B:LEU174 4.3 30.0 1.0
CB B:CYS170 4.6 22.2 1.0
SG B:CYS170 4.7 23.9 1.0
CD2 B:LEU188 4.7 17.3 1.0
CD2 B:TYR186 4.7 17.4 1.0
CD B:PRO194 4.8 14.1 1.0
O B:CYS170 4.9 24.1 1.0
O B:PHE280 4.9 15.7 1.0
CA B:GLY193 5.0 12.0 1.0

Fluorine binding site 5 out of 6 in 7m2l

Go back to Fluorine Binding Sites List in 7m2l
Fluorine binding site 5 out of 6 in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:27.1
occ:1.00
 F10 B:F6F502 0.0 27.1 1.0
C8 B:F6F502 1.3 29.1 1.0
F11 B:F6F502 2.1 32.2 1.0
F9 B:F6F502 2.1 33.0 1.0
O7 B:F6F502 2.2 26.1 1.0
O B:PHE280 3.1 15.7 1.0
C B:PHE280 3.3 17.8 1.0
CD1 B:LEU174 3.4 29.4 1.0
C1 B:F6F502 3.5 23.4 1.0
CA B:PHE280 3.5 19.1 1.0
CD B:PRO194 3.9 14.1 1.0
CB B:PHE280 4.0 20.8 1.0
N B:GLY281 4.1 14.6 1.0
C2 B:F6F502 4.1 23.4 1.0
CA B:GLY193 4.3 12.0 1.0
CG B:LEU174 4.3 23.5 1.0
C6 B:F6F502 4.5 24.4 1.0
CD2 B:LEU174 4.6 30.0 1.0
CD1 B:PHE280 4.7 23.4 1.0
CA B:GLY281 4.7 15.8 1.0
CD1 B:LEU188 4.7 17.1 1.0
N B:PHE280 4.8 17.9 1.0
CG B:PHE280 4.8 22.9 1.0
N B:PRO194 4.9 13.0 1.0

Fluorine binding site 6 out of 6 in 7m2l

Go back to Fluorine Binding Sites List in 7m2l
Fluorine binding site 6 out of 6 in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two of the Beta- Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:32.2
occ:1.00
 F11 B:F6F502 0.0 32.2 1.0
C8 B:F6F502 1.3 29.1 1.0
F10 B:F6F502 2.1 27.1 1.0
F9 B:F6F502 2.1 33.0 1.0
O7 B:F6F502 2.2 26.1 1.0
C1 B:F6F502 2.7 23.4 1.0
C2 B:F6F502 3.0 23.4 1.0
CB B:CYS170 3.3 22.2 1.0
CD1 B:PHE280 3.5 23.4 1.0
SG B:CYS170 3.6 23.9 1.0
C6 B:F6F502 3.7 24.4 1.0
CB B:PHE280 4.0 20.8 1.0
CA B:PHE280 4.0 19.1 1.0
C3 B:F6F502 4.1 22.8 1.0
CD1 B:LEU174 4.2 29.4 1.0
CG B:PHE280 4.2 22.9 1.0
CA B:CYS170 4.3 21.6 1.0
CE1 B:PHE280 4.5 28.4 1.0
O B:PHE280 4.5 15.7 1.0
OH B:TYR186 4.5 22.5 1.0
C B:PHE280 4.5 17.8 1.0
C B:CYS170 4.6 26.2 1.0
C5 B:F6F502 4.6 29.9 1.0
O B:CYS170 4.7 24.1 1.0
C4 B:F6F502 4.8 22.0 1.0
CG B:LEU174 4.9 23.5 1.0

Reference:

E.Hilario, M.F.Dunn, L.J.Mueller. The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. To Be Published.
Page generated: Fri Aug 2 09:16:18 2024

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