Calcium 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
Zinc	(Zn)	4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1, PDB code: 8c3p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca906 b:34.4 occ:1.00 OD1 A:ASP773 2.2 35.7 1.0 OD1 A:ASP769 2.3 38.0 1.0 OD1 A:ASP767 2.3 38.8 1.0 OD1 A:ASP765 2.4 38.4 1.0 O A:LEU771 2.4 31.1 1.0 O A:HOH1118 2.5 37.8 1.0 CG A:ASP767 3.3 40.9 1.0 CG A:ASP769 3.3 37.5 1.0 CG A:ASP773 3.5 39.7 1.0 C A:LEU771 3.5 33.6 1.0 CG A:ASP765 3.5 34.7 1.0 OD2 A:ASP767 3.5 44.5 1.0 OD2 A:ASP769 3.7 32.8 1.0 N A:LEU771 3.9 30.6 1.0 CA A:ASP765 4.0 37.2 1.0 N A:ASP773 4.1 28.5 1.0 CA A:LEU771 4.1 34.0 1.0 OD2 A:ASP773 4.2 39.8 1.0 CB A:ASP765 4.2 39.8 1.0 C A:HIS772 4.2 39.8 1.0 CA A:ASP773 4.3 38.4 1.0 CB A:LEU771 4.4 28.3 1.0 N A:ASP769 4.4 32.9 1.0 OD2 A:ASP765 4.4 41.4 1.0 O A:PHE764 4.4 35.5 1.0 CB A:ASP773 4.5 38.2 1.0 N A:HIS772 4.5 28.3 1.0 O A:HIS772 4.5 32.1 1.0 CB A:ASP769 4.6 29.8 1.0 C A:ASP765 4.7 35.9 1.0 N A:ASP767 4.7 35.2 1.0 CB A:ASP767 4.7 35.2 1.0 N A:GLY770 4.8 41.5 1.0 CA A:HIS772 4.8 36.1 1.0 N A:TYR768 4.8 37.5 1.0 N A:TYR766 4.9 37.3 1.0 CA A:ASP769 4.9 33.1 1.0 C A:ASP769 5.0 32.6 1.0 C A:ASP767 5.0 38.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca907 b:60.9 occ:1.00 OG A:SER833 2.4 43.0 1.0 O A:HOH1128 2.5 32.2 1.0 O A:SER830 2.7 39.3 1.0 O A:ASN827 3.3 35.1 1.0 O A:HOH1003 3.6 30.1 1.0 CB A:SER833 3.6 33.9 1.0 C A:SER830 3.8 40.2 1.0 O A:CYS831 3.8 40.6 1.0 CA A:CYS831 3.9 45.3 1.0 C A:CYS831 3.9 43.8 1.0 N A:SER833 3.9 42.8 1.0 C A:ASN827 4.3 34.0 1.0 CA A:SER833 4.3 36.4 1.0 N A:CYS831 4.3 37.9 1.0 O A:HOH1157 4.3 30.7 1.0 OE2 A:GLU828 4.6 62.3 1.0 CA A:GLU828 4.6 32.3 1.0 N A:SER834 4.6 39.3 1.0 N A:ASN832 4.7 43.6 1.0 C A:SER833 4.7 31.5 1.0 N A:GLU828 4.8 31.5 1.0 C A:GLU828 5.0 36.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca906 b:37.3 occ:1.00 OD1 B:ASP773 2.3 40.8 1.0 OD1 B:ASP769 2.3 35.1 1.0 OD1 B:ASP767 2.3 36.0 1.0 O B:LEU771 2.4 29.4 1.0 OD1 B:ASP765 2.5 37.6 1.0 CG B:ASP769 3.3 33.6 1.0 CG B:ASP767 3.4 38.5 1.0 CG B:ASP773 3.4 44.0 1.0 C B:LEU771 3.5 35.2 1.0 OD2 B:ASP769 3.6 29.8 1.0 CG B:ASP765 3.6 35.0 1.0 OD2 B:ASP767 3.7 43.4 1.0 CA B:ASP765 3.9 33.4 1.0 N B:ASP773 3.9 28.8 1.0 N B:LEU771 4.0 31.1 1.0 OD2 B:ASP773 4.1 38.4 1.0 CA B:ASP773 4.1 31.9 1.0 C B:HIS772 4.2 34.6 1.0 CA B:LEU771 4.2 36.0 1.0 CB B:ASP765 4.2 27.4 1.0 CB B:ASP773 4.3 42.1 1.0 O B:PHE764 4.3 30.7 1.0 N B:ASP769 4.4 35.7 1.0 C B:ASP765 4.5 33.4 1.0 O B:HIS772 4.5 37.9 1.0 N B:HIS772 4.5 33.0 1.0 CB B:LEU771 4.5 31.2 1.0 N B:ASP767 4.5 36.8 1.0 CB B:ASP769 4.6 29.3 1.0 OD2 B:ASP765 4.6 40.1 1.0 N B:TYR766 4.6 34.9 1.0 CB B:ASP767 4.7 26.6 1.0 N B:TYR768 4.7 34.6 1.0 CA B:HIS772 4.7 27.3 1.0 N B:GLY770 4.8 28.5 1.0 CA B:ASP769 4.9 29.8 1.0 C B:ASP767 4.9 37.2 1.0 N B:ASP765 4.9 34.6 1.0 CD B:LYS777 5.0 48.1 1.0 CA B:ASP767 5.0 33.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca907 b:41.8 occ:0.51 O B:SER830 2.4 34.5 1.0 O B:ASN827 2.4 30.7 1.0 O B:HOH1177 2.5 40.4 1.0 OG B:SER833 2.5 43.7 1.0 O B:HOH1178 2.8 34.8 1.0 C B:ASN827 3.4 39.4 1.0 C B:SER830 3.4 41.1 1.0 CB B:SER833 3.5 31.1 1.0 CA B:GLU828 3.8 39.8 1.0 N B:GLU828 4.0 38.8 1.0 CA B:CYS831 4.1 40.5 1.0 C B:GLU828 4.2 39.6 1.0 N B:CYS831 4.2 43.1 1.0 OE1 B:GLU828 4.2 56.7 1.0 N B:SER833 4.2 39.0 1.0 O B:GLU828 4.3 35.1 1.0 CB B:ASN827 4.4 29.2 1.0 C B:CYS831 4.4 47.6 1.0 N B:SER830 4.4 41.4 1.0 O B:HOH1001 4.4 44.5 1.0 CA B:SER830 4.4 29.6 1.0 O B:HOH1049 4.4 32.3 1.0 CA B:ASN827 4.5 35.2 1.0 CA B:SER833 4.5 37.4 1.0 O B:CYS831 4.6 42.4 1.0 N B:ASN832 4.9 44.6 1.0 CB B:SER830 4.9 34.4 1.0 N B:GLU829 4.9 34.5 1.0 SG B:CYS414 4.9 41.2 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