Sodium in PDB 2ez8: Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Lactyl-Thiamin Diphosphate

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

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Lactyl-Thiamin Diphosphate, PDB code: 2ez8 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)	24.96 / 1.96
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.133, 154.462, 165.656, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.2

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Lactyl-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-Lactyl-Thiamin Diphosphate (pdb code 2ez8). 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-Lactyl-Thiamin Diphosphate, PDB code: 2ez8:
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-Lactyl-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-Lactyl-Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1513 b:5.6 occ:0.50 O A:MET452 2.7 8.5 1.0 OE1 A:GLN455 2.8 8.6 1.0 O A:HOH1689 3.0 9.8 1.0 CD A:GLN455 3.7 9.0 1.0 C A:MET452 3.8 8.5 1.0 NE2 A:GLN455 4.1 7.6 1.0 CD2 A:HIS58 4.2 5.5 1.0 O A:SER451 4.6 9.2 1.0 N A:THR453 4.6 8.4 1.0 CA A:MET452 4.6 8.6 1.0 CA A:THR453 4.6 9.1 1.0 NE2 A:HIS58 4.8 6.8 1.0 CG A:GLN455 4.9 8.5 1.0 CG A:HIS58 5.0 7.8 1.0 OE2 A:GLU60 5.0 10.1 1.0

Sodium binding site 2 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Lactyl-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-Lactyl-Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1511 b:6.0 occ:0.50 OE1 B:GLN455 2.7 10.4 1.0 O B:MET452 2.8 7.6 1.0 O B:HOH1686 3.0 9.1 1.0 CD B:GLN455 3.6 10.9 1.0 C B:MET452 3.8 8.2 1.0 NE2 B:GLN455 4.0 9.2 1.0 CD2 B:HIS58 4.1 8.9 1.0 CA B:THR453 4.6 6.8 1.0 O B:SER451 4.6 9.4 1.0 N B:THR453 4.6 6.9 1.0 CA B:MET452 4.7 8.3 1.0 NE2 B:HIS58 4.7 6.9 1.0 CG B:GLN455 4.8 9.0 1.0 CG B:HIS58 4.8 8.2 1.0 OE2 B:GLU60 5.0 11.9 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