Zinc in PDB 5lqq: Structure of Autotaxin (ENPP2) with LM350

All present enzymatic activity of Structure of Autotaxin (ENPP2) with LM350:
3.1.4.39;

The structure of Structure of Autotaxin (ENPP2) with LM350, PDB code: 5lqq was solved by W.J.Keune, T.Heidebrecht, E.Castelmur, R.P.Joosten, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.655, 89.067, 77.509, 90.00, 102.88, 90.00
R / Rfree (%)	21.7 / 26.2

The structure of Structure of Autotaxin (ENPP2) with LM350 also contains other interesting chemical elements:

Iodine	(I)	10 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Structure of Autotaxin (ENPP2) with LM350 (pdb code 5lqq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Autotaxin (ENPP2) with LM350, PDB code: 5lqq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Autotaxin (ENPP2) with LM350


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Autotaxin (ENPP2) with LM350 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn909 b:66.8 occ:1.00 OD2 A:ASP311 2.2 57.6 1.0 NE2 A:HIS474 2.3 47.5 1.0 NE2 A:HIS315 2.4 62.9 1.0 OD1 A:ASP311 2.7 57.1 1.0 CG A:ASP311 2.8 57.6 1.0 O A:HOH1073 2.8 53.7 1.0 CE1 A:HIS474 3.1 46.7 1.0 CE1 A:HIS315 3.2 63.3 1.0 CD2 A:HIS474 3.3 47.9 1.0 CD2 A:HIS315 3.6 63.8 1.0 CB A:ASP311 4.2 57.8 1.0 ND1 A:HIS474 4.3 46.5 1.0 OG1 A:THR209 4.4 44.2 1.0 ND1 A:HIS315 4.4 64.6 1.0 CG A:HIS474 4.4 47.2 1.0 CE1 A:HIS359 4.4 47.0 1.0 ZN A:ZN910 4.5 95.8 1.0 CG A:HIS315 4.6 64.8 1.0 NE2 A:HIS359 4.7 46.6 1.0 OD1 A:ASP171 4.9 52.0 1.0 CE A:MET361 4.9 52.5 1.0 OD2 A:ASP171 4.9 52.8 1.0

Zinc binding site 2 out of 2 in the Structure of Autotaxin (ENPP2) with LM350


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Autotaxin (ENPP2) with LM350 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn910 b:95.8 occ:1.00 OD1 A:ASP171 1.9 52.0 1.0 OG1 A:THR209 2.0 44.2 1.0 NE2 A:HIS359 2.5 46.6 1.0 OD2 A:ASP358 2.6 46.1 1.0 CG A:ASP171 2.7 51.6 1.0 CB A:THR209 2.8 43.4 1.0 OD2 A:ASP171 3.1 52.8 1.0 CE1 A:HIS359 3.1 47.0 1.0 CG2 A:THR209 3.1 43.2 1.0 CA A:THR209 3.2 42.8 1.0 CG A:ASP358 3.4 45.9 1.0 CD2 A:HIS359 3.5 46.0 1.0 OD1 A:ASP358 3.6 46.2 1.0 OD2 A:ASP311 3.7 57.6 1.0 N A:THR209 3.7 42.8 1.0 CB A:ASP171 4.0 50.9 1.0 ND1 A:HIS359 4.2 46.9 1.0 N A:GLY172 4.3 49.5 1.0 CG A:ASP311 4.3 57.6 1.0 CE1 A:HIS474 4.4 46.7 1.0 CA A:ASP171 4.4 50.0 1.0 CG A:HIS359 4.4 46.4 1.0 C A:LYS208 4.5 42.7 1.0 ZN A:ZN909 4.5 66.8 1.0 C A:THR209 4.6 42.4 1.0 NE2 A:HIS474 4.6 47.5 1.0 CB A:ASP358 4.7 45.3 1.0 C A:ASP171 4.7 50.2 1.0 OH A:TYR306 4.7 52.0 1.0 OD1 A:ASP311 4.8 57.1 1.0 O A:LYS208 5.0 42.4 1.0

L.M.Miller, W.J.Keune, D.Castagna, L.C.Young, E.L.Duffy, F.Potjewyd, F.Salgado-Polo, P.Engel Garcia, D.Semaan, J.M.Pritchard, A.Perrakis, S.J.Macdonald, C.Jamieson, A.J.Watson. Structure-Activity Relationships of Small Molecule Autotaxin Inhibitors with A Discrete Binding Mode. J. Med. Chem. V. 60 722 2017.
ISSN: ISSN 1520-4804
PubMed: 27982588
DOI: 10.1021/ACS.JMEDCHEM.6B01597