Sodium in PDB 2ezt: Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate

All present enzymatic activity of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate:
1.2.3.3;

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate, PDB code: 2ezt was solved by G.Wille, D.Meyer, A.Steinmetz, E.Hinze, R.Golbik, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.07 / 2.29
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.790, 154.022, 165.320, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.7

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate (pdb code 2ezt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate, PDB code: 2ezt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1514 b:2.0 occ:0.50 O A:MET452 2.7 7.7 1.0 OE1 A:GLN455 2.7 5.0 1.0 O A:HOH1688 2.9 4.4 1.0 CD A:GLN455 3.6 6.2 1.0 C A:MET452 3.7 7.8 1.0 NE2 A:GLN455 4.0 5.5 1.0 CD2 A:HIS58 4.2 2.6 1.0 O A:SER451 4.6 8.7 1.0 N A:THR453 4.6 7.4 1.0 CA A:MET452 4.6 7.7 1.0 CA A:THR453 4.7 6.8 1.0 CG A:GLN455 4.8 5.8 1.0 NE2 A:HIS58 4.9 3.3 1.0 OE2 A:GLU60 4.9 10.8 1.0 CG A:HIS58 5.0 5.1 1.0

Sodium binding site 2 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1511 b:2.0 occ:0.50 OE1 B:GLN455 2.7 8.7 1.0 O B:MET452 2.7 7.0 1.0 O B:HOH1682 2.9 4.9 1.0 CD B:GLN455 3.6 7.0 1.0 C B:MET452 3.8 7.5 1.0 NE2 B:GLN455 4.0 4.9 1.0 CD2 B:HIS58 4.1 5.8 1.0 O B:SER451 4.6 8.7 1.0 N B:THR453 4.6 6.3 1.0 CA B:THR453 4.7 6.4 1.0 CA B:MET452 4.7 7.7 1.0 NE2 B:HIS58 4.8 7.0 1.0 CG B:GLN455 4.8 7.5 1.0 CG B:HIS58 4.8 6.5 1.0 OE2 B:GLU60 5.0 8.1 1.0

G.Wille, D.Meyer, A.Steinmetz, E.Hinze, R.Golbik, K.Tittmann. The Catalytic Cycle of A Thiamin Diphosphate Enzyme Examined By Cryocrystallography. Nat.Chem.Biol. V. 2 324 2006.
ISSN: ISSN 1552-4450
PubMed: 16680160
DOI: 10.1038/NCHEMBIO788