Sodium in PDB 2clk: Tryptophan Synthase in Complex with D-Glyceraldehyde 3- Phosphate (G3P)

All present enzymatic activity of Tryptophan Synthase in Complex with D-Glyceraldehyde 3- Phosphate (G3P):
4.2.1.20;

The structure of Tryptophan Synthase in Complex with D-Glyceraldehyde 3- Phosphate (G3P), PDB code: 2clk was solved by H.Ngo, R.Harris, N.Kimmich, P.Casino, D.Niks, L.Blumenstein, T.R.Barends, V.Kulik, M.Weyand, I.Schlichting, M.F.Dunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.5
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.045, 59.558, 67.409, 90.00, 94.56, 90.00
R / Rfree (%)	17.9 / 20.2

The binding sites of Sodium atom in the Tryptophan Synthase in Complex with D-Glyceraldehyde 3- Phosphate (G3P) (pdb code 2clk). 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 Tryptophan Synthase in Complex with D-Glyceraldehyde 3- Phosphate (G3P), PDB code: 2clk:

Sodium binding site 1 out of 1 in the Tryptophan Synthase in Complex with D-Glyceraldehyde 3- Phosphate (G3P)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tryptophan Synthase in Complex with D-Glyceraldehyde 3- Phosphate (G3P) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1393 b:10.3 occ:1.00 O B:GLY232 2.3 10.7 1.0 O B:SER308 2.4 9.9 1.0 O B:HOH2237 2.4 11.5 1.0 O B:HOH2243 2.4 14.0 1.0 O B:PHE306 2.4 14.4 1.0 C B:GLY232 3.4 9.2 1.0 C B:SER308 3.5 9.9 1.0 C B:PHE306 3.6 12.3 1.0 CG B:PRO270 3.8 10.0 1.0 CD B:PRO270 3.9 9.9 1.0 N B:SER308 3.9 11.7 1.0 O B:GLY268 4.1 11.8 1.0 CA B:GLY232 4.1 9.5 1.0 CB B:PHE306 4.3 11.5 1.0 CA B:SER308 4.3 10.4 1.0 OG B:SER297 4.4 17.8 1.0 CA B:PHE306 4.4 12.7 1.0 CD2 B:PHE306 4.4 14.6 1.0 C B:PRO307 4.4 13.3 1.0 O B:VAL231 4.5 9.4 1.0 N B:GLY233 4.5 8.9 1.0 N B:VAL309 4.5 9.8 1.0 N B:PRO307 4.6 11.7 1.0 CA B:VAL309 4.6 8.1 1.0 N B:PHE306 4.6 12.8 1.0 O B:LEU304 4.6 14.6 1.0 CB B:VAL309 4.6 9.6 1.0 CA B:PRO307 4.6 11.5 1.0 CA B:GLY233 4.8 7.9 1.0 OE2 B:GLU256 4.8 11.2 1.0 CG B:PHE306 4.8 12.4 1.0 N B:GLY232 5.0 7.7 1.0

H.Ngo, R.Harris, N.Kimmich, P.Casino, D.Niks, L.Blumenstein, T.R.Barends, V.Kulik, M.Weyand, I.Schlichting, M.F.Dunn. Synthesis and Characterization of Allosteric Probes of Substrate Channeling in the Tryptophan Synthase Bienzyme Complex. Biochemistry V. 46 7713 2007.
ISSN: ISSN 0006-2960
PubMed: 17559195
DOI: 10.1021/BI700385F