Magnesium 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:

Sodium

(Na)

2 atoms

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

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:13.3 occ:1.00 O1A A:TPP1616 2.0 11.9 1.0 OD1 A:ASP447 2.1 10.9 1.0 O3B A:TPP1616 2.2 9.9 1.0 O A:GLN476 2.2 12.3 1.0 OD1 A:ASN474 2.2 14.1 1.0 O A:HOH2098 2.2 10.5 1.0 CG A:ASN474 3.1 12.0 1.0 PA A:TPP1616 3.2 12.1 1.0 PB A:TPP1616 3.2 10.0 1.0 CG A:ASP447 3.2 12.1 1.0 C A:GLN476 3.3 12.1 1.0 O3A A:TPP1616 3.4 11.0 1.0 ND2 A:ASN474 3.5 11.2 1.0 O2B A:TPP1616 3.8 9.3 1.0 OD2 A:ASP447 3.8 12.8 1.0 N A:ASP447 3.9 11.0 1.0 N A:GLN476 4.0 12.5 1.0 O7 A:TPP1616 4.0 11.8 1.0 N A:GLY448 4.1 11.4 1.0 O A:PHE472 4.1 12.7 1.0 CA A:GLN476 4.2 12.5 1.0 N A:GLY478 4.2 11.3 1.0 N A:TYR477 4.3 12.0 1.0 O2A A:TPP1616 4.3 10.8 1.0 CA A:TYR477 4.4 11.6 1.0 N A:ASN474 4.4 12.5 1.0 CB A:ASP447 4.4 11.2 1.0 O1B A:TPP1616 4.5 9.2 1.0 CA A:ASP447 4.5 11.5 1.0 CB A:ASN474 4.5 12.5 1.0 CZ A:PHE497 4.6 12.7 1.0 CA A:GLY446 4.6 10.7 1.0 C A:GLY446 4.7 11.3 1.0 CB A:GLN476 4.7 12.6 1.0 C A:ASP447 4.8 11.3 1.0 N A:CYS475 4.8 12.1 1.0 CA A:ASN474 4.8 12.6 1.0 C A:TYR477 4.9 11.9 1.0 CA A:GLY448 5.0 11.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1613 b:13.2 occ:1.00 O1A B:TPP1618 2.0 10.8 1.0 O B:GLN476 2.1 11.4 1.0 OD1 B:ASP447 2.1 12.1 1.0 O3B B:TPP1618 2.1 13.3 1.0 O B:HOH2091 2.1 11.2 1.0 OD1 B:ASN474 2.2 12.6 1.0 CG B:ASN474 3.1 12.8 1.0 PA B:TPP1618 3.2 10.5 1.0 PB B:TPP1618 3.2 11.5 1.0 C B:GLN476 3.3 10.9 1.0 CG B:ASP447 3.3 13.1 1.0 ND2 B:ASN474 3.4 10.3 1.0 O3A B:TPP1618 3.5 11.0 1.0 O2B B:TPP1618 3.7 12.9 1.0 OD2 B:ASP447 3.9 11.5 1.0 N B:ASP447 3.9 11.3 1.0 N B:GLN476 3.9 11.0 1.0 N B:GLY448 4.0 11.1 1.0 O7 B:TPP1618 4.1 11.8 1.0 CA B:GLN476 4.1 11.4 1.0 N B:GLY478 4.1 9.8 1.0 O B:PHE472 4.2 14.1 1.0 N B:TYR477 4.2 10.5 1.0 CA B:TYR477 4.3 10.4 1.0 O2A B:TPP1618 4.3 9.7 1.0 N B:ASN474 4.4 12.2 1.0 O1B B:TPP1618 4.5 10.6 1.0 CB B:ASP447 4.5 10.7 1.0 CB B:ASN474 4.5 12.0 1.0 CA B:ASP447 4.5 11.3 1.0 CZ B:PHE497 4.6 15.4 1.0 CB B:GLN476 4.6 11.6 1.0 C B:GLY446 4.7 11.4 1.0 CA B:GLY446 4.7 11.7 1.0 C B:TYR477 4.8 10.2 1.0 C B:ASP447 4.8 11.4 1.0 N B:CYS475 4.8 12.1 1.0 CA B:ASN474 4.9 12.4 1.0 CA B:GLY448 4.9 11.1 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