Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Hydroxyethyl-Thiamin Diphosphate, PDB code: 2ezt:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1510 b:6.1 occ:1.00 O1A A:TDM1611 2.1 7.3 1.0 OD1 A:ASP447 2.1 3.9 1.0 OD1 A:ASN474 2.1 7.3 1.0 O3B A:TDM1611 2.2 7.2 1.0 O A:GLN476 2.2 6.0 1.0 O A:HOH2083 2.2 3.3 1.0 CG A:ASN474 3.1 4.9 1.0 PB A:TDM1611 3.3 5.8 1.0 CG A:ASP447 3.3 6.1 1.0 PA A:TDM1611 3.3 4.4 1.0 ND2 A:ASN474 3.3 4.7 1.0 C A:GLN476 3.3 5.4 1.0 O3A A:TDM1611 3.5 6.0 1.0 O2B A:TDM1611 3.8 4.9 1.0 N A:ASP447 3.8 8.3 1.0 OD2 A:ASP447 3.9 8.1 1.0 N A:GLN476 4.0 5.4 1.0 O A:PHE472 4.1 7.8 1.0 N A:GLY448 4.1 7.6 1.0 CA A:GLN476 4.2 5.3 1.0 O7 A:TDM1611 4.2 6.6 1.0 N A:TYR477 4.3 5.4 1.0 N A:GLY478 4.3 5.5 1.0 N A:ASN474 4.4 7.2 1.0 CA A:TYR477 4.4 5.7 1.0 CB A:ASN474 4.4 5.2 1.0 CB A:ASP447 4.4 6.9 1.0 O2A A:TDM1611 4.5 6.2 1.0 CA A:ASP447 4.5 7.5 1.0 CZ A:PHE497 4.6 6.4 1.0 O1B A:TDM1611 4.6 5.7 1.0 C A:GLY446 4.7 9.0 1.0 CA A:GLY446 4.7 8.7 1.0 N A:CYS475 4.7 6.5 1.0 CA A:ASN474 4.8 6.1 1.0 CB A:GLN476 4.8 5.7 1.0 C A:ASP447 4.8 7.8 1.0 C A:TYR477 4.9 5.6 1.0 C A:ASN474 5.0 6.5 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1513 b:7.7 occ:1.00 OD1 B:ASP447 2.1 5.8 1.0 OD1 B:ASN474 2.1 10.4 1.0 O1A B:TDM1614 2.1 9.2 1.0 O B:GLN476 2.1 6.1 1.0 O3B B:TDM1614 2.2 11.7 1.0 O B:HOH2080 2.2 4.7 1.0 CG B:ASN474 3.1 8.1 1.0 CG B:ASP447 3.2 5.9 1.0 C B:GLN476 3.3 6.1 1.0 PB B:TDM1614 3.3 8.0 1.0 PA B:TDM1614 3.3 6.9 1.0 ND2 B:ASN474 3.4 3.6 1.0 O3A B:TDM1614 3.6 9.0 1.0 OD2 B:ASP447 3.8 6.5 1.0 O2B B:TDM1614 3.8 6.7 1.0 N B:GLN476 3.9 6.8 1.0 N B:ASP447 3.9 6.4 1.0 N B:GLY448 4.1 6.4 1.0 CA B:GLN476 4.1 6.8 1.0 O7 B:TDM1614 4.2 7.3 1.0 N B:GLY478 4.2 4.9 1.0 O B:PHE472 4.2 7.8 1.0 N B:TYR477 4.3 5.9 1.0 CA B:TYR477 4.4 5.7 1.0 N B:ASN474 4.4 8.4 1.0 CB B:ASN474 4.4 7.7 1.0 CB B:ASP447 4.5 6.6 1.0 O2A B:TDM1614 4.5 4.7 1.0 CZ B:PHE497 4.5 9.0 1.0 CB B:GLN476 4.6 6.5 1.0 CA B:ASP447 4.6 6.6 1.0 O1B B:TDM1614 4.6 7.4 1.0 N B:CYS475 4.7 7.9 1.0 C B:GLY446 4.7 6.4 1.0 CA B:GLY446 4.8 6.5 1.0 CA B:ASN474 4.8 8.2 1.0 C B:ASP447 4.8 7.0 1.0 C B:TYR477 4.9 5.4 1.0 C B:ASN474 5.0 7.8 1.0 CA B:GLY448 5.0 7.2 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