Sodium in PDB 6bve: Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid

All present enzymatic activity of Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid:
5.3.1.1;

The structure of Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid, PDB code: 6bve was solved by P.Jimenez-Sandoval, E.Castro-Torres, L.G.Brieba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.47 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.880, 73.099, 85.175, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19

The binding sites of Sodium atom in the Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid (pdb code 6bve). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid, PDB code: 6bve:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:20.8 occ:1.00 O A:HOH536 2.3 27.6 1.0 O A:ILE219 2.4 18.1 1.0 O A:MET214 2.4 21.5 1.0 O A:GLN216 2.4 18.4 1.0 C A:MET214 3.5 19.5 1.0 C A:GLN216 3.5 19.6 1.0 C A:ILE219 3.5 16.7 1.0 O A:HOH405 3.9 25.6 1.0 O A:HOH547 3.9 24.6 1.0 N A:ILE219 4.0 20.5 1.0 N A:GLN216 4.1 18.5 1.0 CA A:ILE219 4.2 16.6 1.0 CA A:MET214 4.2 16.2 1.0 CA A:PRO217 4.2 22.5 1.0 C A:ALA215 4.3 26.0 1.0 C A:PRO217 4.3 18.3 1.0 O A:PRO217 4.3 19.7 1.0 N A:PRO217 4.3 20.2 1.0 CA A:GLN216 4.4 17.4 1.0 CB A:ILE219 4.5 15.5 1.0 N A:ALA215 4.5 17.5 1.0 N A:ASP220 4.6 15.4 1.0 CA A:ALA215 4.7 21.1 1.0 O A:ALA215 4.7 27.8 1.0 CE A:MET214 4.8 18.8 1.0 O A:ILE213 4.8 16.1 1.0 CA A:ASP220 4.9 15.1 1.0 CB A:MET214 4.9 13.5 1.0 N A:GLU218 4.9 17.1 1.0

Sodium binding site 2 out of 2 in the Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Triosephosphate Isomerase of Synechocystis in Complex with 2- Phosphoglycolic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:16.1 occ:1.00 O B:GLN216 2.3 16.9 1.0 O B:MET214 2.4 17.3 1.0 O B:HOH543 2.4 22.0 1.0 O B:ILE219 2.4 13.7 1.0 O B:HOH541 2.4 31.0 1.0 O B:HOH457 2.4 29.1 1.0 C B:MET214 3.5 14.2 1.0 C B:GLN216 3.5 18.6 1.0 C B:ILE219 3.5 14.8 1.0 O B:HOH408 3.8 23.2 1.0 O B:HOH549 3.9 30.1 1.0 N B:ILE219 4.0 14.8 1.0 N B:GLN216 4.1 18.4 1.0 C B:ALA215 4.1 18.8 1.0 CA B:ILE219 4.2 13.8 1.0 CA B:MET214 4.3 14.3 1.0 O B:PRO217 4.3 16.4 1.0 C B:PRO217 4.3 17.4 1.0 CA B:PRO217 4.3 16.5 1.0 O B:ALA215 4.4 19.2 1.0 CA B:GLN216 4.4 15.2 1.0 N B:ALA215 4.4 13.6 1.0 N B:PRO217 4.4 14.5 1.0 CB B:ILE219 4.5 14.2 1.0 CA B:ALA215 4.5 15.6 1.0 N B:ASP220 4.6 12.1 1.0 CE B:MET214 4.7 17.4 1.0 O B:ILE213 4.8 12.9 1.0 N B:GLU218 4.9 15.5 1.0 CA B:ASP220 4.9 16.1 1.0 C B:GLU218 5.0 13.6 1.0

E.Castro-Torres, P.Jimenez-Sandoval, E.Fernandez-De Gortari, M.Lopez-Castillo, N.Baruch-Torres, M.Lopez-Hidalgo, A.Peralta-Castro, C.Diaz-Quezada, R.R.Sotelo-Mundo, C.G.Benitez-Cardoza, L.M.Espinoza-Fonseca, A.Ochoa-Leyva, L.G.Brieba. Structural Basis For the Limited Response to Oxidative and Thiol-Conjugating Agents By Triosephosphate Isomerase From the Photosynthetic Bacteriasynechocystis. Front Mol Biosci V. 5 103 2018.
ISSN: ESSN 2296-889X
PubMed: 30538993
DOI: 10.3389/FMOLB.2018.00103