Zinc in PDB 5inh: Crystal Structure of Autotaxin/ENPP2 with A Covalent Fragment

All present enzymatic activity of Crystal Structure of Autotaxin/ENPP2 with A Covalent Fragment:
3.1.4.39;

The structure of Crystal Structure of Autotaxin/ENPP2 with A Covalent Fragment, PDB code: 5inh was solved by M.G.Klein, R.Tjhen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.51 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.358, 80.745, 76.480, 90.00, 102.86, 90.00
R / Rfree (%)	17.2 / 20.7

The structure of Crystal Structure of Autotaxin/ENPP2 with A Covalent Fragment also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Autotaxin/ENPP2 with A Covalent Fragment (pdb code 5inh). 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 with A Covalent Fragment, PDB code: 5inh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin/ENPP2 with A Covalent Fragment


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 with A Covalent Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:24.0 occ:1.00 OD1 A:ASP171 2.0 25.3 1.0 OG1 A:THR209 2.0 22.3 1.0 OD2 A:ASP358 2.1 23.1 1.0 NE2 A:HIS359 2.1 20.8 1.0 O1 A:6C1914 2.6 22.0 1.0 CG A:ASP171 2.7 23.8 1.0 B2 A:6C1914 2.8 20.7 1.0 OD2 A:ASP171 2.9 24.9 1.0 CD2 A:HIS359 3.0 19.9 1.0 CG A:ASP358 3.0 21.7 1.0 CE1 A:HIS359 3.1 19.9 1.0 CB A:THR209 3.1 21.9 1.0 OD1 A:ASP358 3.3 21.1 1.0 CA A:THR209 3.5 20.6 1.0 CG2 A:THR209 3.6 22.3 1.0 O3 A:6C1914 3.8 18.5 1.0 N A:THR209 3.9 19.9 1.0 O10 A:6C1914 4.0 28.2 1.0 C4 A:6C1914 4.0 24.5 1.0 CB A:ASP171 4.1 23.2 1.0 CG A:HIS359 4.1 19.6 1.0 ND1 A:HIS359 4.1 20.5 1.0 N A:GLY172 4.2 21.9 1.0 CG A:ASP311 4.2 26.3 1.0 CE1 A:HIS474 4.3 21.9 1.0 OD2 A:ASP311 4.3 29.6 1.0 OD1 A:ASP311 4.3 25.5 1.0 CB A:ASP358 4.4 20.6 1.0 ZN A:ZN902 4.4 25.3 1.0 C9 A:6C1914 4.4 27.5 1.0 CA A:ASP171 4.4 22.8 1.0 NE2 A:HIS474 4.5 21.9 1.0 C A:ASP171 4.6 22.4 1.0 C A:LYS208 4.7 21.1 1.0 CB A:ASP311 4.8 24.6 1.0 C11 A:6C1914 4.9 29.9 1.0 C A:THR209 4.9 20.2 1.0 CA A:GLY172 4.9 20.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin/ENPP2 with A Covalent Fragment


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 with A Covalent Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:25.3 occ:1.00 OXT A:ACT913 2.0 33.7 1.0 OD2 A:ASP311 2.1 29.6 1.0 NE2 A:HIS315 2.1 25.2 1.0 NE2 A:HIS474 2.1 21.9 1.0 O1 A:6C1914 2.2 22.0 1.0 OD1 A:ASP311 2.7 25.5 1.0 CG A:ASP311 2.7 26.3 1.0 C A:ACT913 3.0 35.1 1.0 CE1 A:HIS474 3.1 21.9 1.0 CD2 A:HIS315 3.1 25.4 1.0 CE1 A:HIS315 3.1 25.3 1.0 CD2 A:HIS474 3.2 22.0 1.0 O A:ACT913 3.3 38.8 1.0 B2 A:6C1914 3.5 20.7 1.0 O3 A:6C1914 3.8 18.5 1.0 O10 A:6C1914 4.0 28.2 1.0 CE1 A:HIS359 4.2 19.9 1.0 ND1 A:HIS315 4.2 26.3 1.0 CB A:ASP311 4.2 24.6 1.0 ND1 A:HIS474 4.2 21.0 1.0 C4 A:6C1914 4.2 24.5 1.0 CG A:HIS315 4.2 26.5 1.0 CG A:HIS474 4.3 21.0 1.0 CH3 A:ACT913 4.3 36.4 1.0 O A:HOH1015 4.3 46.9 1.0 NE2 A:HIS359 4.4 20.8 1.0 ZN A:ZN901 4.4 24.0 1.0 C9 A:6C1914 4.5 27.5 1.0 C18 A:6C1914 4.5 35.6 1.0 OD1 A:ASP171 4.6 25.3 1.0 OG1 A:THR209 4.6 22.3 1.0 CE A:MET361 4.7 23.6 1.0

M.Lanier, D.C.Cole, Y.Istratiy, M.G.Klein, P.A.Schwartz, R.Tjhen, A.Jennings, M.S.Hixon. Repurposing Suzuki Coupling Reagents As A Directed Fragment Library Targeting Serine Hydrolases and Related Enzymes. J. Med. Chem. V. 60 5209 2017.
ISSN: ISSN 1520-4804
PubMed: 28564542
DOI: 10.1021/ACS.JMEDCHEM.6B01224