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Sodium in PDB 6xoy: Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate

Enzymatic activity of Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate

All present enzymatic activity of Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate:
4.2.1.20;

Protein crystallography data

The structure of Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate, PDB code: 6xoy was solved by R.S.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.67 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.45, 57.72, 67.27, 90, 95.47, 90
R / Rfree (%) 17.7 / 21.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate (pdb code 6xoy). 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 Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate, PDB code: 6xoy:

Sodium binding site 1 out of 1 in 6xoy

Go back to Sodium Binding Sites List in 6xoy
Sodium binding site 1 out of 1 in the Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Salmonella Typhimurium Tryptophan Synthase Complexed with D-Tryptophan and D-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:25.7
occ:1.00
 O B:HOH566 2.2 26.9 1.0
O B:GLY232 2.3 26.9 1.0
O B:SER308 2.3 21.9 1.0
O B:HOH674 2.4 28.5 1.0
O B:PHE306 2.6 25.7 1.0
HB3 B:PHE306 3.2 31.4 1.0
HD2 B:PHE306 3.3 32.0 1.0
C B:GLY232 3.4 29.2 1.0
HA2 B:GLY232 3.4 27.6 1.0
HD2 B:PRO270 3.5 26.2 1.0
HG3 B:PRO270 3.5 32.4 1.0
C B:SER308 3.5 27.4 1.0
C B:PHE306 3.7 25.4 1.0
H B:SER308 3.7 25.2 1.0
HG2 B:PRO270 3.8 32.4 1.0
HB B:VAL309 3.8 28.9 1.0
O B:GLY268 3.9 23.2 1.0
CG B:PRO270 3.9 26.9 1.0
HD3 B:PRO270 3.9 26.2 1.0
CD B:PRO270 3.9 21.8 1.0
HA B:VAL309 4.0 24.9 1.0
CA B:GLY232 4.0 23.0 1.0
H B:PHE306 4.0 33.9 1.0
CB B:PHE306 4.0 26.2 1.0
N B:SER308 4.1 21.0 1.0
CD2 B:PHE306 4.1 26.6 1.0
HA2 B:GLY233 4.3 27.5 1.0
CA B:PHE306 4.3 29.9 1.0
O B:LEU304 4.4 26.3 1.0
O B:VAL231 4.4 25.6 1.0
N B:VAL309 4.4 22.6 1.0
HG23 B:VAL309 4.5 34.0 1.0
CA B:SER308 4.5 21.0 1.0
CA B:VAL309 4.5 20.8 1.0
CB B:VAL309 4.5 24.0 1.0
HG12 B:VAL231 4.5 30.4 1.0
N B:PHE306 4.5 28.2 1.0
N B:GLY233 4.5 23.9 1.0
CG B:PHE306 4.6 26.0 1.0
HA B:PRO307 4.6 29.0 1.0
HA3 B:GLY232 4.7 27.6 1.0
N B:PRO307 4.7 24.4 1.0
HD2 B:PRO257 4.7 25.0 1.0
C B:PRO307 4.8 25.7 1.0
HB2 B:PHE306 4.8 31.4 1.0
OE2 B:GLU256 4.8 24.4 1.0
C B:GLY268 4.8 23.6 1.0
HA B:SER308 4.8 25.2 1.0
N B:GLY232 4.9 20.6 1.0
CA B:GLY233 4.9 22.9 1.0
CA B:PRO307 4.9 24.1 1.0
C B:VAL231 5.0 26.4 1.0

Reference:

R.S.Phillips, A.P.Harris. Structural Basis of the Stereochemistry of Inhibition of Tryptophan Synthase By Tryptophan and Derivatives. Biochemistry V. 60 231 2021.
ISSN: ISSN 0006-2960
PubMed: 33428374
DOI: 10.1021/ACS.BIOCHEM.0C00635
Page generated: Tue Oct 8 14:53:14 2024

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