Zinc in PDB 3wax: Crystal Structure of Autotaxin in Complex with 3BOA

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with 3BOA:
3.1.4.39;

The structure of Crystal Structure of Autotaxin in Complex with 3BOA, PDB code: 3wax was solved by H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.24 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.607, 94.479, 75.305, 90.00, 93.90, 90.00
R / Rfree (%)	17.8 / 22.4

The structure of Crystal Structure of Autotaxin in Complex with 3BOA also contains other interesting chemical elements:

Potassium	(K)	1 atom
Calcium	(Ca)	1 atom
Chlorine	(Cl)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Autotaxin in Complex with 3BOA (pdb code 3wax). 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 in Complex with 3BOA, PDB code: 3wax:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin in Complex with 3BOA


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 in Complex with 3BOA within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn912 b:20.4 occ:1.00 OD1 A:ASP171 1.9 19.3 1.0 OG1 A:THR209 2.0 18.6 1.0 OD2 A:ASP358 2.1 19.3 1.0 NE2 A:HIS359 2.1 19.5 1.0 OBD A:DWX936 2.4 22.5 0.5 OBD A:DWX936 2.4 22.5 0.5 CG A:ASP171 2.7 22.6 1.0 OD2 A:ASP171 2.9 26.0 1.0 CD2 A:HIS359 2.9 20.1 1.0 CG A:ASP358 3.0 18.3 1.0 CE1 A:HIS359 3.1 18.7 1.0 CB A:THR209 3.1 21.4 1.0 BBC A:DWX936 3.2 43.6 0.5 OD1 A:ASP358 3.2 21.2 1.0 BBC A:DWX936 3.3 43.7 0.5 CA A:THR209 3.5 18.9 1.0 CG2 A:THR209 3.7 18.8 1.0 OBE A:DWX936 3.7 22.6 0.5 OBE A:DWX936 3.8 22.5 0.5 N A:THR209 3.9 16.7 1.0 CG A:HIS359 4.1 16.6 1.0 CB A:ASP171 4.1 19.9 1.0 ND1 A:HIS359 4.1 16.9 1.0 N A:GLY172 4.2 19.1 1.0 OD1 A:ASP311 4.3 20.7 1.0 CG A:ASP311 4.3 19.0 1.0 CAZ A:DWX936 4.3 26.0 0.5 CE1 A:HIS474 4.3 21.9 1.0 OD2 A:ASP311 4.3 22.2 1.0 CB A:ASP358 4.3 17.9 1.0 CAZ A:DWX936 4.4 26.0 0.5 CBA A:DWX936 4.4 25.6 0.5 CA A:ASP171 4.4 18.3 1.0 CBA A:DWX936 4.5 25.6 0.5 ZN A:ZN913 4.5 22.1 1.0 NE2 A:HIS474 4.5 19.3 1.0 C A:ASP171 4.6 20.8 1.0 C A:LYS208 4.6 18.6 1.0 CB A:ASP311 4.9 19.6 1.0 CA A:GLY172 4.9 19.6 1.0 C A:THR209 4.9 18.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin in Complex with 3BOA


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 in Complex with 3BOA within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn913 b:22.1 occ:1.00 NE2 A:HIS474 2.0 19.3 1.0 NE2 A:HIS315 2.1 22.6 1.0 OD2 A:ASP311 2.2 22.2 1.0 OBD A:DWX936 2.4 22.5 0.5 OBD A:DWX936 2.4 22.5 0.5 OD1 A:ASP311 2.6 20.7 1.0 CG A:ASP311 2.7 19.0 1.0 CD2 A:HIS474 3.0 15.9 1.0 CE1 A:HIS474 3.0 21.9 1.0 BBC A:DWX936 3.0 43.6 0.5 CD2 A:HIS315 3.1 22.6 1.0 BBC A:DWX936 3.1 43.7 0.5 CE1 A:HIS315 3.2 22.2 1.0 OBE A:DWX936 3.7 22.6 0.5 OBE A:DWX936 3.8 22.5 0.5 ND1 A:HIS474 4.1 18.3 1.0 CE1 A:HIS359 4.1 18.7 1.0 CG A:HIS474 4.2 14.7 1.0 CB A:ASP311 4.2 19.6 1.0 CG A:HIS315 4.2 24.5 1.0 ND1 A:HIS315 4.3 21.2 1.0 CAZ A:DWX936 4.3 26.0 0.5 NE2 A:HIS359 4.3 19.5 1.0 CAZ A:DWX936 4.3 26.0 0.5 ZN A:ZN912 4.5 20.4 1.0 OD1 A:ASP171 4.6 19.3 1.0 CE A:MET361 4.6 17.2 1.0 OG1 A:THR209 4.8 18.6 1.0 O A:HOH1302 4.8 33.0 1.0 CBA A:DWX936 4.9 25.6 0.5 CBA A:DWX936 4.9 25.6 0.5 O A:ASP311 4.9 22.5 1.0

M.Kawaguchi, T.Okabe, S.Okudaira, H.Nishimasu, R.Ishitani, H.Kojima, O.Nureki, J.Aoki, T.Nagano. Screening and X-Ray Crystal Structure-Based Optimization of Autotaxin (ENPP2) Inhibitors, Using A Newly Developed Fluorescence Probe Acs Chem.Biol. V. 8 1713 2013.
ISSN: ISSN 1554-8929
PubMed: 23688339
DOI: 10.1021/CB400150C