Sodium in PDB 7kxc: The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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 Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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 Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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 Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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: 7kxc 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) 39.57 / 1.51
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.13, 59.359, 67.477, 90, 95.16, 90
R / Rfree (%) 19.8 / 23.1

Other elements in 7kxc:

The structure of The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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) 1 atom
Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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 7kxc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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: 7kxc:

Sodium binding site 1 out of 1 in 7kxc

Go back to Sodium Binding Sites List in 7kxc
Sodium binding site 1 out of 1 in the The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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 Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One 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:25.7
occ:1.00
 O B:HOH706 1.9 22.7 1.0
O B:GLY232 2.4 15.8 1.0
O B:SER308 2.4 13.5 1.0
O B:HOH741 2.4 19.5 1.0
O B:PHE306 2.6 14.4 1.0
C B:GLY232 3.5 13.8 1.0
C B:PHE306 3.7 14.2 1.0
C B:SER308 3.7 12.7 1.0
O B:GLY268 3.7 12.3 1.0
CD B:PRO270 3.9 12.3 1.0
CB B:PHE306 3.9 15.0 1.0
CG B:PRO270 4.0 12.8 1.0
CA B:GLY232 4.0 12.7 1.0
CD2 B:PHE306 4.1 15.5 1.0
N B:SER308 4.1 12.9 1.0
CA B:PHE306 4.3 14.4 1.0
O B:LEU304 4.3 14.7 1.0
O B:VAL231 4.4 11.8 1.0
N B:PHE306 4.5 14.3 1.0
CG B:PHE306 4.5 15.3 1.0
CA B:SER308 4.5 12.5 1.0
C B:GLY268 4.6 12.0 1.0
N B:VAL309 4.6 12.2 1.0
CA B:VAL309 4.6 11.9 1.0
CB B:VAL309 4.6 12.1 1.0
N B:PRO307 4.6 13.7 1.0
N B:GLY233 4.6 13.6 1.0
OE2 B:GLU256 4.8 13.6 1.0
C B:PRO307 4.8 13.2 1.0
CA B:PRO307 4.9 13.3 1.0
N B:GLY232 4.9 12.4 1.0
C B:VAL231 5.0 11.6 1.0

Reference:

E.Hilario, M.F.Dunn, L.J.Mueller. The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'-Trifluoromethoxybenzenesulfonyl) -2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One of the Beta-Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring. To Be Published.
Page generated: Fri Dec 17 11:20:01 2021

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