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Sodium in PDB 6wdu: The External Aldimine Form of the Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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 Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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 Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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 Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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: 6wdu 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) 36.91 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.655, 59.415, 67.345, 90, 94.89, 90
R / Rfree (%) 16.2 / 19.5

Sodium Binding Sites:

The binding sites of Sodium atom in the The External Aldimine Form of the Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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 6wdu). 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 External Aldimine Form of the Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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: 6wdu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6wdu

Go back to Sodium Binding Sites List in 6wdu
Sodium binding site 1 out of 2 in the The External Aldimine Form of the Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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 Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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:Na407

b:16.4
occ:1.00
O B:GLY232 2.2 15.0 1.0
O B:SER308 2.3 13.7 1.0
O B:HOH704 2.3 15.5 1.0
O B:HOH628 2.4 19.1 1.0
O B:PHE306 2.5 16.1 1.0
C B:GLY232 3.3 13.2 1.0
C B:SER308 3.5 13.0 1.0
C B:PHE306 3.6 15.7 1.0
CG B:PRO270 3.9 13.3 1.0
N B:SER308 4.0 15.4 1.0
CA B:GLY232 4.0 12.0 1.0
CD B:PRO270 4.0 12.8 1.0
O B:GLY268 4.1 13.0 1.0
CA B:SER308 4.3 13.9 1.0
CB B:PHE306 4.4 15.3 1.0
O B:VAL231 4.4 12.1 1.0
CA B:PHE306 4.4 15.9 1.0
CD2 B:PHE306 4.4 15.4 1.0
OG B:SER297 4.4 17.9 1.0
N B:GLY233 4.4 12.5 1.0
N B:VAL309 4.5 12.1 1.0
C B:PRO307 4.5 15.8 1.0
CA B:VAL309 4.6 11.7 1.0
N B:PRO307 4.6 15.2 1.0
N B:PHE306 4.6 15.2 1.0
CA B:PRO307 4.6 16.4 1.0
CB B:VAL309 4.7 11.5 1.0
CA B:GLY233 4.7 12.1 1.0
O B:LEU304 4.8 16.1 1.0
OE2 B:GLU256 4.8 13.3 1.0
CG B:PHE306 4.9 15.9 1.0
N B:GLY232 4.9 12.1 1.0
C B:VAL231 5.0 11.1 1.0

Sodium binding site 2 out of 2 in 6wdu

Go back to Sodium Binding Sites List in 6wdu
Sodium binding site 2 out of 2 in the The External Aldimine Form of the Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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 2 of The External Aldimine Form of the Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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:Na408

b:22.3
occ:1.00
O B:HOH832 2.1 35.8 1.0
O B:THR71 2.9 13.2 1.0
O B:THR69 3.0 19.1 1.0
O B:HOH756 3.1 36.7 1.0
O B:THR66 3.3 18.4 1.0
OG1 B:THR66 3.4 17.4 1.0
CB B:THR66 3.8 15.8 1.0
O B:HOH848 4.0 34.9 1.0
C B:THR71 4.0 12.3 1.0
C B:THR66 4.0 17.7 1.0
C B:THR69 4.0 18.2 1.0
OG1 B:THR69 4.2 17.1 1.0
N B:THR71 4.4 12.2 1.0
O B:HOH532 4.5 37.2 1.0
CA B:THR66 4.6 16.1 1.0
N B:THR69 4.6 19.7 1.0
N B:ALA67 4.7 18.6 1.0
C B:ARG70 4.8 16.5 1.0
CA B:ARG70 4.8 17.4 1.0
N B:ARG70 4.8 17.7 1.0
CA B:THR71 4.8 12.2 1.0
N B:THR72 4.8 12.2 1.0
CA B:THR69 4.8 18.6 1.0
O B:HOH675 4.9 14.8 1.0
CA B:ALA67 4.9 20.4 1.0
OG1 B:THR72 5.0 15.4 1.0

Reference:

E.Hilario, L.Fan, M.F.Dunn, L.J.Mueller. The External Aldimine Form of the Salmonella Thypi Wild-Type Tryptophan Synthase in Open Conformation Showing Multiple Side Chain Conformations For the Residue Beta Q114 and Sodium Ion at the Metal Coordination 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: Tue Oct 8 14:33:29 2024

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