Calcium in PDB 8c7r: Crystal Structure of Rat Autotaxin and Compound Mey-003

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

The structure of Crystal Structure of Rat Autotaxin and Compound Mey-003, PDB code: 8c7r 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)	43.64 / 2.53
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.529, 61.843, 63.85, 104.01, 98.43, 93.27
R / Rfree (%)	20.5 / 25.4

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

Iodine	(I)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin and Compound Mey-003 (pdb code 8c7r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin and Compound Mey-003, PDB code: 8c7r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin and Compound Mey-003


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 Rat Autotaxin and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca909 b:60.5 occ:1.00 OG1 A:THR526 2.7 35.1 1.0 O A:ASN524 2.9 34.1 1.0 OE2 A:GLU507 2.9 34.1 1.0 NH1 A:ARG825 3.0 33.1 1.0 O A:HOH1025 3.1 26.5 1.0 NH2 A:ARG825 3.5 26.1 1.0 N A:THR526 3.6 26.2 1.0 CZ A:ARG825 3.7 28.1 1.0 CG A:ARG827 3.7 39.9 1.0 C A:GLY525 3.7 27.5 1.0 CB A:THR526 3.8 36.3 1.0 CD1 A:ILE506 3.9 29.4 1.0 CA A:GLY525 3.9 28.1 1.0 C A:ASN524 3.9 32.1 1.0 CD A:GLU507 4.0 33.9 1.0 O A:HOH1026 4.1 36.5 1.0 CG2 A:THR853 4.2 29.6 1.0 CA A:THR526 4.2 30.5 1.0 CD A:ARG827 4.3 51.3 1.0 O A:GLY525 4.3 31.1 1.0 N A:GLY525 4.4 29.3 1.0 OE1 A:GLU507 4.5 33.4 1.0 O A:HOH1051 4.5 25.1 1.0 CB A:ARG827 4.7 33.8 1.0 OH A:TYR221 4.8 27.4 1.0 NH1 A:ARG827 4.8 81.3 1.0 NE A:ARG825 5.0 29.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin and Compound Mey-003


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 Rat Autotaxin and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca910 b:40.5 occ:1.00 OD1 A:ASN741 2.2 34.8 1.0 OD1 A:ASP743 2.2 34.3 1.0 OD1 A:ASP739 2.3 28.7 1.0 OD1 A:ASP747 2.3 37.7 1.0 O A:LEU745 2.3 32.4 1.0 CG A:ASP743 3.1 33.9 1.0 CG A:ASN741 3.2 39.8 1.0 CG A:ASP739 3.4 34.4 1.0 C A:LEU745 3.4 34.1 1.0 OD2 A:ASP743 3.4 36.9 1.0 ND2 A:ASN741 3.5 41.7 1.0 CG A:ASP747 3.5 37.8 1.0 CA A:ASP739 3.8 32.9 1.0 N A:LEU745 3.9 27.0 1.0 N A:ASP747 3.9 36.2 1.0 C A:ARG746 4.0 37.6 1.0 CA A:ASP747 4.0 38.0 1.0 CB A:ASP739 4.1 29.9 1.0 O A:ARG746 4.1 36.2 1.0 CA A:LEU745 4.1 36.9 1.0 O A:PHE738 4.2 29.3 1.0 N A:ASP743 4.2 30.5 1.0 OE1 A:GLU751 4.3 51.4 1.0 OD2 A:ASP739 4.3 30.3 1.0 CB A:ASP747 4.3 38.7 1.0 CB A:ASP743 4.4 31.7 1.0 OD2 A:ASP747 4.4 40.3 1.0 CB A:LEU745 4.4 38.1 1.0 N A:ARG746 4.5 27.8 1.0 C A:ASP739 4.5 31.2 1.0 CB A:ASN741 4.6 32.6 1.0 N A:ASN741 4.6 32.6 1.0 CA A:ASP743 4.7 32.8 1.0 CA A:ARG746 4.7 35.0 1.0 N A:GLY744 4.8 29.3 1.0 N A:TYR742 4.8 32.9 1.0 N A:TYR740 4.8 35.5 1.0 N A:ASP739 4.9 32.4 1.0 C A:ASN741 4.9 32.5 1.0 C A:ASP743 4.9 27.4 1.0 CA A:ASN741 4.9 33.4 1.0 CD A:GLU751 4.9 52.2 1.0 C A:PHE738 4.9 35.9 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