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Sodium 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
Fluorine (F) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7m2l

Go back to Sodium Binding Sites List in 7m2l
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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
B:Na508

b:16.4
occ:1.00
 O B:GLY232 2.2 17.7 1.0
O B:SER308 2.3 12.9 1.0
O B:HOH624 2.4 24.0 1.0
O B:HOH746 2.4 16.8 1.0
O B:PHE306 2.5 20.8 1.0
C B:GLY232 3.4 18.5 1.0
C B:SER308 3.5 15.8 1.0
C B:PHE306 3.6 25.1 1.0
O B:HOH602 3.7 58.6 1.0
CG B:PRO270 3.8 14.2 1.0
CD2 B:PHE306 3.8 24.1 1.0
CD B:PRO270 3.9 13.9 1.0
CA B:GLY232 4.0 15.2 1.0
N B:SER308 4.0 14.8 1.0
O B:GLY268 4.1 14.9 1.0
CB B:PHE306 4.1 26.3 1.0
CA B:PHE306 4.3 29.5 1.0
CG B:PHE306 4.4 28.0 1.0
CA B:SER308 4.4 14.5 1.0
N B:VAL309 4.4 14.0 1.0
CA B:VAL309 4.5 13.8 1.0
O B:VAL231 4.5 16.2 1.0
N B:GLY233 4.5 14.3 1.0
O B:LEU304 4.5 16.9 1.0
N B:PHE306 4.5 28.6 1.0
CB B:VAL309 4.5 15.1 1.0
N B:PRO307 4.6 23.1 1.0
C B:PRO307 4.6 20.7 1.0
CE2 B:PHE306 4.7 22.7 1.0
OE2 B:GLU256 4.8 13.5 1.0
CA B:GLY233 4.9 10.7 1.0
CA B:PRO307 4.9 20.6 1.0
N B:GLY232 4.9 11.4 1.0
C B:GLY268 5.0 13.6 1.0
C B:VAL231 5.0 14.3 1.0

Sodium binding site 2 out of 2 in 7m2l

Go back to Sodium Binding Sites List in 7m2l
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
B:Na509

b:29.8
occ:1.00
 OE2 B:GLU296 2.4 37.0 1.0
OD1 B:ASP305 2.4 31.3 1.0
O B:HOH820 2.4 27.6 1.0
O B:HOH736 2.5 28.6 1.0
O B:SER297 2.5 28.0 1.0
O B:HOH752 2.8 38.3 1.0
CG B:ASP305 3.1 31.5 1.0
OD2 B:ASP305 3.2 32.8 1.0
CD B:GLU296 3.2 38.6 1.0
C B:SER297 3.5 28.0 1.0
CG B:GLU296 3.6 37.8 1.0
O B:HOH650 3.6 28.0 1.0
N B:SER297 3.8 26.6 1.0
OG B:SER297 3.9 32.4 1.0
CA B:SER297 4.1 28.4 1.0
O B:HOH886 4.2 36.6 1.0
OE1 B:GLU296 4.3 31.2 1.0
O B:HOH753 4.3 37.1 1.0
N B:TYR298 4.4 19.6 1.0
CB B:ASP305 4.5 23.6 1.0
C B:GLU296 4.5 34.0 1.0
CB B:SER297 4.6 25.3 1.0
CA B:TYR298 4.7 18.5 1.0
CB B:GLU296 4.7 29.6 1.0
CA B:GLU296 4.7 30.8 1.0
O B:HOH866 4.7 35.6 1.0
O B:ASP305 4.8 31.5 1.0
OG1 B:THR165 4.9 26.6 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: Tue Oct 8 17:48:30 2024

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