Magnesium in PDB 6efg: Pyruvate Decarboxylase From Kluyveromyces Lactis

All present enzymatic activity of Pyruvate Decarboxylase From Kluyveromyces Lactis:
4.1.1.1;

The structure of Pyruvate Decarboxylase From Kluyveromyces Lactis, PDB code: 6efg was solved by S.Kutter, S.Konig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.25 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.360, 78.480, 100.570, 80.10, 67.72, 77.40
R / Rfree (%)	22.1 / 29

The binding sites of Magnesium atom in the Pyruvate Decarboxylase From Kluyveromyces Lactis (pdb code 6efg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Decarboxylase From Kluyveromyces Lactis, PDB code: 6efg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:30.9 occ:1.00 OD1 A:ASP444 1.9 22.1 1.0 O1A A:TPP600 2.0 22.2 1.0 O A:HOH715 2.1 28.7 1.0 O1B A:TPP600 2.1 27.2 1.0 O A:GLY473 2.2 26.5 1.0 OD1 A:ASN471 2.2 21.8 1.0 CG A:ASP444 3.1 28.6 1.0 PA A:TPP600 3.2 22.6 1.0 CG A:ASN471 3.2 24.3 1.0 PB A:TPP600 3.3 30.1 1.0 C A:GLY473 3.4 23.1 1.0 O3A A:TPP600 3.5 24.3 1.0 ND2 A:ASN471 3.6 26.3 1.0 OD2 A:ASP444 3.7 30.5 1.0 N A:GLY445 3.8 27.2 1.0 O3B A:TPP600 3.9 27.3 1.0 N A:ASP444 4.0 26.6 1.0 O A:LEU469 4.0 31.0 1.0 O7 A:TPP600 4.0 23.7 1.0 N A:GLY473 4.2 29.0 1.0 CB A:ASP444 4.3 26.2 1.0 N A:TYR474 4.3 23.5 1.0 CA A:GLY473 4.3 25.8 1.0 N A:THR475 4.3 25.6 1.0 O2A A:TPP600 4.3 20.4 1.0 CA A:GLY443 4.4 25.7 1.0 CA A:TYR474 4.4 25.1 1.0 OG1 A:THR475 4.4 25.9 1.0 N A:ASN471 4.5 25.2 1.0 C A:GLY443 4.5 25.7 1.0 CA A:ASP444 4.5 25.6 1.0 O2B A:TPP600 4.5 28.3 1.0 CB A:ASN471 4.6 24.2 1.0 CA A:GLY445 4.6 27.5 1.0 C A:ASP444 4.7 24.2 1.0 C A:ASN471 4.8 21.6 1.0 CA A:ASN471 4.8 23.9 1.0 C A:TYR474 4.9 25.2 1.0 CB A:THR475 4.9 27.0 1.0 N A:ASP472 4.9 25.4 1.0

Magnesium binding site 2 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:38.7 occ:1.00 O1B B:TPP600 2.0 34.7 1.0 O1A B:TPP600 2.0 25.4 1.0 OD1 B:ASP444 2.1 30.1 1.0 O B:GLY473 2.1 34.8 1.0 OD1 B:ASN471 2.2 31.9 1.0 O B:HOH705 2.3 22.0 1.0 PA B:TPP600 3.1 29.8 1.0 PB B:TPP600 3.1 31.2 1.0 CG B:ASN471 3.1 33.0 1.0 C B:GLY473 3.2 29.9 1.0 CG B:ASP444 3.3 32.7 1.0 O3A B:TPP600 3.4 26.6 1.0 ND2 B:ASN471 3.4 31.6 1.0 O3B B:TPP600 3.5 30.0 1.0 N B:ASP444 3.8 28.1 1.0 N B:GLY445 3.9 29.9 1.0 OD2 B:ASP444 3.9 33.5 1.0 N B:GLY473 4.0 31.0 1.0 O B:LEU469 4.0 24.0 1.0 CA B:GLY473 4.1 31.2 1.0 O7 B:TPP600 4.1 25.4 1.0 N B:TYR474 4.2 28.4 1.0 N B:THR475 4.3 30.0 1.0 O2A B:TPP600 4.3 28.7 1.0 CA B:GLY443 4.3 24.0 1.0 CA B:TYR474 4.4 26.9 1.0 O2B B:TPP600 4.4 26.2 1.0 C B:GLY443 4.4 26.0 1.0 CB B:ASP444 4.4 31.3 1.0 CA B:ASP444 4.5 29.5 1.0 OG1 B:THR475 4.5 30.5 1.0 CB B:ASN471 4.5 33.9 1.0 N B:ASN471 4.6 32.5 1.0 CA B:GLY445 4.6 29.1 1.0 C B:ASP444 4.7 29.9 1.0 C B:TYR474 4.9 32.0 1.0 CB B:THR475 4.9 29.8 1.0 C B:ASN471 4.9 34.8 1.0 CA B:ASN471 4.9 33.8 1.0

Magnesium binding site 3 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:23.9 occ:1.00 O D:GLY473 1.8 25.9 1.0 OD1 D:ASN471 2.0 29.3 1.0 O3B D:TPP600 2.1 25.1 1.0 O D:HOH703 2.1 18.4 1.0 OD1 D:ASP444 2.2 34.0 1.0 O2A D:TPP600 2.3 24.4 1.0 CG D:ASN471 2.9 30.8 1.0 C D:GLY473 3.0 25.0 1.0 PB D:TPP600 3.1 27.5 1.0 ND2 D:ASN471 3.2 32.7 1.0 CG D:ASP444 3.2 35.5 1.0 PA D:TPP600 3.3 25.1 1.0 O2B D:TPP600 3.5 27.7 1.0 O3A D:TPP600 3.5 27.6 1.0 OD2 D:ASP444 3.6 31.8 1.0 N D:TYR474 3.9 25.9 1.0 O D:LEU469 3.9 30.7 1.0 N D:THR475 3.9 28.6 1.0 CA D:GLY473 4.0 26.3 1.0 N D:GLY473 4.0 26.2 1.0 N D:ASP444 4.0 30.5 1.0 CA D:TYR474 4.1 28.2 1.0 N D:GLY445 4.2 31.3 1.0 OG1 D:THR475 4.2 25.9 1.0 O7 D:TPP600 4.2 26.1 1.0 CB D:ASN471 4.3 29.8 1.0 O1B D:TPP600 4.4 27.1 1.0 N D:ASN471 4.4 31.6 1.0 CB D:ASP444 4.5 33.4 1.0 O1A D:TPP600 4.5 28.6 1.0 C D:TYR474 4.6 28.1 1.0 CA D:GLY443 4.6 31.2 1.0 CB D:THR475 4.7 26.6 1.0 CA D:ASP444 4.7 31.7 1.0 CA D:ASN471 4.7 28.3 1.0 C D:ASN471 4.7 32.1 1.0 C D:GLY443 4.7 31.0 1.0 O D:ASN471 4.9 32.6 1.0 CA D:THR475 4.9 26.8 1.0 C D:ASP444 5.0 29.2 1.0 CA D:GLY445 5.0 29.5 1.0 N D:ASP472 5.0 32.9 1.0

Magnesium binding site 4 out of 4 in the Pyruvate Decarboxylase From Kluyveromyces Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:21.4 occ:1.00 O3B E:TPP600 1.9 26.8 1.0 O2A E:TPP600 2.0 30.8 1.0 O E:HOH710 2.1 17.1 1.0 O E:GLY473 2.1 24.1 1.0 OD1 E:ASN471 2.1 27.5 1.0 OD1 E:ASP444 2.2 24.8 1.0 PB E:TPP600 3.0 30.6 1.0 CG E:ASN471 3.0 26.1 1.0 PA E:TPP600 3.2 31.4 1.0 ND2 E:ASN471 3.3 25.2 1.0 C E:GLY473 3.3 25.2 1.0 O3A E:TPP600 3.4 29.6 1.0 O2B E:TPP600 3.4 26.6 1.0 CG E:ASP444 3.4 26.7 1.0 OD2 E:ASP444 4.0 24.8 1.0 N E:GLY445 4.0 26.6 1.0 N E:THR475 4.0 26.1 1.0 O7 E:TPP600 4.0 26.5 1.0 N E:ASP444 4.1 25.6 1.0 N E:GLY473 4.1 29.6 1.0 O E:LEU469 4.1 23.3 1.0 CA E:GLY473 4.2 26.6 1.0 N E:TYR474 4.2 24.7 1.0 O1B E:TPP600 4.3 25.2 1.0 CA E:TYR474 4.3 27.0 1.0 OG1 E:THR475 4.4 25.6 1.0 O1A E:TPP600 4.4 28.0 1.0 CB E:ASN471 4.4 25.4 1.0 CA E:GLY443 4.5 27.9 1.0 N E:ASN471 4.5 26.8 1.0 C E:GLY443 4.6 26.0 1.0 CB E:ASP444 4.6 25.6 1.0 CB E:THR475 4.7 24.4 1.0 C E:TYR474 4.7 28.3 1.0 CA E:ASP444 4.7 26.4 1.0 CA E:GLY445 4.8 27.7 1.0 CA E:ASN471 4.8 26.6 1.0 C E:ASN471 4.9 24.9 1.0 C E:ASP444 4.9 28.1 1.0 CA E:THR475 5.0 25.8 1.0

S.Kutter, S.Konig. The Crystal Structures of Pyruvate Decarboxylase From Kluyveromyces Lactis in the Absence of Ligands and in the Presence of the Substrate Surrogate Pyruvamide To Be Published.