Atomistry » Sodium » PDB 7lsv-7m4l » 7m2l
Atomistry »
  Sodium »
    PDB 7lsv-7m4l »
      7m2l »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy