Zinc in PDB 8c3o: Crystal Structure of Autotaxin Gamma and Compound Mey-003

All present enzymatic activity of Crystal Structure of Autotaxin Gamma and Compound Mey-003:
3.1.4.39;

The structure of Crystal Structure of Autotaxin Gamma and Compound Mey-003, PDB code: 8c3o 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)	57.64 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.925, 288.478, 57.643, 90, 90.12, 90
R / Rfree (%)	21.4 / 27.1

The structure of Crystal Structure of Autotaxin Gamma and Compound Mey-003 also contains other interesting chemical elements:

Iodine	(I)	37 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Autotaxin Gamma and Compound Mey-003 (pdb code 8c3o). 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 and Compound Mey-003, PDB code: 8c3o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn907 b:61.2 occ:1.00 OD2 A:ASP312 2.2 40.6 1.0 NE2 A:HIS475 2.3 28.1 1.0 NE2 A:HIS316 2.3 37.5 1.0 OD1 A:ASP312 2.8 33.3 1.0 CG A:ASP312 2.8 35.2 1.0 CE1 A:HIS475 3.1 26.5 1.0 CE1 A:HIS316 3.3 41.0 1.0 CD2 A:HIS316 3.3 43.4 1.0 CD2 A:HIS475 3.4 25.5 1.0 OD2 A:ASP172 4.0 35.4 1.0 OG1 A:THR210 4.2 33.3 1.0 CB A:ASP312 4.3 36.7 1.0 CE1 A:HIS360 4.3 26.4 1.0 ND1 A:HIS475 4.3 23.9 1.0 ND1 A:HIS316 4.4 46.5 1.0 CG A:HIS316 4.4 46.5 1.0 NE2 A:HIS360 4.5 24.2 1.0 CG A:HIS475 4.5 23.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn908 b:24.1 occ:0.19 OD1 A:ASP172 2.1 33.4 1.0 OG1 A:THR210 2.1 33.3 1.0 OD2 A:ASP359 2.2 26.3 1.0 NE2 A:HIS360 2.3 24.2 1.0 CG A:ASP172 2.7 29.6 1.0 CB A:THR210 2.8 26.0 1.0 OD2 A:ASP172 2.9 35.4 1.0 CA A:THR210 2.9 20.9 1.0 CG A:ASP359 3.0 24.0 1.0 CD2 A:HIS360 3.0 20.9 1.0 CG2 A:THR210 3.0 22.1 1.0 CE1 A:HIS360 3.2 26.4 1.0 OD1 A:ASP359 3.4 21.7 1.0 N A:THR210 3.8 20.6 1.0 CB A:ASP172 4.0 26.9 1.0 CG A:HIS360 4.1 19.8 1.0 C A:THR210 4.1 15.3 1.0 ND1 A:HIS360 4.1 22.0 1.0 N A:GLY173 4.2 23.7 1.0 CA A:ASP172 4.2 25.1 1.0 CB A:ASP359 4.2 19.0 1.0 O A:THR210 4.4 14.8 1.0 C A:LYS209 4.5 18.5 1.0 OH A:TYR307 4.5 32.0 1.0 C A:ASP172 4.6 24.6 1.0 O A:LYS209 4.6 20.6 1.0 CE1 A:HIS475 4.8 26.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:58.1 occ:1.00 OD1 B:ASP312 2.1 42.7 1.0 NE2 B:HIS475 2.3 27.2 1.0 NE2 B:HIS316 2.3 39.5 1.0 CG B:ASP312 2.8 40.1 1.0 OD2 B:ASP312 2.9 44.7 1.0 CE1 B:HIS475 3.1 27.2 1.0 CD2 B:HIS316 3.2 42.8 1.0 CE1 B:HIS316 3.3 44.2 1.0 CD2 B:HIS475 3.4 25.9 1.0 CE1 B:HIS360 4.2 23.5 1.0 OD1 B:ASP172 4.2 27.7 1.0 CB B:ASP312 4.2 39.7 1.0 ND1 B:HIS475 4.3 27.7 1.0 OG1 B:THR210 4.3 22.7 1.0 CG B:HIS316 4.4 47.9 1.0 ND1 B:HIS316 4.4 48.0 1.0 NE2 B:HIS360 4.4 25.8 1.0 CG B:HIS475 4.5 24.0 1.0 CE B:MET362 4.8 39.5 1.0 O B:ASP312 4.8 47.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn905 b:25.6 occ:0.16 OG1 B:THR210 2.0 22.7 1.0 OD2 B:ASP359 2.0 26.2 1.0 OD1 B:ASP172 2.1 27.7 1.0 NE2 B:HIS360 2.3 25.8 1.0 OD2 B:ASP172 2.4 34.0 1.0 CG B:ASP172 2.4 32.9 1.0 CB B:THR210 2.7 18.8 1.0 CG B:ASP359 2.9 22.5 1.0 CD2 B:HIS360 3.0 21.1 1.0 CG2 B:THR210 3.0 18.2 1.0 CA B:THR210 3.0 19.4 1.0 CE1 B:HIS360 3.3 23.5 1.0 OD1 B:ASP359 3.4 23.8 1.0 CB B:ASP172 3.7 30.8 1.0 N B:THR210 3.9 22.3 1.0 CB B:ASP359 4.0 19.1 1.0 CA B:ASP172 4.0 26.8 1.0 CG B:HIS360 4.1 19.8 1.0 N B:GLY173 4.2 23.6 1.0 ND1 B:HIS360 4.2 20.8 1.0 C B:THR210 4.2 16.0 1.0 OD1 B:ASP312 4.5 42.7 1.0 OH B:TYR307 4.5 31.1 1.0 C B:ASP172 4.5 23.8 1.0 O B:THR210 4.6 17.3 1.0 C B:LYS209 4.7 19.8 1.0 CG B:ASP312 4.8 40.1 1.0 CE1 B:HIS475 5.0 27.2 1.0 O B:LYS209 5.0 21.8 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