Magnesium in PDB 7a1a: 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae

The structure of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae, PDB code: 7a1a was solved by G.Hofer, W.Keller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.95 / 1.53
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.894, 99.894, 129.168, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.5

The structure of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae (pdb code 7a1a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae, PDB code: 7a1a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:16.6 occ:1.00 O A:HOH653 2.0 19.7 1.0 O A:HOH656 2.0 20.1 1.0 O A:HOH711 2.1 23.0 1.0 OD1 A:ASP293 2.2 16.3 1.0 OE2 A:GLU8 2.2 14.7 1.0 NE2 A:HIS167 2.3 12.6 1.0 CG A:ASP293 3.0 23.2 1.0 HG2 A:GLU8 3.0 20.8 1.0 CE1 A:HIS167 3.2 9.8 1.0 CD A:GLU8 3.2 14.6 1.0 OD2 A:ASP293 3.2 23.0 1.0 CD2 A:HIS167 3.3 11.4 1.0 HE1 A:HIS167 3.3 11.7 1.0 HD2 A:HIS167 3.4 13.7 1.0 CG A:GLU8 3.6 17.4 1.0 O A:HOH822 3.7 19.6 1.0 O A:HOH725 3.9 17.2 1.0 HA A:ASP293 4.0 12.8 1.0 O A:HOH688 4.0 19.9 1.0 HE1 A:HIS222 4.2 18.1 1.0 HG3 A:GLU8 4.2 20.8 1.0 HD2 A:PHE296 4.2 14.5 1.0 OE1 A:GLU8 4.3 12.6 1.0 ND1 A:HIS167 4.3 11.4 1.0 CB A:ASP293 4.3 12.7 1.0 O A:GLU8 4.3 16.0 1.0 NE2 A:HIS222 4.3 12.8 1.0 CG A:HIS167 4.4 13.6 1.0 HB3 A:GLU8 4.6 16.0 1.0 O A:HOH760 4.6 25.7 1.0 HD2 A:PRO168 4.6 11.6 1.0 CE1 A:HIS222 4.6 15.1 1.0 CA A:ASP293 4.6 10.7 1.0 CB A:GLU8 4.7 13.3 1.0 HB2 A:ASP293 4.7 15.3 1.0 CD2 A:PHE296 4.8 12.1 1.0 HE2 A:PHE296 4.8 17.8 1.0 HB2 A:ALA10 4.8 17.7 1.0 O A:HOH610 5.0 13.8 1.0 HB3 A:ASP293 5.0 15.3 1.0

Magnesium binding site 2 out of 2 in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:16.1 occ:0.73 O B:HOH720 2.1 24.2 1.0 O B:HOH697 2.1 20.5 1.0 OD1 B:ASP293 2.2 21.9 1.0 OE2 B:GLU8 2.2 19.1 1.0 O B:HOH756 2.2 37.6 1.0 NE2 B:HIS167 2.4 14.1 1.0 HG2 B:GLU8 3.0 20.6 1.0 CG B:ASP293 3.1 27.6 1.0 CD B:GLU8 3.2 17.3 1.0 CE1 B:HIS167 3.3 11.5 1.0 CD2 B:HIS167 3.3 14.0 1.0 OD2 B:ASP293 3.4 43.4 1.0 HE1 B:HIS167 3.4 13.8 1.0 HD2 B:HIS167 3.5 16.8 1.0 O B:HOH812 3.6 22.8 1.0 CG B:GLU8 3.6 17.1 1.0 O B:HOH731 3.9 17.4 1.0 HA B:ASP293 4.0 15.6 1.0 HD2 B:PHE296 4.1 19.1 1.0 O B:HOH626 4.1 18.8 1.0 HG3 B:GLU8 4.2 20.6 1.0 HE1 B:HIS222 4.3 21.1 1.0 OE1 B:GLU8 4.3 15.8 1.0 CB B:ASP293 4.3 14.6 1.0 O B:GLU8 4.3 19.2 1.0 NE2 B:HIS222 4.4 16.0 1.0 O B:HOH724 4.4 25.6 1.0 ND1 B:HIS167 4.4 13.2 1.0 O B:HOH762 4.4 31.9 1.0 CG B:HIS167 4.4 13.1 1.0 HE2 B:PHE296 4.6 20.7 1.0 HD2 B:PRO168 4.6 13.2 1.0 CD2 B:PHE296 4.6 15.9 1.0 HB3 B:GLU8 4.6 17.5 1.0 HB2 B:ASP293 4.6 17.5 1.0 CA B:ASP293 4.6 13.0 1.0 CE1 B:HIS222 4.7 17.6 1.0 O B:HOH686 4.7 23.0 1.0 CB B:GLU8 4.8 14.6 1.0 CE2 B:PHE296 4.9 17.2 1.0 HB2 B:ALA10 5.0 20.0 1.0

G.Hofer, X.Sheng, S.Braeuer, S.E.Payer, K.Plasch, W.Goessler, K.Faber, W.Keller, F.Himo, S.M.Glueck. Metal Ion Promiscuity and Structure of 2,3-Dihydroxybenzoic Acid Decarboxylase of Aspergillus Oryzae. Chembiochem 2020.
ISSN: ESSN 1439-7633
PubMed: 33090643
DOI: 10.1002/CBIC.202000600