Magnesium in PDB 8zk9: Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid

The structure of Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid, PDB code: 8zk9 was solved by S.Dong, L.Liu, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.27 / 2.03
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	115.916, 136.52, 77.234, 90, 90, 90
R / Rfree (%)	22 / 25.4

The binding sites of Magnesium atom in the Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid (pdb code 8zk9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid, PDB code: 8zk9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid


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 the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:24.8 occ:1.00 OD1 A:ASN462 1.9 32.9 1.0 O1B A:TPP601 2.0 28.7 1.0 O A:GLY464 2.0 33.1 1.0 O2A A:TPP601 2.1 25.8 1.0 OD1 A:ASP435 2.1 30.1 1.0 O A:HOH755 2.6 25.8 1.0 CG A:ASN462 2.9 32.3 1.0 PB A:TPP601 3.2 28.4 1.0 CG A:ASP435 3.2 29.3 1.0 C A:GLY464 3.3 34.3 1.0 PA A:TPP601 3.3 29.0 1.0 ND2 A:ASN462 3.3 30.9 1.0 O3A A:TPP601 3.5 17.6 1.0 OD2 A:ASP435 3.7 35.4 1.0 O2B A:TPP601 3.7 34.1 1.0 N A:GLY464 4.0 38.3 1.0 O A:LEU460 4.0 35.9 1.0 N A:THR466 4.0 33.6 1.0 N A:ASP435 4.0 28.5 1.0 N A:GLY436 4.1 28.1 1.0 O7 A:TPP601 4.1 34.9 1.0 N A:TYR465 4.2 29.4 1.0 CA A:GLY464 4.2 35.6 1.0 CB A:ASN462 4.3 34.2 1.0 CA A:TYR465 4.3 32.6 1.0 O1A A:TPP601 4.4 27.2 1.0 N A:ASN462 4.4 30.7 1.0 OG1 A:THR466 4.4 32.0 1.0 O3B A:TPP601 4.5 28.1 1.0 CB A:ASP435 4.5 29.8 1.0 O A:HOH779 4.6 30.1 1.0 CB A:THR466 4.7 31.8 1.0 CA A:ASN462 4.7 36.3 1.0 CA A:ASP435 4.7 28.6 1.0 C A:ASN462 4.7 35.0 1.0 C A:TYR465 4.7 35.7 1.0 N A:GLU463 4.8 31.0 1.0 CA A:GLY434 4.8 28.2 1.0 C A:GLY434 4.8 30.6 1.0 C A:ASP435 4.9 28.6 1.0 CA A:GLY436 4.9 27.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid


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 the Decarboxylase KDC4427 Mutant E468L in Complex with Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:26.0 occ:1.00 OD1 B:ASN462 2.0 35.9 1.0 O3B B:TPP601 2.0 34.5 1.0 O B:GLY464 2.1 28.6 1.0 O2A B:TPP601 2.1 34.5 1.0 OD1 B:ASP435 2.2 32.5 1.0 O B:HOH734 2.3 26.3 1.0 CG B:ASN462 3.0 31.6 1.0 PB B:TPP601 3.1 31.3 1.0 C B:GLY464 3.3 30.4 1.0 PA B:TPP601 3.3 30.5 1.0 CG B:ASP435 3.3 30.3 1.0 ND2 B:ASN462 3.4 31.6 1.0 O1B B:TPP601 3.5 34.3 1.0 O3A B:TPP601 3.5 22.3 1.0 OD2 B:ASP435 3.8 32.4 1.0 O7 B:TPP601 3.9 41.5 1.0 N B:THR466 4.0 29.0 1.0 N B:GLY436 4.1 28.5 1.0 N B:ASP435 4.1 27.3 1.0 O B:LEU460 4.1 32.8 1.0 N B:GLY464 4.1 36.5 1.0 N B:TYR465 4.2 28.8 1.0 CA B:TYR465 4.2 35.6 1.0 CA B:GLY464 4.3 31.2 1.0 CB B:ASN462 4.4 32.4 1.0 OG1 B:THR466 4.4 37.4 1.0 O2B B:TPP601 4.5 35.6 1.0 N B:ASN462 4.5 32.9 1.0 CB B:ASP435 4.6 30.1 1.0 O B:HOH758 4.6 33.1 1.0 CB B:THR466 4.6 32.5 1.0 C B:TYR465 4.6 31.9 1.0 O1A B:TPP601 4.7 26.8 1.0 CA B:GLY434 4.7 28.1 1.0 CA B:ASP435 4.7 27.4 1.0 C B:GLY434 4.8 28.1 1.0 CA B:ASN462 4.8 31.9 1.0 C B:ASN462 4.9 36.5 1.0 CA B:GLY436 4.9 27.3 1.0 C B:ASP435 4.9 36.2 1.0 N B:GLU463 4.9 38.0 1.0 CA B:THR466 4.9 35.4 1.0

S.Dong, L.Liu, H.Zhang. Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Indole-3-Pyruvic Acid To Be Published.