Magnesium in PDB 1qpb: Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide

All present enzymatic activity of Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide:
4.1.1.1;

The structure of Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide, PDB code: 1qpb was solved by G.Lu, D.Dobritzsch, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.0 / 2.4
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.049, 119.700, 81.283, 90.00, 120.21, 90.00
R / Rfree (%)	23.3 / 28.7

The binding sites of Magnesium atom in the Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide (pdb code 1qpb). 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 Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide, PDB code: 1qpb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:26.7 occ:1.00 O A:GLY473 2.0 22.1 1.0 OD1 A:ASN471 2.2 31.6 1.0 O3B A:TPP600 2.4 24.3 1.0 O A:HOH2077 2.4 10.2 1.0 OD1 A:ASP444 2.5 27.8 1.0 O1A A:TPP600 2.5 18.8 1.0 CG A:ASN471 2.8 31.9 1.0 ND2 A:ASN471 3.0 32.2 1.0 C A:GLY473 3.2 21.4 1.0 PB A:TPP600 3.4 23.2 1.0 PA A:TPP600 3.6 24.7 1.0 CG A:ASP444 3.6 26.6 1.0 O3A A:TPP600 3.7 23.7 1.0 N A:THR475 3.8 22.5 1.0 CG2 A:THR475 3.8 18.8 1.0 O1B A:TPP600 3.9 21.4 1.0 N A:GLY473 3.9 29.7 1.0 CB A:ASN471 4.1 30.0 1.0 N A:TYR474 4.1 20.9 1.0 OD2 A:ASP444 4.1 26.9 1.0 CA A:GLY473 4.1 24.8 1.0 CA A:TYR474 4.2 22.9 1.0 OG1 A:THR475 4.3 22.0 1.0 C A:ASN471 4.3 33.6 1.0 N A:ASN471 4.4 31.3 1.0 N A:ASP444 4.4 23.2 1.0 O A:ASN471 4.4 35.0 1.0 CA A:ASN471 4.5 31.0 1.0 O A:LEU469 4.5 27.8 1.0 N A:GLY445 4.5 18.5 1.0 C A:TYR474 4.5 21.0 1.0 O7 A:TPP600 4.5 27.0 1.0 CB A:THR475 4.6 20.8 1.0 N A:ASP472 4.6 32.9 1.0 O2B A:TPP600 4.7 23.5 1.0 C A:ASP472 4.7 31.1 1.0 O2A A:TPP600 4.8 21.4 1.0 CA A:THR475 4.8 23.3 1.0 CB A:ASP444 4.9 25.4 1.0 CA A:GLY443 4.9 19.4 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Decarboyxlase From Yeast (Form B) Complexed with Pyruvamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:71.5 occ:1.00 O B:GLY473 2.0 23.2 1.0 OD1 B:ASN471 2.2 33.2 1.0 O3B B:TPP600 2.4 16.2 1.0 O B:HOH2043 2.5 13.8 1.0 OD1 B:ASP444 2.6 33.5 1.0 O1A B:TPP600 2.6 18.8 1.0 CG B:ASN471 2.9 31.5 1.0 C B:GLY473 3.0 22.1 1.0 ND2 B:ASN471 3.3 27.6 1.0 CG2 B:THR475 3.4 27.8 1.0 CG B:ASP444 3.5 33.9 1.0 PB B:TPP600 3.6 20.4 1.0 N B:THR475 3.6 27.9 1.0 N B:GLY473 3.7 24.5 1.0 OD2 B:ASP444 3.7 34.1 1.0 PA B:TPP600 3.8 17.4 1.0 CA B:GLY473 3.9 21.2 1.0 O1B B:TPP600 3.9 19.5 1.0 N B:TYR474 3.9 24.0 1.0 O3A B:TPP600 4.0 19.6 1.0 CA B:TYR474 4.1 24.4 1.0 CB B:ASN471 4.1 30.9 1.0 OG1 B:THR475 4.2 33.8 1.0 CB B:THR475 4.2 29.4 1.0 C B:ASN471 4.3 31.0 1.0 C B:TYR474 4.4 25.8 1.0 N B:ASN471 4.4 29.7 1.0 O B:ASN471 4.5 32.8 1.0 CA B:ASN471 4.5 29.0 1.0 CA B:THR475 4.5 28.0 1.0 O7 B:TPP600 4.6 14.6 1.0 N B:ASP472 4.6 28.5 1.0 N B:GLY445 4.6 28.1 1.0 C B:ASP472 4.6 27.1 1.0 O B:LEU469 4.7 33.1 1.0 O2A B:TPP600 4.8 12.6 1.0 N B:ASP444 4.8 28.2 1.0 O2B B:TPP600 4.8 20.4 1.0 CB B:ASP444 4.9 31.9 1.0

G.Lu, D.Dobritzsch, S.Baumann, G.Schneider, S.Konig. The Structural Basis of Substrate Activation in Yeast Pyruvate Decarboxylase A Crystallographic and Kinetic Study Eur.J.Biochem. V. 267 861 2000.
ISSN: ISSN 0014-2956
PubMed: 10651824
DOI: 10.1046/J.1432-1327.2000.01070.X