Magnesium in PDB 2ezu: Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Acetyl-Thiamin Diphosphate

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

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Acetyl-Thiamin Diphosphate, PDB code: 2ezu 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)	25.00 / 2.16
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.276, 154.724, 166.003, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 18.4

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Acetyl-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-Acetyl-Thiamin Diphosphate (pdb code 2ezu). 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-Acetyl-Thiamin Diphosphate, PDB code: 2ezu:
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-Acetyl-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-Acetyl-Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:6.0 occ:1.00 O12 A:HTL1614 2.0 9.9 1.0 O A:GLN476 2.1 9.3 1.0 O23 A:HTL1614 2.1 7.7 1.0 OD1 A:ASP447 2.1 5.8 1.0 OD1 A:ASN474 2.2 7.2 1.0 O A:HOH2095 2.2 2.1 1.0 CG A:ASN474 3.1 6.2 1.0 P2 A:HTL1614 3.2 7.0 1.0 P1 A:HTL1614 3.2 8.4 1.0 C A:GLN476 3.3 8.4 1.0 CG A:ASP447 3.3 7.5 1.0 ND2 A:ASN474 3.4 7.4 1.0 O11 A:HTL1614 3.4 7.5 1.0 O21 A:HTL1614 3.7 5.6 1.0 OD2 A:ASP447 3.9 7.5 1.0 N A:GLN476 3.9 8.5 1.0 N A:ASP447 4.0 7.5 1.0 N A:GLY448 4.0 7.5 1.0 O5G A:HTL1614 4.1 7.9 1.0 CA A:GLN476 4.1 8.4 1.0 O A:PHE472 4.2 8.6 1.0 N A:GLY478 4.2 7.8 1.0 N A:TYR477 4.2 8.3 1.0 CA A:TYR477 4.3 8.4 1.0 O13 A:HTL1614 4.4 8.6 1.0 N A:ASN474 4.5 7.5 1.0 CB A:ASP447 4.5 7.0 1.0 O22 A:HTL1614 4.5 7.3 1.0 CB A:ASN474 4.5 7.2 1.0 CA A:ASP447 4.6 7.4 1.0 CZ A:PHE497 4.6 11.2 1.0 CA A:GLY446 4.7 8.0 1.0 CB A:GLN476 4.7 7.9 1.0 C A:GLY446 4.7 8.0 1.0 C A:TYR477 4.8 7.8 1.0 C A:ASP447 4.8 7.9 1.0 N A:CYS475 4.8 7.4 1.0 CA A:ASN474 4.9 7.3 1.0 CA A:GLY448 4.9 7.3 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate 2-Acetyl-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-Acetyl-Thiamin Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1612 b:7.0 occ:1.00 O12 B:HTL1617 2.0 10.7 1.0 OD1 B:ASP447 2.0 6.6 1.0 O B:HOH1629 2.1 7.5 1.0 O B:GLN476 2.1 8.2 1.0 O23 B:HTL1617 2.2 9.4 1.0 OD1 B:ASN474 2.2 6.5 1.0 CG B:ASN474 3.2 7.7 1.0 P1 B:HTL1617 3.2 7.5 1.0 CG B:ASP447 3.2 9.0 1.0 P2 B:HTL1617 3.3 8.4 1.0 C B:GLN476 3.3 7.6 1.0 ND2 B:ASN474 3.5 2.0 1.0 O11 B:HTL1617 3.5 7.9 1.0 O21 B:HTL1617 3.8 7.4 1.0 OD2 B:ASP447 3.9 8.5 1.0 N B:ASP447 3.9 7.6 1.0 N B:GLN476 3.9 7.9 1.0 N B:GLY448 4.0 8.7 1.0 O5G B:HTL1617 4.1 11.1 1.0 O B:PHE472 4.2 8.7 1.0 CA B:GLN476 4.2 8.0 1.0 N B:GLY478 4.2 6.0 1.0 N B:TYR477 4.3 6.5 1.0 O13 B:HTL1617 4.3 7.2 1.0 CA B:TYR477 4.4 6.4 1.0 CB B:ASP447 4.4 7.1 1.0 N B:ASN474 4.5 8.6 1.0 CA B:ASP447 4.5 8.1 1.0 CZ B:PHE497 4.5 10.7 1.0 O22 B:HTL1617 4.6 6.5 1.0 CB B:ASN474 4.6 7.6 1.0 C B:GLY446 4.6 7.7 1.0 CA B:GLY446 4.7 7.3 1.0 CB B:GLN476 4.7 8.7 1.0 C B:ASP447 4.7 8.7 1.0 N B:CYS475 4.8 8.0 1.0 CA B:ASN474 4.9 8.2 1.0 C B:TYR477 4.9 6.1 1.0 CA B:GLY448 4.9 8.2 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