Magnesium in PDB 7wkm: Crystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol

The structure of Crystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol, PDB code: 7wkm 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)	24.96 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.415, 99.415, 128.921, 90, 90, 90
R / Rfree (%)	14.3 / 17.8

The binding sites of Magnesium atom in the Crystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol (pdb code 7wkm). 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 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol, PDB code: 7wkm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexed 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 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:18.9 occ:1.00 OD1 A:ASP293 2.0 15.5 1.0 O3 A:CAQ401 2.1 18.4 1.0 O A:HOH688 2.1 15.7 1.0 OE2 A:GLU8 2.1 16.0 1.0 NE2 A:HIS167 2.2 14.3 1.0 O A:HOH522 2.2 25.1 1.0 CG A:ASP293 3.0 16.4 1.0 CE1 A:HIS167 3.1 13.7 1.0 CD2 A:HIS167 3.2 15.8 1.0 CD A:GLU8 3.2 18.1 1.0 C3 A:CAQ401 3.3 17.4 1.0 OD2 A:ASP293 3.3 19.5 1.0 CG A:GLU8 3.7 15.9 1.0 O A:HOH704 3.7 15.7 1.0 C2 A:CAQ401 3.8 17.0 1.0 O A:HOH620 4.1 16.7 1.0 ND1 A:HIS167 4.3 14.0 1.0 NE2 A:HIS222 4.3 16.0 1.0 OE1 A:GLU8 4.3 16.4 1.0 O A:GLU8 4.3 15.2 1.0 CB A:ASP293 4.3 14.8 1.0 CG A:HIS167 4.3 12.0 1.0 C4 A:CAQ401 4.5 15.1 1.0 CE1 A:HIS222 4.6 17.1 1.0 CA A:ASP293 4.6 13.3 1.0 O4 A:CAQ401 4.7 16.0 1.0 CD2 A:PHE296 4.8 15.0 1.0 CB A:GLU8 4.8 13.9 1.0 O A:HOH673 4.9 13.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 2,3-Dihydroxybenzoate Decarboxylase Complexed 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 2,3-Dihydroxybenzoate Decarboxylase Complexed with Catechol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:23.1 occ:1.00 OD1 B:ASP293 2.0 15.3 1.0 OE2 B:GLU8 2.1 15.8 1.0 O B:HOH704 2.1 15.9 1.0 O4 B:CAQ401 2.1 18.1 1.0 NE2 B:HIS167 2.2 15.6 1.0 O B:HOH658 2.6 30.9 1.0 CG B:ASP293 2.9 18.2 1.0 CE1 B:HIS167 3.1 15.5 1.0 CD B:GLU8 3.2 16.0 1.0 CD2 B:HIS167 3.2 16.2 1.0 OD2 B:ASP293 3.3 19.1 1.0 C4 B:CAQ401 3.4 17.2 1.0 CG B:GLU8 3.6 13.7 1.0 O B:HOH696 3.8 15.7 1.0 C5 B:CAQ401 3.9 18.0 1.0 O B:HOH710 4.0 18.0 1.0 O B:GLU8 4.2 16.0 1.0 CB B:ASP293 4.2 15.8 1.0 ND1 B:HIS167 4.3 15.7 1.0 OE1 B:GLU8 4.3 16.4 1.0 CG B:HIS167 4.3 13.8 1.0 NE2 B:HIS222 4.3 15.6 1.0 CA B:ASP293 4.5 15.1 1.0 C3 B:CAQ401 4.5 17.3 1.0 CE1 B:HIS222 4.6 19.3 1.0 O3 B:CAQ401 4.7 17.0 1.0 CB B:GLU8 4.7 14.8 1.0 CD2 B:PHE296 4.7 18.4 1.0 O B:HOH584 5.0 15.8 1.0

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