Magnesium in PDB 4cok: Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus

All present enzymatic activity of Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus:
4.1.1.1;

The structure of Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus, PDB code: 4cok was solved by L.J.Vanzyl, W.-D.Schubert, M.Tuffin, D.A.Cowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.06 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.070, 140.960, 91.060, 90.00, 125.78, 90.00
R / Rfree (%)	13.19 / 16.294

The binding sites of Magnesium atom in the Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus (pdb code 4cok). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus, PDB code: 4cok:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:8.5 occ:1.00 O2A A:TPP600 2.0 9.4 1.0 OD1 A:ASP436 2.0 9.6 1.0 O2B A:TPP600 2.1 10.7 1.0 O A:HOH2515 2.1 8.1 1.0 OD1 A:ASN463 2.1 10.1 1.0 O A:GLY465 2.1 10.8 1.0 CG A:ASN463 3.1 11.7 1.0 PA A:TPP600 3.2 10.3 1.0 PB A:TPP600 3.3 15.7 1.0 CG A:ASP436 3.3 10.0 1.0 C A:GLY465 3.4 10.0 1.0 ND2 A:ASN463 3.5 10.8 1.0 O3A A:TPP600 3.5 9.6 1.0 O1B A:TPP600 3.8 23.8 1.0 OD2 A:ASP436 3.9 10.6 1.0 N A:ASP436 4.0 9.1 1.0 N A:GLY465 4.1 10.3 1.0 N A:GLY437 4.1 9.5 1.0 O A:ILE461 4.1 10.7 1.0 N A:THR467 4.1 13.4 1.0 O7 A:TPP600 4.1 10.8 1.0 N A:TYR466 4.3 11.5 1.0 CA A:GLY465 4.3 10.8 1.0 CA A:TYR466 4.3 11.6 1.0 N A:ASN463 4.3 10.5 1.0 O1A A:TPP600 4.4 10.4 1.0 O3B A:TPP600 4.5 26.0 1.0 CB A:ASN463 4.5 11.5 1.0 CB A:ASP436 4.5 8.4 1.0 CA A:GLY435 4.6 8.2 1.0 O A:HOH2535 4.6 14.7 1.0 C A:GLY435 4.6 8.9 1.0 C A:ASN463 4.7 11.8 1.0 CA A:ASP436 4.7 8.4 1.0 OG1 A:THR467 4.7 16.9 1.0 CA A:ASN463 4.7 10.9 1.0 N A:HIS464 4.8 11.8 1.0 C A:TYR466 4.8 13.8 1.0 CB A:THR467 4.8 15.5 1.0 C A:ASP436 4.9 9.8 1.0

Magnesium binding site 2 out of 2 in the Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:11.1 occ:1.00 O2A B:TPP600 2.0 11.6 1.0 OD1 B:ASP436 2.0 12.4 1.0 OD1 B:ASN463 2.1 12.3 1.0 O1B B:TPP600 2.1 12.5 1.0 O B:GLY465 2.1 12.9 1.0 O B:HOH2437 2.2 10.8 1.0 CG B:ASN463 3.1 14.4 1.0 PA B:TPP600 3.2 12.3 1.0 PB B:TPP600 3.2 17.2 1.0 CG B:ASP436 3.3 10.3 1.0 C B:GLY465 3.3 12.8 1.0 ND2 B:ASN463 3.5 13.5 1.0 O3A B:TPP600 3.5 11.2 1.0 O3B B:TPP600 3.8 24.7 1.0 OD2 B:ASP436 3.9 13.3 1.0 N B:ASP436 4.0 9.5 1.0 N B:GLY465 4.0 12.8 1.0 N B:THR467 4.1 15.6 1.0 N B:GLY437 4.1 9.6 1.0 O7 B:TPP600 4.1 12.6 1.0 O B:ILE461 4.2 12.5 1.0 CA B:GLY465 4.2 14.3 1.0 N B:TYR466 4.2 14.1 1.0 CA B:TYR466 4.3 12.4 1.0 O2B B:TPP600 4.4 26.5 1.0 N B:ASN463 4.4 10.4 1.0 O1A B:TPP600 4.4 12.0 1.0 CB B:ASN463 4.4 11.5 1.0 CB B:ASP436 4.5 8.9 1.0 OG1 B:THR467 4.6 18.4 1.0 CA B:GLY435 4.6 8.3 1.0 O B:HOH2453 4.6 17.3 1.0 C B:ASN463 4.7 13.2 1.0 C B:GLY435 4.7 10.1 1.0 CA B:ASP436 4.7 10.3 1.0 CA B:ASN463 4.7 11.6 1.0 N B:HIS464 4.7 12.9 1.0 C B:TYR466 4.8 15.0 1.0 CB B:THR467 4.8 16.2 1.0 C B:ASP436 4.9 11.0 1.0

L.J.Vanzyl, W.-D.Schubert, M.Tuffin, D.A.Cowan. Functional and Structural Characterization of Pyruvate Decarboxylase From Gluconoacetobacter Diazotrophicus To Be Published.