Magnesium in PDB 8zk8: Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Indole-3-Pyruvic Acid

The structure of Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Indole-3-Pyruvic Acid, PDB code: 8zk8 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)	19.98 / 2.16
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.871, 136.857, 77.265, 90, 90, 90
R / Rfree (%)	18.2 / 22

The binding sites of Magnesium atom in the Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Indole-3-Pyruvic Acid (pdb code 8zk8). 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 Indole-3-Pyruvic Acid, PDB code: 8zk8:
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 Indole-3-Pyruvic 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 Indole-3-Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:23.3 occ:1.00 OD1 A:ASN462 1.9 29.4 1.0 O A:HOH747 2.0 25.1 1.0 O2A A:TPP601 2.0 26.3 1.0 O A:GLY464 2.1 30.1 1.0 O2B A:TPP601 2.1 25.9 1.0 OD1 A:ASP435 2.1 27.4 1.0 CG A:ASN462 3.0 32.9 1.0 CG A:ASP435 3.2 30.0 1.0 C A:GLY464 3.3 39.3 1.0 PA A:TPP601 3.3 29.4 1.0 PB A:TPP601 3.3 31.1 1.0 ND2 A:ASN462 3.4 34.5 1.0 O3A A:TPP601 3.4 14.7 1.0 OD2 A:ASP435 3.7 32.4 1.0 O3B A:TPP601 3.8 31.4 1.0 N A:GLY464 4.0 29.8 1.0 N A:GLY436 4.1 26.3 1.0 O A:LEU460 4.1 33.5 1.0 N A:ASP435 4.1 26.2 1.0 O7 A:TPP601 4.1 30.9 1.0 N A:TYR465 4.2 31.0 1.0 N A:THR466 4.2 26.5 1.0 CG2 A:THR466 4.2 30.0 1.0 CA A:GLY464 4.3 27.8 1.0 CA A:TYR465 4.3 26.2 1.0 CB A:ASN462 4.3 32.8 1.0 N A:ASN462 4.4 31.7 1.0 O1A A:TPP601 4.5 22.5 1.0 CB A:ASP435 4.5 26.3 1.0 O1B A:TPP601 4.6 27.0 1.0 CA A:ASP435 4.7 25.5 1.0 CA A:ASN462 4.7 33.9 1.0 C A:ASN462 4.8 34.4 1.0 CA A:GLY434 4.8 29.7 1.0 N A:GLU463 4.8 29.0 1.0 C A:TYR465 4.8 31.2 1.0 C A:GLY434 4.9 32.9 1.0 C A:ASP435 4.9 24.8 1.0 CA A:GLY436 4.9 26.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Decarboxylase KDC4427 Mutant E468L in Complex with Indole-3-Pyruvic 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 Indole-3-Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:27.5 occ:1.00 O B:HOH735 1.9 30.7 1.0 O2A B:TPP601 2.0 36.8 1.0 OD1 B:ASN462 2.1 35.6 1.0 O B:GLY464 2.1 30.4 1.0 O3B B:TPP601 2.1 34.2 1.0 OD1 B:ASP435 2.2 33.0 1.0 CG B:ASN462 3.1 35.5 1.0 PA B:TPP601 3.2 35.1 1.0 PB B:TPP601 3.2 39.2 1.0 CG B:ASP435 3.3 32.5 1.0 C B:GLY464 3.3 32.3 1.0 O3A B:TPP601 3.4 24.1 1.0 ND2 B:ASN462 3.4 38.4 1.0 OD2 B:ASP435 3.8 31.7 1.0 O1B B:TPP601 3.9 32.4 1.0 N B:THR466 4.0 32.1 1.0 O7 B:TPP601 4.1 35.4 1.0 N B:ASP435 4.1 32.3 1.0 N B:GLY464 4.1 35.2 1.0 N B:GLY436 4.1 28.7 1.0 O B:LEU460 4.1 37.9 1.0 N B:TYR465 4.2 32.0 1.0 CA B:TYR465 4.3 35.1 1.0 CA B:GLY464 4.3 34.9 1.0 O1A B:TPP601 4.4 26.2 1.0 CB B:ASN462 4.4 32.8 1.0 O2B B:TPP601 4.5 32.6 1.0 N B:ASN462 4.5 32.6 1.0 CB B:ASP435 4.6 26.9 1.0 O B:HOH804 4.6 36.5 1.0 OG1 B:THR466 4.7 33.0 1.0 CB B:THR466 4.7 29.0 1.0 C B:TYR465 4.7 34.8 1.0 CA B:ASP435 4.7 28.6 1.0 CA B:GLY434 4.7 28.4 1.0 CA B:ASN462 4.8 33.8 1.0 C B:ASN462 4.8 33.8 1.0 C B:GLY434 4.8 31.6 1.0 N B:GLU463 4.9 36.3 1.0 C B:ASP435 4.9 31.4 1.0 CA B:GLY436 4.9 30.5 1.0 CA B:THR466 4.9 31.7 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.