Sodium in PDB 3sth: Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii

All present enzymatic activity of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii:
1.2.1.12;

The structure of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii, PDB code: 3sth was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), B.L.Staker, T.E.Edwards, B.Sankaran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.367, 104.322, 146.625, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.6

The binding sites of Sodium atom in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii (pdb code 3sth). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii, PDB code: 3sth:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii


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 Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:25.3 occ:1.00 O A:ARG24 2.2 23.1 1.0 O A:VAL27 2.3 22.3 1.0 O A:ALA21 2.4 23.6 1.0 O A:HOH434 2.5 11.4 1.0 O A:HOH402 2.7 21.9 1.0 C A:ARG24 3.4 24.6 1.0 C A:ALA21 3.4 24.8 1.0 C A:VAL27 3.5 21.7 1.0 CA A:MET22 3.7 28.4 1.0 O A:MET22 3.8 29.8 1.0 C A:MET22 3.9 28.2 1.0 N A:MET22 4.0 26.9 1.0 N A:ARG24 4.0 26.3 1.0 CA A:ARG24 4.3 25.9 1.0 N A:GLY25 4.3 25.1 1.0 CA A:GLY25 4.3 25.1 1.0 N A:VAL27 4.4 19.5 1.0 N A:GLU28 4.4 23.5 1.0 OE1 A:GLU28 4.4 42.1 1.0 CA A:VAL27 4.4 19.6 1.0 CA A:GLU28 4.4 26.8 1.0 C A:GLY25 4.6 23.4 1.0 CA A:ALA21 4.6 24.4 1.0 N A:GLU23 4.7 27.8 1.0 CB A:VAL27 4.7 19.4 1.0 CB A:ARG24 4.8 25.7 1.0 CB A:MET22 5.0 30.2 1.0 CD A:GLU28 5.0 38.3 1.0 O A:GLY25 5.0 23.7 1.0 N A:ASP26 5.0 21.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii


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 Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:22.5 occ:1.00 O B:VAL27 2.1 21.3 1.0 O B:ARG24 2.3 22.4 1.0 O B:HOH421 2.3 24.8 1.0 O B:HOH615 2.4 28.6 1.0 O B:ALA21 2.4 21.5 1.0 C B:VAL27 3.3 20.8 1.0 C B:ARG24 3.5 23.4 1.0 C B:ALA21 3.5 21.4 1.0 CA B:MET22 3.8 24.0 1.0 N B:MET22 4.1 22.5 1.0 O B:MET22 4.1 26.1 1.0 C B:MET22 4.1 24.5 1.0 N B:ARG24 4.2 24.3 1.0 N B:GLU28 4.2 21.6 1.0 CA B:GLU28 4.2 22.3 1.0 N B:VAL27 4.3 20.3 1.0 CA B:VAL27 4.3 19.7 1.0 CA B:ARG24 4.3 24.4 1.0 N B:GLY25 4.4 23.6 1.0 CA B:GLY25 4.4 23.6 1.0 CG B:GLU28 4.5 29.7 1.0 O B:HOH617 4.6 21.6 1.0 CB B:ARG24 4.6 24.5 1.0 CA B:ALA21 4.6 20.5 1.0 CB B:VAL27 4.7 18.6 1.0 C B:GLY25 4.7 23.0 1.0 CE B:MET22 4.9 31.6 1.0 N B:GLU23 4.9 24.4 1.0 CB B:ALA21 5.0 19.6 1.0 CB B:GLU28 5.0 24.1 1.0 SD B:MET22 5.0 31.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:32.0 occ:1.00 O C:ARG24 2.2 24.2 0.5 O C:ARG24 2.3 24.1 0.5 O C:VAL27 2.3 26.4 1.0 O C:HOH429 2.4 21.1 1.0 O C:ALA21 2.5 27.1 1.0 O C:MET22 3.3 31.9 1.0 C C:ARG24 3.4 24.4 0.5 C C:ARG24 3.5 24.4 0.5 C C:VAL27 3.5 26.0 1.0 C C:ALA21 3.6 25.3 1.0 C C:MET22 3.7 29.5 1.0 CA C:MET22 3.7 28.2 1.0 OE1 C:GLU28 3.7 40.9 1.0 N C:ARG24 3.9 23.1 0.5 N C:ARG24 4.0 23.1 0.5 N C:MET22 4.1 25.7 1.0 CA C:ARG24 4.2 23.6 0.5 CA C:ARG24 4.2 23.6 0.5 NZ C:LYS71 4.3 45.7 1.0 CD C:GLU28 4.4 40.1 1.0 N C:VAL27 4.4 24.7 1.0 N C:GLU28 4.4 27.6 1.0 CA C:GLU28 4.4 28.8 1.0 N C:GLY25 4.5 25.7 1.0 CA C:VAL27 4.5 24.6 1.0 N C:GLU23 4.6 28.9 1.0 CB C:ARG24 4.6 22.5 0.5 CA C:GLY25 4.6 26.8 1.0 C C:GLU23 4.7 31.8 1.0 C C:GLY25 4.8 26.9 1.0 CB C:VAL27 4.8 23.1 1.0 CB C:ARG24 4.8 22.7 0.5 CA C:ALA21 4.9 23.6 1.0 OE2 C:GLU28 4.9 43.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:23.4 occ:1.00 O D:ARG24 2.2 25.6 0.5 O D:ARG24 2.2 25.6 0.5 O D:VAL27 2.4 28.2 1.0 O D:ALA21 2.5 25.3 1.0 O D:HOH544 2.5 26.7 1.0 O D:HOH377 2.6 29.5 1.0 O D:MET22 3.3 28.3 1.0 C D:ARG24 3.4 26.2 0.5 C D:ARG24 3.4 26.3 0.5 C D:ALA21 3.5 24.6 1.0 C D:VAL27 3.6 27.8 1.0 C D:MET22 3.6 26.4 1.0 CA D:MET22 3.6 25.8 1.0 N D:MET22 4.0 24.4 1.0 N D:ARG24 4.0 25.2 0.5 N D:ARG24 4.0 25.1 0.5 NZ D:LYS71 4.2 44.9 1.0 CA D:ARG24 4.2 25.4 0.5 CA D:ARG24 4.3 25.7 0.5 OE1 D:GLU28 4.4 43.8 1.0 N D:VAL27 4.4 26.9 1.0 N D:GLY25 4.4 27.6 1.0 CD D:GLU28 4.4 42.5 1.0 N D:GLU28 4.4 29.1 1.0 CA D:GLU28 4.4 30.6 1.0 N D:GLU23 4.5 25.3 1.0 CB D:ARG24 4.5 24.3 0.5 OE2 D:GLU28 4.5 45.5 1.0 CA D:VAL27 4.5 26.9 1.0 CA D:GLY25 4.6 28.7 1.0 C D:GLU23 4.6 26.4 1.0 C D:GLY25 4.8 28.4 1.0 CA D:ALA21 4.8 23.4 1.0 CB D:VAL27 4.8 25.7 1.0 CB D:ARG24 4.8 24.7 0.5 CB D:MET22 4.9 26.0 1.0

R.Dubey, B.L.Staker, I.T.Foe, M.Bogyo, P.J.Myler, H.M.Ngo, M.J.Gubbels. Membrane Skeletal Association and Post-Translational Allosteric Regulation of Toxoplasma Gondii GAPDH1. Mol.Microbiol. V. 103 618 2017.
ISSN: ISSN 0950-382X
PubMed: 27859784
DOI: 10.1111/MMI.13577