Magnesium in PDB 2vk4: Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis

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

The structure of Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis, PDB code: 2vk4 was solved by S.Kutter, S.Relle, G.Wille, M.S.Weiss, S.Konig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.709, 203.175, 79.815, 90.00, 91.81, 90.00
R / Rfree (%)	17.8 / 23

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis (pdb code 2vk4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis, PDB code: 2vk4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of 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 Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:15.7 occ:1.00 O3B A:TPP600 1.9 16.7 1.0 O A:GLY473 2.0 13.1 1.0 O A:HOH2238 2.1 20.8 1.0 O1A A:TPP600 2.1 12.1 1.0 OD2 A:ASP444 2.1 15.7 1.0 OD1 A:ASN471 2.2 18.5 1.0 PB A:TPP600 3.1 13.7 1.0 CG A:ASN471 3.1 17.7 1.0 PA A:TPP600 3.2 12.6 1.0 C A:GLY473 3.2 12.9 1.0 CG A:ASP444 3.3 14.3 1.0 ND2 A:ASN471 3.5 14.5 1.0 O3A A:TPP600 3.5 13.1 1.0 O1B A:TPP600 3.6 12.5 1.0 OD1 A:ASP444 3.9 19.6 1.0 N A:THR475 3.9 14.2 1.0 N A:GLY445 4.1 13.2 1.0 O7 A:TPP600 4.1 14.6 1.0 N A:TYR474 4.1 12.9 1.0 O A:LEU469 4.2 16.3 1.0 CA A:GLY473 4.2 13.2 1.0 N A:GLY473 4.2 15.4 1.0 CA A:TYR474 4.2 13.5 1.0 N A:ASP444 4.2 13.2 1.0 O2A A:TPP600 4.3 10.3 1.0 O2B A:TPP600 4.3 12.3 1.0 OG1 A:THR475 4.4 16.4 1.0 CB A:ASN471 4.5 15.9 1.0 C A:TYR474 4.6 13.3 1.0 CB A:ASP444 4.6 12.3 1.0 CA A:GLY443 4.6 12.9 1.0 N A:ASN471 4.6 15.1 1.0 C A:GLY443 4.7 13.1 1.0 CA A:ASP444 4.8 13.1 1.0 CB A:THR475 4.8 15.7 1.0 C A:ASN471 4.8 15.1 1.0 CA A:GLY445 4.9 13.0 1.0 C A:ASP444 4.9 12.2 1.0 CA A:ASN471 4.9 15.5 1.0 CA A:THR475 5.0 15.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of 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 Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:17.1 occ:1.00 O B:GLY473 2.0 12.3 1.0 OD1 B:ASN471 2.1 13.9 1.0 O B:HOH2256 2.1 11.8 1.0 OD2 B:ASP444 2.1 11.6 1.0 O1A B:TPP600 2.1 9.6 1.0 O3B B:TPP600 2.2 12.8 1.0 CG B:ASN471 3.1 13.5 1.0 C B:GLY473 3.2 12.2 1.0 PB B:TPP600 3.3 12.7 1.0 CG B:ASP444 3.3 14.3 1.0 PA B:TPP600 3.3 11.4 1.0 O3A B:TPP600 3.5 13.7 1.0 ND2 B:ASN471 3.6 13.8 1.0 OD1 B:ASP444 3.8 12.1 1.0 O1B B:TPP600 3.9 12.8 1.0 N B:GLY473 3.9 12.3 1.0 N B:GLY445 4.0 14.6 1.0 CA B:GLY473 4.1 11.1 1.0 O B:LEU469 4.1 12.8 1.0 N B:THR475 4.1 14.0 1.0 N B:TYR474 4.1 12.1 1.0 O7 B:TPP600 4.2 11.9 1.0 N B:ASP444 4.2 15.3 1.0 CA B:TYR474 4.3 13.1 1.0 N B:ASN471 4.4 13.0 1.0 O2A B:TPP600 4.5 14.7 1.0 CB B:ASN471 4.5 12.9 1.0 OG1 B:THR475 4.5 11.9 1.0 O2B B:TPP600 4.5 12.5 1.0 CB B:ASP444 4.6 14.7 1.0 O B:HOH2262 4.6 10.3 1.0 CA B:GLY443 4.6 14.9 1.0 C B:TYR474 4.7 13.1 1.0 CA B:ASP444 4.7 14.7 1.0 C B:ASN471 4.7 12.4 1.0 CA B:ASN471 4.7 12.7 1.0 C B:GLY443 4.8 16.0 1.0 CA B:GLY445 4.8 14.2 1.0 C B:ASP444 4.8 14.1 1.0 CB B:THR475 4.8 12.8 1.0 N B:ASP472 4.9 13.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of 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 Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:12.4 occ:1.00 OD1 C:ASN471 2.0 12.1 1.0 O3B C:TPP600 2.0 8.3 1.0 OD2 C:ASP444 2.1 9.1 1.0 O C:HOH2374 2.1 6.7 1.0 O C:GLY473 2.1 11.2 1.0 O1A C:TPP600 2.2 11.0 1.0 CG C:ASN471 3.0 10.9 1.0 PB C:TPP600 3.2 12.6 1.0 CG C:ASP444 3.3 11.3 1.0 PA C:TPP600 3.3 13.0 1.0 ND2 C:ASN471 3.3 12.2 1.0 C C:GLY473 3.3 11.8 1.0 O3A C:TPP600 3.5 10.8 1.0 O1B C:TPP600 3.5 11.7 1.0 OD1 C:ASP444 3.8 12.6 1.0 O C:LEU469 4.0 12.6 1.0 N C:THR475 4.0 12.0 1.0 N C:GLY445 4.1 9.1 1.0 N C:ASP444 4.1 8.3 1.0 O7 C:TPP600 4.1 14.9 1.0 N C:GLY473 4.2 14.6 1.0 CA C:GLY473 4.2 12.6 1.0 N C:TYR474 4.3 11.5 1.0 CA C:TYR474 4.4 11.4 1.0 OG1 C:THR475 4.4 10.7 1.0 CB C:ASN471 4.4 9.5 1.0 O2A C:TPP600 4.4 11.4 1.0 N C:ASN471 4.5 9.2 1.0 O2B C:TPP600 4.5 7.2 1.0 CB C:ASP444 4.5 10.5 1.0 CA C:GLY443 4.5 8.1 1.0 O C:HOH2302 4.6 8.9 1.0 C C:GLY443 4.6 8.2 1.0 CA C:ASP444 4.7 8.9 1.0 CB C:THR475 4.7 11.9 1.0 C C:TYR474 4.7 11.7 1.0 C C:ASN471 4.7 11.5 1.0 CA C:ASN471 4.8 9.6 1.0 C C:ASP444 4.9 9.5 1.0 CA C:GLY445 4.9 10.0 1.0 O C:ASN471 5.0 11.5 1.0 CA C:THR475 5.0 10.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of 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 Crystal Structure of Pyruvate Decarboxylase From Kluyveromyces Lactis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:20.7 occ:1.00 OD2 D:ASP444 1.9 17.4 1.0 OD1 D:ASN471 1.9 21.4 1.0 O D:GLY473 2.1 14.5 1.0 O D:HOH2237 2.1 11.4 1.0 O1A D:TPP600 2.2 17.1 1.0 O3B D:TPP600 2.2 19.0 1.0 CG D:ASN471 3.0 19.6 1.0 CG D:ASP444 3.1 16.6 1.0 C D:GLY473 3.3 15.1 1.0 ND2 D:ASN471 3.3 15.4 1.0 PB D:TPP600 3.4 15.9 1.0 PA D:TPP600 3.5 14.5 1.0 OD1 D:ASP444 3.6 18.9 1.0 O3A D:TPP600 3.7 15.4 1.0 O1B D:TPP600 3.8 18.4 1.0 N D:ASP444 3.9 13.7 1.0 O D:LEU469 3.9 16.2 1.0 N D:GLY445 4.0 14.0 1.0 N D:GLY473 4.0 16.3 1.0 CA D:GLY473 4.2 15.8 1.0 N D:THR475 4.2 17.1 1.0 N D:TYR474 4.3 15.5 1.0 CB D:ASN471 4.3 19.5 1.0 N D:ASN471 4.4 19.6 1.0 CB D:ASP444 4.4 15.1 1.0 O7 D:TPP600 4.5 14.2 1.0 CA D:TYR474 4.5 15.7 1.0 CA D:GLY443 4.5 14.5 1.0 O2A D:TPP600 4.5 15.0 1.0 OG1 D:THR475 4.5 14.0 1.0 CA D:ASP444 4.5 14.7 1.0 C D:GLY443 4.6 13.9 1.0 O2B D:TPP600 4.7 16.0 1.0 CA D:ASN471 4.7 19.1 1.0 C D:ASN471 4.7 19.0 1.0 C D:ASP444 4.8 14.2 1.0 CA D:GLY445 4.8 11.7 1.0 C D:TYR474 4.9 16.3 1.0 CB D:THR475 4.9 16.9 1.0 N D:ASP472 4.9 19.2 1.0 O D:ASN471 5.0 18.8 1.0

S.Konig, M.Spinka, S.Kutter. Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story. J.Mol.Catal., B Enzym. V. 61 100 2014.
ISSN: ISSN 1381-1177
DOI: 10.1016/J.MOLCATB.2009.02.010