Sodium in PDB 7ly8: The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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 Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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 Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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 Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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: 7ly8 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)*	36.85 / 1.55
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	183.645, 58.8, 67.205, 90, 95.13, 90
*R / R_free (%)*	17.3 / 19.4

Other elements in 7ly8:

The structure of The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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:

Fluorine	(F)	9 atoms
Chlorine	(Cl)	5 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 Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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 7ly8). 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 Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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: 7ly8:

Sodium binding site 1 out of 1 in 7ly8

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Sodium Binding Sites List in 7ly8

Sodium binding site 1 out of 1 in the The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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 Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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:Na408 b:13.0 occ:1.00	O	B:GLY232	2.3	11.5	1.0
	O	B:SER308	2.3	11.8	1.0
	O	B:HOH647	2.4	14.3	1.0
	O	B:PHE306	2.4	14.4	1.0
	O	B:HOH565	2.4	12.9	1.0
	C	B:GLY232	3.4	11.3	1.0
	C	B:SER308	3.5	12.6	1.0
	C	B:PHE306	3.6	14.5	1.0
	CG	B:PRO270	3.7	12.3	1.0
	N	B:SER308	4.0	13.8	1.0
	CD	B:PRO270	4.0	12.1	1.0
	CA	B:GLY232	4.1	11.2	1.0
	O	B:GLY268	4.3	13.5	1.0
	CB	B:PHE306	4.3	14.7	1.0
	O	B:LEU304	4.3	15.8	1.0
	CA	B:SER308	4.3	12.9	1.0
	CD2	B:PHE306	4.3	14.3	1.0
	CA	B:PHE306	4.4	15.2	1.0
	OG	B:SER297	4.4	16.8	1.0
	N	B:PHE306	4.5	15.2	1.0
	C	B:PRO307	4.5	14.9	1.0
	N	B:VAL309	4.5	11.8	1.0
	O	B:VAL231	4.5	10.9	1.0
	N	B:PRO307	4.5	15.0	1.0
	N	B:GLY233	4.5	11.2	1.0
	CA	B:VAL309	4.6	11.3	1.0
	CA	B:PRO307	4.6	15.0	1.0
	CG	B:PHE306	4.7	14.8	1.0
	CB	B:VAL309	4.7	11.4	1.0
	OE2	B:GLU256	4.8	12.7	1.0
	CA	B:GLY233	4.8	11.1	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 Two Molecules of N-(4'-Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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 Apr 7 15:02:04 2023

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