Calcium in PDB 7wmd: Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don

The structure of Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don, PDB code: 7wmd was solved by M.Chen, H.Yang, F.Lv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.43 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.539, 90.536, 57.294, 90, 103.81, 90
R / Rfree (%)	16.8 / 21.7

The binding sites of Calcium atom in the Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don (pdb code 7wmd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don, PDB code: 7wmd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:4.5 occ:1.00 O A:HOH848 2.2 21.0 1.0 ND2 A:ASN400 2.2 20.6 1.0 OD1 A:ASP398 2.4 20.4 1.0 OD1 A:ASP433 2.4 35.7 1.0 OD2 A:ASP398 2.5 27.5 1.0 O A:HOH990 2.5 13.2 1.0 CG A:ASP398 2.8 23.1 1.0 OD2 A:ASP433 3.0 44.7 1.0 CG A:ASP433 3.1 37.6 1.0 CG A:ASN400 3.3 27.4 1.0 OD1 A:ASN400 3.7 21.7 1.0 O A:HOH712 3.8 35.2 1.0 CB A:ASP398 4.3 24.2 1.0 CB A:ASP433 4.4 33.5 1.0 CB A:ASN400 4.6 23.8 1.0 CA A:ASN400 4.9 19.4 1.0

Calcium binding site 2 out of 3 in the Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:20.9 occ:1.00 OE2 A:GLU306 2.4 33.4 1.0 O A:HOH932 2.5 26.5 1.0 CD A:GLU306 3.1 35.8 1.0 OE1 A:GLU306 3.3 41.7 1.0 NZ A:LYS349 3.7 19.3 1.0 O A:HOH742 3.8 36.0 1.0 CE A:LYS349 4.2 18.1 1.0 OD1 A:ASP410 4.4 20.8 1.0 CG A:GLU306 4.5 27.7 1.0 N A:ALA240 4.7 35.6 1.0 OD2 A:ASP410 4.9 19.1 1.0 CB A:ALA240 4.9 36.5 1.0

Calcium binding site 3 out of 3 in the Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pqq-Dependent Alcohol Dehydrogenase Detoxifying Don within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:2.1 occ:1.00 NZ A:LYS137 2.3 18.2 1.0 OE2 A:GLU205 2.3 29.8 1.0 OD1 A:ASP136 2.4 19.7 1.0 O A:HOH988 2.5 22.4 1.0 OD2 A:ASP136 2.7 21.8 1.0 OE1 A:GLU205 2.7 27.4 1.0 CD A:GLU205 2.9 25.5 1.0 CG A:ASP136 2.9 20.4 1.0 CE A:LYS137 3.2 20.4 1.0 CD A:LYS137 3.4 16.3 1.0 O A:HOH789 4.1 28.8 1.0 CG A:LYS137 4.2 17.6 1.0 CG A:GLU205 4.4 19.3 1.0 CB A:ASP136 4.4 19.2 1.0 O A:HOH889 4.6 22.8 1.0 N A:ASP136 5.0 17.6 1.0

H.Yang, R.Yan, Y.Li, Z.Lu, X.Bie, H.Zhao, F.Lu, M.Chen. Structure-Function Analysis of A Quinone-Dependent Dehydrogenase Capable of Deoxynivalenol Detoxification. J.Agric.Food Chem. V. 70 6764 2022.
ISSN: ESSN 1520-5118
PubMed: 35613468
DOI: 10.1021/ACS.JAFC.2C01083