Magnesium in PDB 7a19: 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae

The structure of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae, PDB code: 7a19 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)	47.64 / 1.21
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.794, 99.794, 129.177, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 17.1

The binding sites of Magnesium atom in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae (pdb code 7a19). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae, PDB code: 7a19:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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:7.7 occ:1.00 OE2 A:GLU8 2.0 8.9 1.0 OD1 A:ASP293 2.1 10.2 1.0 O A:HOH685 2.1 9.6 1.0 O A:HOH859 2.1 12.6 1.0 O A:HOH803 2.1 13.7 1.0 NE2 A:HIS167 2.2 8.7 1.0 CG A:ASP293 3.0 10.0 1.0 HG2 A:GLU8 3.1 10.7 1.0 CD2 A:HIS167 3.2 8.2 1.0 CD A:GLU8 3.2 8.2 1.0 CE1 A:HIS167 3.2 7.7 1.0 HD2 A:HIS167 3.3 9.9 1.0 HE1 A:HIS167 3.3 9.2 1.0 OD2 A:ASP293 3.4 10.1 1.0 HE2 A:HIS222 3.6 11.4 1.0 CG A:GLU8 3.7 8.9 1.0 O A:HOH1035 3.9 22.5 1.0 HE1 A:HIS222 4.0 10.8 1.0 HA A:ASP293 4.0 10.9 1.0 O A:HOH794 4.1 11.3 1.0 O A:HOH711 4.1 11.7 1.0 OE1 A:GLU8 4.2 8.6 1.0 O A:GLU8 4.2 9.4 1.0 ND1 A:HIS167 4.3 7.6 1.0 HD2 A:PHE296 4.3 14.8 1.0 NE2 A:HIS222 4.3 9.5 1.0 CG A:HIS167 4.3 8.1 1.0 HG3 A:GLU8 4.3 10.7 1.0 CB A:ASP293 4.4 8.5 1.0 CE1 A:HIS222 4.5 9.0 1.0 HD2 A:PRO168 4.5 9.9 1.0 HB3 A:GLU8 4.5 10.2 1.0 O A:HOH918 4.5 12.7 1.0 CA A:ASP293 4.7 9.1 1.0 CB A:GLU8 4.7 8.5 1.0 CD2 A:PHE296 4.8 12.3 1.0 HB2 A:ASP293 4.9 10.2 1.0 HE2 A:PHE296 4.9 15.6 1.0 HB2 A:ALA10 4.9 11.7 1.0 HB3 A:ASP293 5.0 10.2 1.0 O A:HOH663 5.0 9.1 1.0

Magnesium binding site 2 out of 3 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:8.8 occ:1.00 O B:HOH832 2.0 14.2 1.0 OD1 B:ASP293 2.1 10.7 1.0 OE2 B:GLU8 2.1 9.8 1.0 O B:HOH715 2.1 11.3 1.0 O B:HOH831 2.2 15.4 1.0 NE2 B:HIS167 2.2 9.3 1.0 CG B:ASP293 3.0 10.4 1.0 HG2 B:GLU8 3.1 11.2 1.0 CD2 B:HIS167 3.2 9.5 1.0 CD B:GLU8 3.2 8.8 1.0 CE1 B:HIS167 3.2 9.4 1.0 HD2 B:HIS167 3.3 11.4 1.0 OD2 B:ASP293 3.4 10.2 1.0 HE1 B:HIS167 3.4 11.2 1.0 HE2 B:HIS222 3.7 11.8 1.0 CG B:GLU8 3.7 9.3 1.0 O B:HOH1015 3.9 31.3 1.0 HA B:ASP293 4.0 11.3 1.0 HE1 B:HIS222 4.0 12.1 1.0 O B:HOH795 4.0 12.7 1.0 O B:HOH753 4.1 12.2 1.0 HD2 B:PHE296 4.2 16.3 1.0 O B:GLU8 4.3 9.9 1.0 OE1 B:GLU8 4.3 8.9 1.0 NE2 B:HIS222 4.3 9.8 1.0 ND1 B:HIS167 4.3 9.0 1.0 HG3 B:GLU8 4.3 11.2 1.0 CG B:HIS167 4.3 8.9 1.0 CB B:ASP293 4.4 9.3 1.0 O B:HOH906 4.4 15.6 1.0 CE1 B:HIS222 4.5 10.1 1.0 HD2 B:PRO168 4.5 11.3 1.0 HB3 B:GLU8 4.5 11.2 1.0 CA B:ASP293 4.7 9.4 1.0 CD2 B:PHE296 4.7 13.6 1.0 CB B:GLU8 4.7 9.3 1.0 HE2 B:PHE296 4.8 16.9 1.0 HB2 B:ASP293 4.9 11.2 1.0 HB2 B:ALA10 5.0 14.0 1.0 HB3 B:ASP293 5.0 11.2 1.0 HG2 B:PRO168 5.0 14.1 1.0

Magnesium binding site 3 out of 3 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 3 of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:30.0 occ:1.00 O B:HOH871 2.0 30.1 1.0 O B:HOH668 2.1 23.8 1.0 O B:HOH526 2.1 25.9 1.0 O B:HOH896 2.1 30.0 1.0 OE2 B:GLU17 2.3 20.9 1.0 CD B:GLU17 3.1 18.8 1.0 HH21 B:ARG21 3.3 23.4 1.0 OE1 B:GLU17 3.3 18.8 1.0 O B:HOH898 3.8 36.2 1.0 NH2 B:ARG21 4.0 19.5 1.0 O B:HOH903 4.0 25.4 1.0 HE B:ARG21 4.0 21.9 1.0 O B:HOH899 4.2 19.9 1.0 HH22 B:ARG21 4.4 23.4 1.0 O B:HOH541 4.5 18.8 1.0 CG B:GLU17 4.5 17.0 1.0 HG2 B:GLU17 4.6 20.4 1.0 O B:HOH870 4.6 29.7 1.0 NE B:ARG21 4.6 18.3 1.0 CZ B:ARG21 4.7 18.3 1.0 HG3 B:GLU17 4.9 20.4 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