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Magnesium in PDB 2ez9: Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate

Enzymatic activity of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate

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

Protein crystallography data

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate, PDB code: 2ez9 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) 19.62 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.661, 154.517, 165.640, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18

Other elements in 2ez9:

The structure of Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-Thiamin Diphosphate (pdb code 2ez9). 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 Analogue 2-Phosphonolactyl-Thiamin Diphosphate, PDB code: 2ez9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2ez9

Go back to Magnesium Binding Sites List in 2ez9
Magnesium binding site 1 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-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 Analogue 2-Phosphonolactyl-Thiamin Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1510

b:9.5
occ:1.00
OD1 A:ASP447 2.0 8.6 1.0
O1A A:TDK1611 2.0 9.8 1.0
O A:GLN476 2.1 9.2 1.0
O3B A:TDK1611 2.1 8.6 1.0
O A:HOH2104 2.1 8.5 1.0
OD1 A:ASN474 2.2 9.5 1.0
CG A:ASN474 3.1 8.6 1.0
CG A:ASP447 3.2 10.6 1.0
PA A:TDK1611 3.3 9.9 1.0
PB A:TDK1611 3.3 8.7 1.0
C A:GLN476 3.3 9.2 1.0
ND2 A:ASN474 3.4 11.0 1.0
O3A A:TDK1611 3.5 9.2 1.0
O2B A:TDK1611 3.8 8.7 1.0
OD2 A:ASP447 3.8 10.8 1.0
N A:ASP447 3.8 9.3 1.0
N A:GLN476 4.0 8.9 1.0
N A:GLY448 4.1 9.8 1.0
CA A:GLN476 4.2 9.2 1.0
O7 A:TDK1611 4.2 9.9 1.0
O A:PHE472 4.2 10.5 1.0
N A:GLY478 4.2 9.2 1.0
N A:TYR477 4.3 9.1 1.0
CA A:TYR477 4.4 9.2 1.0
O2A A:TDK1611 4.4 8.4 1.0
CB A:ASP447 4.4 9.7 1.0
N A:ASN474 4.5 9.9 1.0
CA A:ASP447 4.5 10.0 1.0
CB A:ASN474 4.5 10.1 1.0
O1B A:TDK1611 4.6 8.8 1.0
CZ A:PHE497 4.6 11.3 1.0
C A:GLY446 4.7 9.7 1.0
CB A:GLN476 4.7 9.7 1.0
CA A:GLY446 4.7 9.5 1.0
C A:ASP447 4.8 9.7 1.0
N A:CYS475 4.8 9.6 1.0
C A:TYR477 4.8 9.2 1.0
CA A:ASN474 4.9 9.4 1.0

Magnesium binding site 2 out of 2 in 2ez9

Go back to Magnesium Binding Sites List in 2ez9
Magnesium binding site 2 out of 2 in the Pyruvate Oxidase Variant F479W in Complex with Reaction Intermediate Analogue 2-Phosphonolactyl-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 Analogue 2-Phosphonolactyl-Thiamin Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1512

b:9.4
occ:1.00
O1A B:TDK1613 2.0 8.2 1.0
O B:GLN476 2.1 8.3 1.0
O3B B:TDK1613 2.1 7.8 1.0
OD1 B:ASP447 2.1 9.4 1.0
O B:HOH1624 2.2 8.0 1.0
OD1 B:ASN474 2.2 9.0 1.0
CG B:ASN474 3.1 9.5 1.0
PB B:TDK1613 3.2 8.6 1.0
PA B:TDK1613 3.2 9.5 1.0
C B:GLN476 3.3 8.0 1.0
CG B:ASP447 3.3 8.9 1.0
ND2 B:ASN474 3.4 10.2 1.0
O3A B:TDK1613 3.4 8.7 1.0
O2B B:TDK1613 3.7 8.3 1.0
OD2 B:ASP447 3.9 9.6 1.0
N B:ASP447 3.9 8.3 1.0
N B:GLN476 4.0 7.6 1.0
N B:GLY448 4.0 9.1 1.0
O7 B:TDK1613 4.1 9.1 1.0
CA B:GLN476 4.1 8.3 1.0
N B:GLY478 4.2 7.3 1.0
N B:TYR477 4.2 7.9 1.0
O B:PHE472 4.3 10.0 1.0
CA B:TYR477 4.3 7.7 1.0
O2A B:TDK1613 4.4 8.8 1.0
O1B B:TDK1613 4.5 8.3 1.0
CB B:ASP447 4.5 8.8 1.0
N B:ASN474 4.5 9.6 1.0
CB B:ASN474 4.6 9.7 1.0
CZ B:PHE497 4.6 11.2 1.0
CA B:ASP447 4.6 8.8 1.0
CB B:GLN476 4.7 8.9 1.0
C B:GLY446 4.7 8.6 1.0
CA B:GLY446 4.7 8.2 1.0
C B:ASP447 4.8 8.7 1.0
C B:TYR477 4.8 7.2 1.0
N B:CYS475 4.9 9.1 1.0
CA B:GLY448 4.9 9.4 1.0
CA B:ASN474 4.9 9.3 1.0

Reference:

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
Page generated: Mon Dec 14 07:22:00 2020

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