Sodium in PDB 7m3s: 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 1.55 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 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 1.55 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 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 1.55 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 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 1.55 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: 7m3s 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 / 1.55
*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 / R_free (%)*	17.7 / 20.1

Other elements in 7m3s:

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 1.55 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)	6 atoms
Chlorine	(Cl)	2 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 1.55 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 7m3s). 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 1.55 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: 7m3s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7m3s

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Sodium Binding Sites List in 7m3s

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 1.55 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 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 1.55 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:Na411 b:16.3 occ:1.00	O	B:SER308	2.2	12.0	1.0
	O	B:GLY232	2.3	17.3	1.0
	O	B:HOH631	2.4	16.3	1.0
	O	B:HOH530	2.5	23.2	1.0
	O	B:PHE306	2.5	20.5	1.0
	C	B:GLY232	3.4	17.9	1.0
	C	B:SER308	3.5	14.7	1.0
	C	B:PHE306	3.6	23.3	1.0
	CG	B:PRO270	3.8	13.3	1.0
	CD2	B:PHE306	3.8	24.0	1.0
	CD	B:PRO270	3.9	13.8	1.0
	CA	B:GLY232	4.0	15.8	1.0
	N	B:SER308	4.0	15.0	1.0
	O	B:GLY268	4.1	13.8	1.0
	CB	B:PHE306	4.2	25.9	1.0
	CA	B:PHE306	4.3	28.2	1.0
	CA	B:SER308	4.4	15.4	1.0
	CG	B:PHE306	4.4	25.3	1.0
	N	B:VAL309	4.4	12.8	1.0
	O	B:VAL231	4.4	15.3	1.0
	CA	B:VAL309	4.4	13.8	1.0
	N	B:GLY233	4.5	13.3	1.0
	CB	B:VAL309	4.5	14.3	1.0
	N	B:PHE306	4.5	26.6	1.0
	O	B:LEU304	4.6	16.8	1.0
	N	B:PRO307	4.6	21.1	1.0
	C	B:PRO307	4.6	20.5	1.0
	CE2	B:PHE306	4.7	21.9	1.0
	CA	B:PRO307	4.8	18.7	1.0
	CA	B:GLY233	4.8	12.0	1.0
	OE2	B:GLU256	4.8	12.5	1.0
	N	B:GLY232	4.9	10.7	1.0
	C	B:VAL231	5.0	12.9	1.0
	C	B:GLY268	5.0	14.1	1.0

Sodium binding site 2 out of 2 in 7m3s

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Sodium Binding Sites List in 7m3s

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 1.55 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 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 1.55 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:Na412 b:29.6 occ:1.00	OD2	B:ASP305	2.4	31.8	1.0
	O	B:HOH642	2.4	28.4	1.0
	O	B:HOH755	2.4	28.0	1.0
	O	B:SER297	2.6	26.8	1.0
	OE1	B:GLU296	2.6	41.1	1.0
	O	B:HOH678	2.7	36.6	1.0
	CG	B:ASP305	3.1	36.1	1.0
	OD1	B:ASP305	3.3	30.4	1.0
	C	B:SER297	3.5	26.6	1.0
	CD	B:GLU296	3.6	37.7	1.0
	O	B:HOH532	3.6	30.4	1.0
	CG	B:GLU296	3.9	52.1	1.0
	N	B:SER297	3.9	24.2	1.0
	OG	B:SER297	4.0	30.5	1.0
	O	B:HOH801	4.1	35.0	1.0
	CA	B:SER297	4.2	23.9	1.0
	CB	B:GLU296	4.3	41.0	1.0
	O	B:HOH734	4.4	37.6	1.0
	N	B:TYR298	4.5	15.7	1.0
	CB	B:ASP305	4.5	25.9	1.0
	C	B:GLU296	4.5	30.9	1.0
	CA	B:TYR298	4.7	14.9	1.0
	CA	B:GLU296	4.7	32.5	1.0
	CB	B:SER297	4.7	22.4	1.0
	OE2	B:GLU296	4.7	49.4	1.0
	O	B:ASP305	4.8	30.3	1.0
	OG1	B:THR165	4.9	28.4	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 1.55 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: Tue Oct 8 17:49:03 2024

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