Calcium in PDB 6xkd: Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1

The structure of Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1, PDB code: 6xkd was solved by D.Fernandez, L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.64 / 3.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	102.35, 102.35, 172.891, 90, 90, 120
R / Rfree (%)	20.1 / 27.3

The structure of Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1 also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1 (pdb code 6xkd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1, PDB code: 6xkd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1009 b:70.6 occ:1.00 OD1 A:ASP788 2.2 63.8 1.0 OD1 A:ASP782 2.4 76.4 1.0 OD1 A:ASP784 2.6 62.9 1.0 OD1 A:ASP780 2.7 50.5 1.0 O A:ARG786 2.7 60.4 1.0 OD2 A:ASP784 3.2 65.8 1.0 CG A:ASP784 3.3 63.8 1.0 CG A:ASP788 3.4 65.2 1.0 CG A:ASP782 3.4 73.8 1.0 C A:ARG786 3.6 60.7 1.0 OD2 A:ASP782 3.6 79.9 1.0 O A:TYR787 3.6 68.1 1.0 C A:TYR787 3.6 64.7 1.0 CA A:ASP788 3.6 65.7 1.0 N A:ASP788 3.7 64.8 1.0 CG A:ASP780 3.8 54.7 1.0 CB A:ASP788 4.1 66.0 1.0 OD2 A:ASP788 4.3 63.3 1.0 N A:TYR787 4.3 62.1 1.0 CA A:ARG786 4.4 60.2 1.0 N A:ARG786 4.4 57.8 1.0 CA A:TYR787 4.4 62.7 1.0 OD2 A:ASP780 4.6 54.4 1.0 CB A:ARG786 4.7 59.3 1.0 CB A:ASP782 4.8 69.1 1.0 CB A:ASP780 4.8 54.5 1.0 CB A:ASP784 4.8 63.2 1.0 CA A:ASP780 4.8 56.2 1.0 N A:ASP782 4.9 65.3 1.0 N A:ASP784 4.9 63.3 1.0 C A:ASP788 5.0 68.2 1.0

Calcium binding site 2 out of 2 in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:64.3 occ:1.00 OD1 B:ASP784 2.3 67.5 1.0 OD1 B:ASP788 2.4 70.2 1.0 OD1 B:ASP782 2.5 64.0 1.0 O B:ARG786 2.5 59.1 1.0 OD1 B:ASP780 2.6 55.5 1.0 OD2 B:ASP782 3.2 63.2 1.0 CG B:ASP782 3.2 62.9 1.0 CG B:ASP784 3.3 64.9 1.0 C B:ARG786 3.4 57.7 1.0 OD2 B:ASP784 3.4 66.8 1.0 CG B:ASP788 3.6 69.5 1.0 C B:TYR787 3.6 64.2 1.0 O B:TYR787 3.6 65.2 1.0 N B:ASP788 3.8 66.6 1.0 CG B:ASP780 3.8 60.6 1.0 CA B:ASP788 3.9 72.1 1.0 N B:TYR787 4.1 59.2 1.0 CA B:ARG786 4.2 55.5 1.0 N B:ARG786 4.2 54.0 1.0 CA B:TYR787 4.3 61.0 1.0 CB B:ASP788 4.3 69.3 1.0 CB B:ARG786 4.4 55.5 1.0 OD2 B:ASP788 4.4 69.9 1.0 OD2 B:ASP780 4.6 62.8 1.0 CB B:ASP784 4.7 61.2 1.0 CB B:ASP782 4.7 61.9 1.0 CB B:ASP780 4.7 59.7 1.0 N B:ASP784 4.7 56.9 1.0 CA B:ASP780 4.7 58.3 1.0 N B:ASP782 5.0 60.3 1.0

J.A.Carozza, J.A.Brown, V.Bohnert, D.Fernandez, Y.Alsaif, R.E.Mardjuki, M.Smith, L.Li. Structure-Aided Development of Small-Molecule Inhibitors of ENPP1, the Extracellular Phosphodiesterase of the Immunotransmitter Cgamp. Cell Chem Biol V. 27 1347 2020.
ISSN: ESSN 2451-9456
PubMed: 32726585
DOI: 10.1016/J.CHEMBIOL.2020.07.007