Sodium in PDB 2ez4: Pyruvate Oxidase Variant F479W

All present enzymatic activity of Pyruvate Oxidase Variant F479W:
1.2.3.3;

The structure of Pyruvate Oxidase Variant F479W, PDB code: 2ez4 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)	29.59 / 2.03
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.346, 154.180, 165.432, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.6

The structure of Pyruvate Oxidase Variant F479W also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyruvate Oxidase Variant F479W (pdb code 2ez4). 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, PDB code: 2ez4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyruvate Oxidase Variant F479W


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1614 b:11.2 occ:0.50 OE1 A:GLN455 2.7 11.7 1.0 O A:MET452 2.8 12.4 1.0 O A:HOH1692 2.8 13.6 1.0 CD A:GLN455 3.6 12.8 1.0 C A:MET452 3.9 12.1 1.0 CD2 A:HIS58 4.0 10.0 1.0 NE2 A:GLN455 4.0 11.4 1.0 N A:THR453 4.7 12.0 1.0 CA A:THR453 4.7 13.0 1.0 NE2 A:HIS58 4.7 11.1 1.0 O A:SER451 4.7 11.2 1.0 CA A:MET452 4.7 11.7 1.0 CG A:GLN455 4.8 12.3 1.0 CG A:HIS58 4.8 11.6 1.0 OE2 A:GLU60 4.9 15.7 1.0

Sodium binding site 2 out of 2 in the Pyruvate Oxidase Variant F479W


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1611 b:6.5 occ:0.50 O B:MET452 2.7 13.4 1.0 OE1 B:GLN455 3.0 16.6 1.0 O B:HOH1688 3.1 15.0 1.0 C B:MET452 3.8 13.5 1.0 CD B:GLN455 3.9 14.5 1.0 CD2 B:HIS58 4.3 11.3 1.0 NE2 B:GLN455 4.4 12.6 1.0 O B:SER451 4.4 12.7 1.0 CA B:MET452 4.5 13.4 1.0 N B:THR453 4.7 12.6 1.0 CA B:THR453 4.8 12.5 1.0 NE2 B:HIS58 4.9 12.0 1.0 OE2 B:GLU60 5.0 15.6 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