Sodium 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:

Calcium	(Ca)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq (pdb code 7wmk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq, PDB code: 7wmk:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pqq-Dependent Alcohol Dehydrogenase Complexed with Pqq within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:0.7 occ:1.00 HZ3 A:LYS137 1.6 28.5 1.0 OE1 A:GLU205 1.8 33.6 1.0 H1 A:ACT603 1.8 27.3 1.0 HZ1 A:LYS137 2.0 28.5 1.0 NZ A:LYS137 2.1 23.8 1.0 O A:ACT603 2.3 25.4 1.0 OD1 A:ASP136 2.3 22.0 1.0 CH3 A:ACT603 2.4 22.8 1.0 CD A:GLU205 2.4 27.3 1.0 OE2 A:GLU205 2.5 29.5 1.0 H3 A:ACT603 2.6 27.3 1.0 OD2 A:ASP136 2.7 21.5 1.0 HZ2 A:LYS137 2.8 28.5 1.0 C A:ACT603 2.8 35.1 1.0 CG A:ASP136 2.8 19.9 1.0 CE A:LYS137 3.2 19.7 1.0 HD2 A:LYS137 3.3 19.4 1.0 H2 A:ACT603 3.3 27.3 1.0 HE2 A:LYS137 3.3 23.6 1.0 HG3 A:LYS137 3.5 17.1 1.0 CD A:LYS137 3.6 16.2 1.0 CG A:GLU205 3.9 23.8 1.0 HE3 A:LYS137 4.0 23.6 1.0 OXT A:ACT603 4.0 44.5 1.0 CG A:LYS137 4.1 14.3 1.0 O A:HOH714 4.1 30.1 1.0 HG2 A:GLU205 4.2 28.5 1.0 H A:ASP136 4.2 19.2 1.0 CB A:ASP136 4.3 16.0 1.0 HG3 A:GLU205 4.3 28.5 1.0 O A:HOH945 4.4 26.8 1.0 HD3 A:LYS137 4.5 19.4 1.0 HG2 A:LYS137 4.6 17.1 1.0 HA A:GLU205 4.6 20.0 1.0 HB3 A:ASP136 4.6 19.2 1.0 HB2 A:ASP136 4.8 19.2 1.0 HB3 A:GLU205 4.9 22.9 1.0 N A:ASP136 4.9 16.1 1.0 CB A:GLU205 5.0 19.1 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