Zinc in PDB 5ijq: Crystal Structure of Autotaxin (ENPP2) Re-Refined

All present enzymatic activity of Crystal Structure of Autotaxin (ENPP2) Re-Refined:
3.1.4.39;

The structure of Crystal Structure of Autotaxin (ENPP2) Re-Refined, PDB code: 5ijq was solved by J.Hausmann, R.P.Joosten, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.808, 63.289, 70.471, 98.78, 106.22, 99.77
R / Rfree (%)	15.4 / 19.7

The structure of Crystal Structure of Autotaxin (ENPP2) Re-Refined also contains other interesting chemical elements:

Iodine	(I)	25 atoms
Calcium	(Ca)	1 atom
Sodium	(Na)	2 atoms

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

Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Autotaxin (ENPP2) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:33.4 occ:1.00 NE2 A:HIS474 2.1 24.6 1.0 NE2 A:HIS315 2.1 28.6 1.0 OD1 A:ASP311 2.1 24.0 1.0 O2 A:PO4908 2.1 42.6 1.0 OD2 A:ASP311 2.6 31.2 1.0 CG A:ASP311 2.7 28.4 1.0 O1 A:PO4908 2.8 46.1 1.0 P A:PO4908 3.0 43.6 1.0 CE1 A:HIS315 3.0 29.4 1.0 CE1 A:HIS474 3.0 25.2 1.0 CD2 A:HIS474 3.1 27.1 1.0 CD2 A:HIS315 3.1 28.8 1.0 O4 A:PO4908 3.9 36.3 1.0 CE1 A:HIS359 4.1 26.9 1.0 ND1 A:HIS315 4.1 32.2 1.0 O3 A:PO4908 4.1 48.3 1.0 ND1 A:HIS474 4.1 26.2 1.0 CB A:ASP311 4.2 31.2 1.0 CG A:HIS315 4.2 30.9 1.0 CG A:HIS474 4.2 26.0 1.0 NE2 A:HIS359 4.3 25.4 1.0 ZN A:ZN907 4.4 50.5 1.0 CE A:MET361 4.5 30.8 1.0 OD1 A:ASP171 4.6 30.8 1.0 OG1 A:THR209 4.8 42.5 1.0 O A:ASP311 4.9 28.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin (ENPP2) Re-Refined


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Autotaxin (ENPP2) Re-Refined within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn907 b:50.5 occ:1.00 OG1 A:THR209 1.6 42.5 1.0 OD1 A:ASP171 1.9 30.8 1.0 NE2 A:HIS359 2.1 25.4 1.0 O1 A:PO4908 2.6 46.1 1.0 CG A:ASP171 2.6 31.3 1.0 OD2 A:ASP358 2.6 42.3 1.0 OD2 A:ASP171 2.8 37.2 1.0 CB A:THR209 2.9 32.9 1.0 CD2 A:HIS359 3.0 28.5 1.0 CE1 A:HIS359 3.0 26.9 1.0 CG A:ASP358 3.4 33.4 1.0 OD1 A:ASP358 3.4 31.7 1.0 CA A:THR209 3.5 28.7 1.0 CG2 A:THR209 3.5 34.0 1.0 O4 A:PO4908 3.8 36.3 1.0 P A:PO4908 3.8 43.6 1.0 N A:THR209 3.8 26.6 1.0 OD1 A:ASP311 3.9 24.0 1.0 CB A:ASP171 4.0 30.5 1.0 ND1 A:HIS359 4.1 28.2 1.0 CG A:HIS359 4.1 28.4 1.0 CG A:ASP311 4.3 28.4 1.0 CE1 A:HIS474 4.3 25.2 1.0 N A:GLY172 4.3 28.9 1.0 ZN A:ZN906 4.4 33.4 1.0 CA A:ASP171 4.4 30.1 1.0 NE2 A:HIS474 4.6 24.6 1.0 C A:ASP171 4.7 31.2 1.0 C A:LYS208 4.7 25.0 1.0 CB A:ASP311 4.7 31.2 1.0 CB A:ASP358 4.8 32.0 1.0 O2 A:PO4908 4.8 42.6 1.0 OD2 A:ASP311 4.8 31.2 1.0 O3 A:PO4908 4.8 48.3 1.0 C A:THR209 4.9 24.5 1.0

J.Hausmann, W.J.Keune, A.L.Hipgrave Ederveen, L.Van Zeijl, R.P.Joosten, A.Perrakis. Structural Snapshots of the Catalytic Cycle of the Phosphodiesterase Autotaxin. J.Struct.Biol. V. 195 199 2016.
ISSN: ESSN 1095-8657
PubMed: 27268273
DOI: 10.1016/J.JSB.2016.06.002