Zinc in PDB 8c3p: Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1

All present enzymatic activity of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1:
3.1.4.39;

The structure of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1, PDB code: 8c3p was solved by M.C.Eymery, A.A.Mccarthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.88 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.94, 57.22, 287.926, 90, 92.72, 90
R / Rfree (%)	22.2 / 28

The structure of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 also contains other interesting chemical elements:

Iodine	(I)	17 atoms
Calcium	(Ca)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 (pdb code 8c3p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1, PDB code: 8c3p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


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 Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn908 b:36.9 occ:0.72 OAD A:NKP902 1.6 51.4 1.0 OD1 A:ASP312 2.0 36.8 1.0 NE2 A:HIS475 2.1 38.9 1.0 NE2 A:HIS316 2.2 37.4 1.0 OD2 A:ASP312 2.3 53.7 1.0 CG A:ASP312 2.3 40.4 1.0 PAC A:NKP902 2.9 53.6 1.0 CD2 A:HIS316 3.0 37.9 1.0 CD2 A:HIS475 3.1 33.5 1.0 CE1 A:HIS475 3.1 28.7 1.0 CE1 A:HIS316 3.2 37.2 1.0 OAF A:NKP902 3.4 57.4 1.0 CE1 A:HIS360 3.6 39.9 1.0 OAA A:NKP902 3.8 35.9 1.0 CB A:ASP312 3.8 38.5 1.0 OAB A:NKP902 4.0 52.9 1.0 CG A:HIS316 4.2 43.0 1.0 NE2 A:HIS360 4.2 40.1 1.0 ND1 A:HIS316 4.2 38.5 1.0 ND1 A:HIS475 4.2 27.1 1.0 CG A:HIS475 4.2 28.5 1.0 ZN A:ZN909 4.4 48.1 0.1 ND1 A:HIS360 4.4 32.2 1.0 CAG A:NKP902 4.5 52.5 1.0 CE A:MET362 4.5 34.1 1.0 CA A:ASP312 4.5 38.2 1.0 O A:ASP312 4.5 36.7 1.0 OG1 A:THR210 4.7 41.7 1.0 C A:ASP312 4.7 32.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


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 Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn909 b:48.1 occ:0.15 CG A:ASP172 2.0 60.4 1.0 OG1 A:THR210 2.1 41.7 1.0 OD1 A:ASP172 2.2 60.9 1.0 CB A:ASP172 2.2 47.0 1.0 NE2 A:HIS360 2.3 40.1 1.0 OD2 A:ASP312 2.3 53.7 1.0 OD2 A:ASP172 2.3 62.8 1.0 CE1 A:HIS360 3.0 39.9 1.0 CA A:ASP172 3.1 45.1 1.0 OAF A:NKP902 3.2 57.4 1.0 CG A:ASP312 3.3 40.4 1.0 CB A:THR210 3.3 41.1 1.0 OD2 A:ASP359 3.4 47.5 1.0 CD2 A:HIS360 3.4 40.6 1.0 CG2 A:THR210 3.6 44.4 1.0 C A:ASP172 3.7 38.9 1.0 N A:GLY173 3.8 34.1 1.0 CB A:ASP312 3.8 38.5 1.0 OD1 A:ASP359 4.0 40.8 1.0 CG A:ASP359 4.1 45.7 1.0 CAG A:NKP902 4.1 52.5 1.0 ND1 A:HIS360 4.2 32.2 1.0 OD1 A:ASP312 4.3 36.8 1.0 CA A:THR210 4.3 34.6 1.0 PAC A:NKP902 4.4 53.6 1.0 ZN A:ZN908 4.4 36.9 0.7 CAH A:NKP902 4.4 57.2 1.0 N A:ASP172 4.4 47.3 1.0 CG A:HIS360 4.4 33.6 1.0 O A:ASP172 4.5 39.4 1.0 CAI A:NKP902 4.5 54.5 1.0 OAA A:NKP902 4.5 35.9 1.0 OAD A:NKP902 4.6 51.4 1.0 CA A:GLY173 4.8 32.2 1.0 N A:THR210 4.9 30.9 1.0 OAE A:NKP902 5.0 63.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn908 b:33.3 occ:0.15 OD1 B:ASP172 2.0 42.9 1.0 OD2 B:ASP359 2.0 37.2 1.0 OG1 B:THR210 2.0 44.0 1.0 NE2 B:HIS360 2.1 38.9 1.0 CG2 B:THR210 2.1 38.0 1.0 CB B:THR210 2.3 34.9 1.0 CA B:THR210 2.6 30.0 1.0 CG B:ASP359 2.7 38.1 1.0 CD2 B:HIS360 2.8 32.2 1.0 CG B:ASP172 2.8 47.4 1.0 CE1 B:HIS360 3.1 33.0 1.0 OD1 B:ASP359 3.2 36.5 1.0 N B:THR210 3.4 33.7 1.0 OD2 B:ASP172 3.4 54.3 1.0 CB B:ASP359 3.8 35.9 1.0 CB B:ASP172 3.9 39.2 1.0 CG B:HIS360 3.9 31.4 1.0 C B:THR210 3.9 25.6 1.0 ND1 B:HIS360 4.0 28.2 1.0 C B:LYS209 4.2 31.7 1.0 CA B:ASP172 4.3 36.1 1.0 O B:THR210 4.3 30.8 1.0 N B:GLY173 4.4 37.5 1.0 OAD B:NKP903 4.5 33.9 1.0 O B:LYS209 4.6 29.7 1.0 OAB B:NKP903 4.7 31.6 1.0 OAF B:NKP903 4.7 39.8 1.0 C B:ASP172 4.8 35.1 1.0 CAG B:NKP903 4.8 47.9 1.0 PAC B:NKP903 4.9 43.3 1.0 OAJ B:NKP903 4.9 61.1 1.0 N B:PHE211 4.9 24.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn909 b:34.3 occ:0.73 OAB B:NKP903 1.9 31.6 1.0 NE2 B:HIS475 2.0 38.4 1.0 NE2 B:HIS316 2.0 34.5 1.0 OD2 B:ASP312 2.1 38.3 1.0 OD1 B:ASP312 2.1 42.4 1.0 CG B:ASP312 2.4 37.2 1.0 CD2 B:HIS316 2.8 29.3 1.0 CE1 B:HIS475 3.0 33.2 1.0 CD2 B:HIS475 3.1 31.3 1.0 CE1 B:HIS316 3.2 36.9 1.0 PAC B:NKP903 3.3 43.3 1.0 OAA B:NKP903 3.8 58.7 1.0 CB B:ASP312 3.9 36.2 1.0 CG B:HIS316 4.0 44.2 1.0 OAD B:NKP903 4.1 33.9 1.0 ND1 B:HIS475 4.1 31.3 1.0 CE1 B:HIS360 4.1 33.0 1.0 ND1 B:HIS316 4.2 47.2 1.0 CG B:HIS475 4.2 29.4 1.0 CE B:MET362 4.3 36.6 1.0 CAG B:NKP903 4.3 47.9 1.0 OAF B:NKP903 4.4 39.8 1.0 O B:ASP312 4.5 42.4 1.0 OG1 B:THR210 4.6 44.0 1.0 OD2 B:ASP172 4.7 54.3 1.0 CA B:ASP312 4.7 41.6 1.0 NE2 B:HIS360 4.7 38.9 1.0 C B:ASP312 4.8 38.2 1.0 OD1 B:ASP172 4.9 42.9 1.0

M.C.Eymery, K.A.Nguyen, S.Basu, J.Hausmann, V.K.T.Nguyen, H.P.Seidel, L.Gutierrez, A.Boumendjel, A.A.Mccarthy. Discovery of Potent Chromone-Based Autotaxin Inhibitors Inspired By Cannabinoids Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115944