Calcium in PDB 7wmk: Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq

The structure of Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq, PDB code: 7wmk 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)	44.15 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.973, 91.19, 57.332, 90, 103.78, 90
R / Rfree (%)	13.8 / 14

The structure of Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq (pdb code 7wmk). 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 Complexed with Pqq, PDB code: 7wmk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq


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 Complexed with Pqq within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:10.9 occ:1.00 HE22 A:GLN191 1.7 52.2 1.0 O7A A:PQQ601 2.3 41.5 1.0 N6 A:PQQ601 2.3 23.5 1.0 O5 A:PQQ601 2.3 21.9 1.0 NE2 A:GLN191 2.4 43.6 1.0 HE21 A:GLN191 2.7 52.2 1.0 OE1 A:GLU306 2.8 34.7 1.0 OD1 A:ASP304 2.8 40.1 1.0 C5 A:PQQ601 3.1 26.6 1.0 C6A A:PQQ601 3.1 23.0 1.0 CD A:GLU306 3.1 30.8 1.0 C7X A:PQQ601 3.1 28.6 1.0 HG3 A:GLU306 3.1 31.3 1.0 C7 A:PQQ601 3.4 42.3 1.0 CD A:GLN191 3.4 40.5 1.0 HE1 A:TRP241 3.5 22.7 1.0 CG A:GLU306 3.6 26.1 1.0 CG A:ASP304 3.7 37.0 1.0 OE1 A:GLN191 3.7 34.8 1.0 HZ1 A:LYS349 3.8 21.5 1.0 OD2 A:ASP304 3.8 40.5 1.0 OE2 A:GLU306 3.8 36.0 1.0 O A:HOH702 3.9 28.9 1.0 O A:HOH730 4.0 23.7 1.0 HG2 A:GLU306 4.1 31.3 1.0 NE1 A:TRP241 4.1 18.9 1.0 HZ2 A:TRP241 4.3 24.6 1.0 O7B A:PQQ601 4.3 23.4 1.0 C9A A:PQQ601 4.4 20.7 1.0 HZ2 A:LYS349 4.4 21.5 1.0 C4 A:PQQ601 4.5 24.1 1.0 NZ A:LYS349 4.5 18.0 1.0 C8 A:PQQ601 4.6 24.9 1.0 HB2 A:GLN191 4.6 28.8 1.0 CG A:GLN191 4.7 24.7 1.0 CE2 A:TRP241 4.7 18.7 1.0 HG2 A:GLN191 4.7 29.6 1.0 CZ2 A:TRP241 4.8 20.6 1.0 HB3 A:GLU306 4.9 25.9 1.0 CD1 A:TRP241 4.9 18.6 1.0 CB A:GLU306 5.0 21.6 1.0

Calcium binding site 2 out of 3 in the Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq


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 Complexed with Pqq within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:9.0 occ:1.00 CL A:CL610 2.3 56.6 1.0 CL A:CL609 2.5 30.9 1.0 HB1 A:ALA158 3.9 20.5 1.0 O A:ALA158 4.1 16.6 1.0 HA A:ALA158 4.2 19.2 1.0 C A:ALA158 4.7 15.8 1.0 CB A:ALA158 4.7 17.1 1.0 CA A:ALA158 4.8 16.0 1.0 HZ1 A:LYS137 4.8 28.5 1.0 HD1 A:TRP159 4.9 17.6 1.0 HZ2 A:LYS137 4.9 28.5 1.0 HE3 A:LYS137 5.0 23.6 1.0

Calcium binding site 3 out of 3 in the Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq


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 Complexed with Pqq within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:16.7 occ:1.00 ND1 A:HIS295 2.3 19.2 1.0 O A:HOH990 2.4 38.1 1.0 CE1 A:HIS295 3.1 19.6 1.0 HE1 A:HIS295 3.1 23.5 1.0 HB2 A:HIS295 3.4 20.3 1.0 O A:HOH993 3.4 43.3 1.0 CG A:HIS295 3.4 16.9 1.0 CB A:HIS295 3.9 17.0 1.0 HA A:HIS295 4.0 20.2 1.0 O A:LYS294 4.0 19.6 1.0 O A:GLY361 4.2 19.9 1.0 NE2 A:HIS295 4.3 18.6 1.0 CD2 A:HIS295 4.5 18.1 1.0 CA A:HIS295 4.5 16.9 1.0 O A:HOH911 4.5 39.2 1.0 HE1 A:PHE356 4.6 20.6 1.0 O A:HOH916 4.6 23.8 1.0 O A:LYS381 4.7 21.7 1.0 HB3 A:HIS295 4.7 20.3 1.0 HB2 A:TYR363 4.8 22.0 1.0 C A:LYS294 5.0 16.9 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