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Sodium in PDB 6dz4: Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.

Enzymatic activity of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.

All present enzymatic activity of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.:
4.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site., PDB code: 6dz4 was solved by E.Hilario, M.F.Dunn, L.J.Mueller, L.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.94 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.509, 59.300, 67.325, 90.00, 94.69, 90.00
R / Rfree (%) 14.7 / 18.6

Other elements in 6dz4:

The structure of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. (pdb code 6dz4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site., PDB code: 6dz4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6dz4

Go back to Sodium Binding Sites List in 6dz4
Sodium binding site 1 out of 2 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:22.6
occ:1.00
 O B:HOH824 2.1 42.1 1.0
O B:THR71 3.0 13.1 1.0
O B:THR69 3.0 18.6 1.0
O B:HOH693 3.0 38.3 1.0
O B:THR66 3.4 17.1 1.0
OG1 B:THR66 3.5 17.1 1.0
CB B:THR66 3.9 15.2 1.0
O B:HOH841 3.9 38.5 1.0
C B:THR71 4.0 11.8 1.0
C B:THR69 4.0 16.3 1.0
C B:THR66 4.0 17.0 1.0
OG1 B:THR69 4.3 14.6 1.0
N B:THR71 4.4 11.5 1.0
N B:THR69 4.7 18.9 1.0
CA B:THR66 4.7 15.5 1.0
CA B:ARG70 4.8 14.9 0.5
C B:ARG70 4.8 14.5 0.5
CA B:ARG70 4.8 15.1 0.5
C B:ARG70 4.8 14.2 0.5
N B:ALA67 4.8 17.8 1.0
N B:ARG70 4.8 15.1 0.5
N B:ARG70 4.8 15.2 0.5
N B:THR72 4.8 11.5 1.0
CA B:THR71 4.8 10.7 1.0
O B:HOH710 4.8 56.5 1.0
CA B:THR69 4.9 17.4 1.0
O B:HOH517 4.9 14.3 1.0
CA B:ALA67 4.9 20.5 1.0
OG1 B:THR72 4.9 16.1 1.0

Sodium binding site 2 out of 2 in 6dz4

Go back to Sodium Binding Sites List in 6dz4
Sodium binding site 2 out of 2 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:15.2
occ:1.00
 O B:GLY232 2.2 15.4 1.0
O B:SER308 2.3 12.7 1.0
O B:HOH690 2.3 14.0 1.0
O B:HOH584 2.4 20.2 1.0
O B:PHE306 2.5 18.6 1.0
C B:GLY232 3.3 12.6 1.0
C B:SER308 3.5 12.6 1.0
C B:PHE306 3.6 16.7 1.0
CG B:PRO270 3.9 11.7 1.0
CA B:GLY232 4.0 11.7 1.0
N B:SER308 4.0 15.6 1.0
CD B:PRO270 4.0 11.3 1.0
O B:GLY268 4.1 12.3 1.0
CA B:SER308 4.4 14.1 1.0
OG B:SER297 4.4 20.6 1.0
CB B:PHE306 4.4 16.0 1.0
CA B:PHE306 4.4 16.4 1.0
O B:VAL231 4.4 11.5 1.0
N B:GLY233 4.4 12.2 1.0
CD2 B:PHE306 4.4 16.6 1.0
N B:VAL309 4.5 11.3 1.0
C B:PRO307 4.5 16.2 1.0
N B:PHE306 4.6 15.5 1.0
CA B:VAL309 4.6 11.2 1.0
N B:PRO307 4.6 15.6 1.0
CB B:VAL309 4.7 11.4 1.0
CA B:PRO307 4.7 15.7 1.0
O B:LEU304 4.7 18.0 1.0
CA B:GLY233 4.8 10.9 1.0
OE2 B:GLU256 4.8 13.7 1.0
N B:GLY232 4.9 10.7 1.0
CG B:PHE306 4.9 17.1 1.0
C B:VAL231 5.0 10.5 1.0

Reference:

E.Hilario, M.F.Dunn, L.J.Mueller, L.Fan. Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl] -Serine (Pls) at the Beta-Site. To Be Published.
Page generated: Tue Oct 8 08:12:56 2024

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