Sodium in PDB 7jmq: The External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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 External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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 External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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 External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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: 7jmq 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) 38.86 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.38, 58.244, 67.154, 90, 94.33, 90
R / Rfree (%) 15.8 / 18.4

Other elements in 7jmq:

The structure of The External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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:

Caesium (Cs) 2 atoms
Chlorine (Cl) 1 atom
Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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 7jmq). 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 External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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: 7jmq:

Sodium binding site 1 out of 1 in 7jmq

Go back to Sodium Binding Sites List in 7jmq
Sodium binding site 1 out of 1 in the The External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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 External Aldimine Form of the Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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:Na429

b:5.8
occ:1.00
O B:HOH502 2.2 5.9 1.0
O B:GLY232 3.0 10.9 1.0
OE1 B:GLU256 3.1 8.4 1.0
O B:HOH592 3.1 13.3 1.0
O B:VAL231 3.2 7.5 1.0
O B:GLY268 3.4 8.4 1.0
O B:SER308 3.5 8.0 1.0
CD B:PRO270 3.7 7.9 1.0
C B:GLY232 3.8 9.3 1.0
CG B:PRO270 3.9 8.1 1.0
CD B:GLU256 3.9 8.1 1.0
C B:VAL231 4.0 7.5 1.0
CG B:GLU256 4.0 7.7 1.0
CG1 B:VAL231 4.1 6.9 1.0
CA B:GLY232 4.1 8.8 1.0
CB B:VAL309 4.3 8.0 1.0
N B:GLY232 4.4 8.1 1.0
CB B:GLU256 4.4 7.1 1.0
CG2 B:VAL309 4.4 8.1 1.0
O B:PHE306 4.5 9.8 1.0
C B:GLY268 4.6 8.0 1.0
C B:SER308 4.6 8.1 1.0
CD B:PRO257 4.6 6.9 1.0
N B:PRO270 4.7 7.8 1.0
CB B:VAL231 4.8 6.9 1.0
CA B:VAL309 4.9 7.8 1.0
CA B:ALA269 4.9 7.9 1.0

Reference:

E.Hilario, M.F.Dunn, L.J.Mueller. The External Aldimine Form of Mutant Beta-S377A Salmonella Thypi Tryptophan Synthase in Open Conformation Showing Dual Side Chain Conformations For the Residue Beta-Q114, Sodium Ion at the Metal Coordination Site, and F9 Inhibitor at the Alpha-Site. 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: Sat Aug 21 17:22:15 2021

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