Magnesium in PDB 7wkl: Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol

The structure of Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol, PDB code: 7wkl was solved by F.Yan, X.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.47 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.282, 105.708, 181.659, 90, 90, 90
R / Rfree (%)	13.9 / 17.8

The binding sites of Magnesium atom in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol (pdb code 7wkl). 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 Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol, PDB code: 7wkl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol


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 Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:24.6 occ:1.00 OD1 A:ASP293 2.1 19.3 1.0 OE2 A:GLU8 2.1 17.5 1.0 O3 A:CAQ401 2.2 19.4 1.0 O A:HOH741 2.2 17.6 1.0 NE2 A:HIS167 2.2 17.3 1.0 O A:HOH512 2.4 30.5 1.0 CG A:ASP293 3.0 18.6 1.0 CD A:GLU8 3.1 18.6 1.0 CE1 A:HIS167 3.2 14.8 1.0 CD2 A:HIS167 3.2 15.0 1.0 OD2 A:ASP293 3.3 19.4 1.0 C3 A:CAQ401 3.4 20.6 1.0 CG A:GLU8 3.6 16.2 1.0 C2 A:CAQ401 3.9 21.4 1.0 O A:HOH681 3.9 16.3 1.0 O A:HOH660 4.1 18.3 1.0 OE1 A:GLU8 4.2 14.3 1.0 CB A:ASP293 4.3 15.1 1.0 ND1 A:HIS167 4.3 16.8 1.0 NE2 A:HIS222 4.3 14.5 1.0 CG A:HIS167 4.3 13.6 1.0 O A:GLU8 4.4 17.0 1.0 C4 A:CAQ401 4.5 18.5 1.0 O B:HOH545 4.5 24.3 1.0 CA A:ASP293 4.6 14.3 1.0 CE1 A:HIS222 4.6 17.3 1.0 O4 A:CAQ401 4.7 17.6 1.0 CD2 A:TYR296 4.7 17.8 1.0 CB A:GLU8 4.7 15.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol


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 Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:27.3 occ:1.00 OD1 B:ASP293 2.0 19.4 1.0 OE2 B:GLU8 2.1 17.0 1.0 O B:HOH617 2.2 19.6 1.0 NE2 B:HIS167 2.2 16.3 1.0 O B:HOH610 2.3 28.3 1.0 O4 B:CAQ401 2.4 18.4 1.0 CG B:ASP293 2.9 20.1 1.0 CD B:GLU8 3.1 16.0 1.0 CD2 B:HIS167 3.1 18.1 1.0 OD2 B:ASP293 3.1 19.9 1.0 CE1 B:HIS167 3.2 16.7 1.0 CG B:GLU8 3.5 14.1 1.0 C4 B:CAQ401 3.6 21.3 1.0 O B:HOH731 3.9 16.6 1.0 C5 B:CAQ401 4.1 21.9 1.0 O B:HOH583 4.1 18.2 1.0 CB B:ASP293 4.2 15.1 1.0 OE1 B:GLU8 4.2 15.1 1.0 O B:GLU8 4.3 16.3 1.0 NE2 B:HIS222 4.3 17.9 1.0 CG B:HIS167 4.3 14.6 1.0 ND1 B:HIS167 4.3 18.1 1.0 CA B:ASP293 4.5 14.8 1.0 O A:HOH582 4.5 25.6 1.0 CE1 B:HIS222 4.6 17.8 1.0 C3 B:CAQ401 4.7 22.0 1.0 CB B:GLU8 4.7 15.2 1.0 O3 B:CAQ401 4.8 21.3 1.0 CD2 B:TYR296 5.0 18.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol


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 Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:23.9 occ:1.00 OD1 C:ASP293 2.1 17.7 1.0 OE2 C:GLU8 2.1 16.4 1.0 O C:HOH694 2.2 15.3 1.0 NE2 C:HIS167 2.2 13.9 1.0 O3 C:CAQ401 2.3 20.0 1.0 O C:HOH515 2.3 28.7 1.0 CG C:ASP293 2.9 17.7 1.0 CD C:GLU8 3.1 14.4 1.0 CD2 C:HIS167 3.2 14.3 1.0 CE1 C:HIS167 3.2 16.0 1.0 OD2 C:ASP293 3.2 17.9 1.0 C3 C:CAQ401 3.6 21.6 1.0 CG C:GLU8 3.6 13.6 1.0 O C:HOH710 3.9 14.8 1.0 O C:HOH701 4.0 16.7 1.0 C2 C:CAQ401 4.1 22.9 1.0 OE1 C:GLU8 4.2 14.6 1.0 CB C:ASP293 4.3 11.9 1.0 O C:GLU8 4.3 17.1 1.0 ND1 C:HIS167 4.3 14.5 1.0 CG C:HIS167 4.3 13.2 1.0 NE2 C:HIS222 4.3 15.4 1.0 O D:HOH751 4.4 24.2 1.0 CE1 C:HIS222 4.6 16.8 1.0 CA C:ASP293 4.6 12.9 1.0 C4 C:CAQ401 4.6 16.8 1.0 CB C:GLU8 4.7 14.4 1.0 CD2 C:TYR296 4.7 18.2 1.0 O4 C:CAQ401 4.8 17.6 1.0 O C:HOH617 4.9 14.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol


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 Dihydroxybenzoate Decarboxylase Mutant F296Y From Aspergillus Oryzae in Complex with Catechol within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:24.3 occ:1.00 OD1 D:ASP293 2.1 18.7 1.0 O D:HOH664 2.1 17.2 1.0 OE2 D:GLU8 2.1 16.9 1.0 NE2 D:HIS167 2.2 13.3 1.0 O3 D:CAQ401 2.3 19.4 1.0 O D:HOH549 2.5 28.6 1.0 CG D:ASP293 2.9 20.0 1.0 CE1 D:HIS167 3.1 13.6 1.0 CD2 D:HIS167 3.1 14.6 1.0 CD D:GLU8 3.1 15.0 1.0 OD2 D:ASP293 3.2 22.6 1.0 CG D:GLU8 3.5 12.9 1.0 C3 D:CAQ401 3.5 21.3 1.0 O D:HOH745 3.9 15.4 1.0 C2 D:CAQ401 4.1 20.9 1.0 O D:HOH584 4.1 16.8 1.0 ND1 D:HIS167 4.2 13.8 1.0 CB D:ASP293 4.3 16.4 1.0 OE1 D:GLU8 4.3 13.9 1.0 CG D:HIS167 4.3 16.2 1.0 NE2 D:HIS222 4.3 14.8 1.0 O D:GLU8 4.4 17.0 1.0 CA D:ASP293 4.6 15.1 1.0 O C:HOH698 4.6 24.6 1.0 C4 D:CAQ401 4.6 20.3 1.0 CE1 D:HIS222 4.6 17.3 1.0 CB D:GLU8 4.7 14.5 1.0 O4 D:CAQ401 4.7 19.6 1.0 CD2 D:TYR296 4.8 19.4 1.0

F.Yan, X.Song. Molecular Mechanism of Reversible Decarboxylase with Efficient CO2 Fixation To Be Published.