Magnesium in PDB 1zpd: Pyruvate Decarboxylase From Zymomonas Mobilis

All present enzymatic activity of Pyruvate Decarboxylase From Zymomonas Mobilis:
4.1.1.1;

The structure of Pyruvate Decarboxylase From Zymomonas Mobilis, PDB code: 1zpd 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)	15.00 / 1.86
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.868, 92.168, 98.256, 102.86, 94.59, 112.69
R / Rfree (%)	16.2 / 19.7

The binding sites of Magnesium atom in the Pyruvate Decarboxylase From Zymomonas Mobilis (pdb code 1zpd). 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 Zymomonas Mobilis, PDB code: 1zpd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyruvate Decarboxylase From Zymomonas Mobilis


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 Zymomonas Mobilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:13.5 occ:1.00 OD1 A:ASP440 1.9 10.9 1.0 OD1 A:ASN467 2.1 12.6 1.0 O A:GLY469 2.2 10.1 1.0 O21 A:DPX600 2.2 12.1 1.0 O A:HOH611 2.2 8.3 1.0 O24 A:DPX600 2.3 14.3 1.0 CG A:ASN467 3.1 10.3 1.0 CG A:ASP440 3.2 10.0 1.0 P19 A:DPX600 3.3 11.2 1.0 C A:GLY469 3.4 16.6 1.0 O22 A:DPX600 3.5 10.9 1.0 ND2 A:ASN467 3.5 9.3 1.0 P23 A:DPX600 3.5 15.1 1.0 OD2 A:ASP440 3.7 13.5 1.0 N A:ASP440 3.9 10.7 1.0 N A:GLY441 4.0 8.5 1.0 N A:GLY469 4.0 13.2 1.0 O A:ILE465 4.1 11.3 1.0 O18 A:DPX600 4.2 13.0 1.0 O A:HOH1256 4.2 36.4 1.0 N A:THR471 4.3 13.2 1.0 CA A:GLY469 4.3 12.6 1.0 CB A:ASP440 4.3 11.8 1.0 N A:TYR470 4.4 10.7 1.0 O20 A:DPX600 4.4 9.7 1.0 O25 A:DPX600 4.4 22.0 1.0 CA A:TYR470 4.5 13.8 1.0 CB A:ASN467 4.5 10.6 1.0 N A:ASN467 4.5 10.7 1.0 CA A:ASP440 4.5 10.5 1.0 O26 A:DPX600 4.6 22.8 1.0 C A:GLY439 4.6 10.0 1.0 CA A:GLY439 4.6 9.6 1.0 O A:HOH824 4.7 10.8 1.0 C A:ASN467 4.8 9.1 1.0 C A:ASP440 4.8 7.5 1.0 CA A:ASN467 4.8 8.9 1.0 N A:TYR468 4.8 10.5 1.0 CA A:GLY441 4.9 10.7 1.0 C A:TYR470 4.9 14.5 1.0 OG1 A:THR471 5.0 17.1 1.0

Magnesium binding site 2 out of 4 in the Pyruvate Decarboxylase From Zymomonas Mobilis


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 Zymomonas Mobilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:13.5 occ:1.00 OD1 B:ASP440 1.9 10.9 1.0 OD1 B:ASN467 2.1 12.5 1.0 O B:GLY469 2.2 10.1 1.0 O21 B:DPX600 2.2 12.1 1.0 O B:HOH611 2.2 8.3 1.0 O24 B:DPX600 2.3 14.4 1.0 CG B:ASN467 3.1 10.3 1.0 CG B:ASP440 3.2 10.0 1.0 P19 B:DPX600 3.2 11.2 1.0 O22 B:DPX600 3.4 10.9 1.0 C B:GLY469 3.4 16.6 1.0 ND2 B:ASN467 3.5 9.3 1.0 P23 B:DPX600 3.5 15.1 1.0 OD2 B:ASP440 3.7 13.5 1.0 N B:ASP440 3.9 10.8 1.0 N B:GLY441 4.0 8.5 1.0 N B:GLY469 4.0 13.2 1.0 O B:ILE465 4.1 11.2 1.0 O18 B:DPX600 4.1 13.0 1.0 N B:THR471 4.3 13.2 1.0 CA B:GLY469 4.3 12.6 1.0 O20 B:DPX600 4.3 9.7 1.0 O25 B:DPX600 4.3 22.0 1.0 N B:TYR470 4.3 10.7 1.0 CB B:ASP440 4.4 11.8 1.0 CA B:TYR470 4.5 13.8 1.0 CB B:ASN467 4.5 10.7 1.0 N B:ASN467 4.5 10.7 1.0 CA B:ASP440 4.6 10.4 1.0 CA B:GLY439 4.6 9.6 1.0 O26 B:DPX600 4.6 22.8 1.0 C B:GLY439 4.6 10.1 1.0 O B:HOH896 4.7 11.1 1.0 C B:ASN467 4.8 9.1 1.0 CA B:ASN467 4.8 8.9 1.0 C B:ASP440 4.8 7.5 1.0 CA B:GLY441 4.9 10.7 1.0 N B:TYR468 4.9 10.4 1.0 OG1 B:THR471 4.9 17.1 1.0 C B:TYR470 4.9 14.5 1.0

Magnesium binding site 3 out of 4 in the Pyruvate Decarboxylase From Zymomonas Mobilis


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 Zymomonas Mobilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:13.5 occ:1.00 OD1 E:ASP440 2.0 10.9 1.0 OD1 E:ASN467 2.1 12.6 1.0 O21 E:DPX600 2.2 12.1 1.0 O E:GLY469 2.2 10.1 1.0 O E:HOH611 2.2 8.3 1.0 O24 E:DPX600 2.3 14.3 1.0 CG E:ASN467 3.1 10.3 1.0 CG E:ASP440 3.2 10.0 1.0 P19 E:DPX600 3.2 11.2 1.0 O22 E:DPX600 3.4 10.9 1.0 C E:GLY469 3.4 16.5 1.0 P23 E:DPX600 3.5 15.1 1.0 ND2 E:ASN467 3.5 9.3 1.0 OD2 E:ASP440 3.8 13.5 1.0 N E:ASP440 4.0 10.8 1.0 N E:GLY441 4.0 8.5 1.0 N E:GLY469 4.1 13.2 1.0 O E:ILE465 4.1 11.3 1.0 O18 E:DPX600 4.1 13.1 1.0 O20 E:DPX600 4.3 9.7 1.0 N E:THR471 4.3 13.2 1.0 CA E:GLY469 4.3 12.6 1.0 O25 E:DPX600 4.3 22.0 1.0 CB E:ASP440 4.4 11.8 1.0 N E:TYR470 4.4 10.7 1.0 CA E:TYR470 4.5 13.8 1.0 CB E:ASN467 4.5 10.6 1.0 N E:ASN467 4.5 10.7 1.0 CA E:ASP440 4.6 10.5 1.0 O26 E:DPX600 4.6 22.8 1.0 CA E:GLY439 4.6 9.6 1.0 C E:GLY439 4.6 10.0 1.0 O E:HOH928 4.8 13.6 1.0 C E:ASP440 4.8 7.5 1.0 C E:ASN467 4.8 9.1 1.0 CA E:ASN467 4.8 8.9 1.0 CA E:GLY441 4.8 10.7 1.0 N E:TYR468 4.9 10.4 1.0 C E:TYR470 4.9 14.5 1.0 OG1 E:THR471 5.0 17.1 1.0

Magnesium binding site 4 out of 4 in the Pyruvate Decarboxylase From Zymomonas Mobilis


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 Zymomonas Mobilis within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:13.5 occ:1.00 OD1 F:ASP440 2.0 10.9 1.0 O F:GLY469 2.1 10.1 1.0 OD1 F:ASN467 2.1 12.6 1.0 O21 F:DPX600 2.2 12.1 1.0 O F:HOH611 2.2 8.3 1.0 O24 F:DPX600 2.3 14.4 1.0 CG F:ASN467 3.1 10.3 1.0 CG F:ASP440 3.2 10.0 1.0 P19 F:DPX600 3.3 11.3 1.0 C F:GLY469 3.4 16.6 1.0 O22 F:DPX600 3.4 10.9 1.0 ND2 F:ASN467 3.5 9.3 1.0 P23 F:DPX600 3.5 15.1 1.0 OD2 F:ASP440 3.8 13.5 1.0 N F:ASP440 3.9 10.8 1.0 N F:GLY441 4.0 8.5 1.0 N F:GLY469 4.0 13.2 1.0 O18 F:DPX600 4.1 13.0 1.0 O F:ILE465 4.2 11.3 1.0 O F:HOH1240 4.2 35.8 1.0 CA F:GLY469 4.3 12.6 1.0 N F:THR471 4.3 13.2 1.0 N F:TYR470 4.3 10.7 1.0 O20 F:DPX600 4.4 9.7 1.0 O25 F:DPX600 4.4 22.0 1.0 CB F:ASP440 4.4 11.8 1.0 CA F:TYR470 4.4 13.8 1.0 CB F:ASN467 4.5 10.7 1.0 O26 F:DPX600 4.5 22.8 1.0 N F:ASN467 4.5 10.7 1.0 CA F:ASP440 4.6 10.4 1.0 CA F:GLY439 4.7 9.6 1.0 C F:GLY439 4.7 10.1 1.0 O F:HOH996 4.7 10.7 1.0 C F:ASN467 4.8 9.1 1.0 C F:ASP440 4.8 7.5 1.0 CA F:ASN467 4.8 8.9 1.0 CA F:GLY441 4.9 10.7 1.0 N F:TYR468 4.9 10.4 1.0 C F:TYR470 4.9 14.5 1.0 OG1 F:THR471 4.9 17.1 1.0

D.Dobritzsch, S.Konig, G.Schneider, G.Lu. High Resolution Crystal Structure of Pyruvate Decarboxylase From Zymomonas Mobilis. Implications For Substrate Activation in Pyruvate Decarboxylases. J.Biol.Chem. V. 273 20196 1998.
ISSN: ISSN 0021-9258
PubMed: 9685367
DOI: 10.1074/JBC.273.32.20196