Sodium in PDB 6vnt: Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution

Enzymatic activity of Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution

All present enzymatic activity of Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution:
4.2.1.20;

Protein crystallography data

The structure of Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution, PDB code: 6vnt was solved by E.Hilario, L.Fan, 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)*	36.31 / 1.25
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	183.022, 59.382, 67.322, 90, 94.92, 90
*R / R_free (%)*	15.3 / 18.1

Other elements in 6vnt:

The structure of Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution (pdb code 6vnt). 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 Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution, PDB code: 6vnt:

Sodium binding site 1 out of 1 in 6vnt

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Sodium Binding Sites List in 6vnt

Sodium binding site 1 out of 1 in the Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na506 b:23.3 occ:1.00	O	B:HOH748	2.2	10.0	0.2
	O	B:HOH748	2.7	16.0	0.8
	OE2	B:GLU256	2.8	13.0	1.0
	O	B:GLY232	2.9	13.9	1.0
	O	B:SER308	3.1	12.7	1.0
	O	B:VAL231	3.3	11.6	1.0
	O	B:GLY268	3.4	11.4	1.0
	CD	B:GLU256	3.7	11.3	1.0
	C	B:GLY232	3.7	12.0	1.0
	CD	B:PRO270	3.8	12.8	1.0
	CG	B:GLU256	3.9	10.4	1.0
	CB	B:VAL309	3.9	10.6	1.0
	CG	B:PRO270	4.0	15.7	1.0
	CA	B:GLY232	4.0	10.6	1.0
	CG2	B:VAL309	4.0	12.0	1.0
	C	B:VAL231	4.1	9.4	1.0
	C	B:SER308	4.2	11.3	1.0
	CG1	B:VAL231	4.2	10.8	1.0
	CA	B:VAL309	4.4	10.3	1.0
	O	B:PHE306	4.4	14.8	1.0
	N	B:GLY232	4.5	9.9	1.0
	CB	B:GLU256	4.5	9.6	1.0
	C	B:GLY268	4.5	10.4	1.0
	CD	B:PRO257	4.8	9.0	1.0
	N	B:VAL309	4.8	10.6	1.0
	N	B:PRO270	4.8	12.3	1.0
	CB	B:VAL231	4.9	9.5	1.0
	OE1	B:GLU256	4.9	12.1	1.0
	N	B:GLY233	5.0	11.0	1.0
	CA	B:ALA269	5.0	10.2	1.0

Reference:

E.Hilario, L.Fan, M.F.Dunn, L.J.Mueller. Tryptophan Synthase in Complex with Inhibitor N-(4'-Trifluoromethoxybenzenesulfonyl) -2-Amino-1-Ethylphosphate (F9F) at the Alpha-Site, Aminoacrylate at the Beta Site, and Sodium Ion at the Metal Coordination Site at 1.25 Angstrom Resolution. To Be Published.

Page generated: Tue Oct 8 14:24:57 2024

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