Zinc 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:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1, PDB code: 6xkd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1007 b:57.9 occ:1.00 OD2 A:ASP405 2.0 54.6 1.0 OD1 A:ASP200 2.0 49.8 1.0 NE2 A:HIS406 2.0 63.2 1.0 O26 A:IJE1011 2.2 59.3 0.5 OG1 A:THR238 2.4 57.9 1.0 CG A:ASP200 2.7 50.2 1.0 OD2 A:ASP200 2.7 53.4 1.0 CE1 A:HIS406 2.9 64.3 1.0 CD2 A:HIS406 3.0 60.5 1.0 CG A:ASP405 3.1 57.8 1.0 CB A:THR238 3.2 58.7 1.0 CA A:THR238 3.3 60.6 1.0 CG2 A:THR238 3.4 58.5 1.0 OD1 A:ASP405 3.5 60.9 1.0 N A:THR238 3.6 61.3 1.0 P24 A:IJE1011 3.7 62.3 0.5 ZN A:ZN1008 3.7 54.2 1.0 ND1 A:HIS406 4.0 61.2 1.0 OD1 A:ASP358 4.1 52.0 1.0 CG A:HIS406 4.1 58.2 1.0 O25 A:IJE1011 4.1 61.2 0.5 CE1 A:HIS517 4.2 55.5 1.0 CB A:ASP200 4.2 50.3 1.0 CG A:ASP358 4.2 52.3 1.0 NE2 A:HIS517 4.2 55.3 1.0 C22 A:IJE1011 4.3 64.1 0.5 CB A:ASP405 4.3 55.2 1.0 N A:GLY201 4.4 56.3 1.0 OD2 A:ASP358 4.5 53.0 1.0 C A:LYS237 4.6 61.2 1.0 C23 A:IJE1011 4.7 62.3 0.5 O27 A:IJE1011 4.7 59.0 0.5 C A:THR238 4.8 61.5 1.0 CA A:ASP200 4.8 51.2 1.0 CB A:ASP358 4.8 53.2 1.0 CE1 A:HIS242 4.9 41.1 1.0 C A:ASP200 4.9 54.2 1.0 ND1 A:HIS517 4.9 56.5 1.0 CA A:GLY201 5.0 55.3 1.0

Zinc binding site 2 out of 4 in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:54.2 occ:1.00 OD1 A:ASP358 2.0 52.0 1.0 NE2 A:HIS517 2.0 55.3 1.0 NE2 A:HIS362 2.1 49.4 1.0 O26 A:IJE1011 2.2 59.3 0.5 O27 A:IJE1011 2.5 59.0 0.5 CG A:ASP358 2.6 52.3 1.0 OD2 A:ASP358 2.6 53.0 1.0 P24 A:IJE1011 2.6 62.3 0.5 CE1 A:HIS517 3.0 55.5 1.0 CD2 A:HIS517 3.0 55.8 1.0 CE1 A:HIS362 3.0 50.5 1.0 CD2 A:HIS362 3.1 48.0 1.0 C23 A:IJE1011 3.4 62.3 0.5 ZN A:ZN1007 3.7 57.9 1.0 CE1 A:HIS406 3.9 64.3 1.0 NE2 A:HIS406 4.0 63.2 1.0 O25 A:IJE1011 4.0 61.2 0.5 C22 A:IJE1011 4.0 64.1 0.5 CB A:ASP358 4.0 53.2 1.0 OD1 A:ASP200 4.1 49.8 1.0 ND1 A:HIS517 4.1 56.5 1.0 CG A:HIS517 4.1 55.3 1.0 ND1 A:HIS362 4.1 50.2 1.0 CG A:HIS362 4.2 48.0 1.0 OG1 A:THR238 4.3 57.9 1.0 CE A:MET408 4.4 62.0 1.0 O A:ASP358 4.8 58.6 1.0 CA A:ASP358 4.9 55.6 1.0

Zinc binding site 3 out of 4 in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:45.3 occ:1.00 OD1 B:ASP200 1.9 45.3 1.0 NE2 B:HIS406 2.0 48.3 1.0 OD2 B:ASP405 2.1 48.6 1.0 OG1 B:THR238 2.5 43.9 1.0 CG B:ASP200 2.6 45.1 1.0 CD2 B:HIS406 2.7 48.2 1.0 OD2 B:ASP200 2.8 46.2 1.0 CG B:ASP405 2.9 50.4 1.0 CB B:THR238 3.0 46.4 1.0 CE1 B:HIS406 3.0 49.6 1.0 CA B:THR238 3.1 47.0 1.0 OD1 B:ASP405 3.1 54.0 1.0 CG2 B:THR238 3.2 44.2 1.0 N B:THR238 3.7 46.8 1.0 CG B:HIS406 3.9 47.8 1.0 ND1 B:HIS406 4.0 48.9 1.0 CB B:ASP200 4.0 43.2 1.0 N B:GLY201 4.1 43.3 1.0 ZN B:ZN1002 4.1 61.0 1.0 C B:THR238 4.3 47.8 1.0 CB B:ASP405 4.3 48.8 1.0 CG B:ASP358 4.3 52.1 1.0 CE1 B:HIS517 4.3 55.8 1.0 OD2 B:ASP358 4.4 51.0 1.0 O B:THR238 4.4 48.3 1.0 NE2 B:HIS517 4.4 56.2 1.0 CA B:ASP200 4.5 43.1 1.0 OD1 B:ASP358 4.5 54.2 1.0 C B:LYS237 4.6 45.8 1.0 C B:ASP200 4.6 43.2 1.0 CE1 B:HIS242 4.7 48.8 1.0 CB B:ASP358 4.7 52.2 1.0 CA B:GLY201 4.7 45.1 1.0 ND1 B:HIS242 4.8 47.7 1.0 O B:LYS237 5.0 43.5 1.0

Zinc binding site 4 out of 4 in the Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ligand-Bound Mouse Cgamp Hydrolase ENPP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:61.0 occ:1.00 NE2 B:HIS517 2.1 56.2 1.0 NE2 B:HIS362 2.2 44.7 1.0 OD2 B:ASP358 2.4 51.0 1.0 OD1 B:ASP358 2.5 54.2 1.0 CG B:ASP358 2.8 52.1 1.0 CE1 B:HIS517 3.0 55.8 1.0 CD2 B:HIS517 3.1 54.1 1.0 OG1 B:THR238 3.1 43.9 1.0 CE1 B:HIS362 3.1 46.9 1.0 CD2 B:HIS362 3.3 46.9 1.0 NE2 B:HIS406 3.8 48.3 1.0 CE1 B:HIS406 3.9 49.6 1.0 ZN B:ZN1001 4.1 45.3 1.0 OD1 B:ASP200 4.1 45.3 1.0 ND1 B:HIS517 4.1 53.4 1.0 CG B:HIS517 4.2 53.0 1.0 CB B:ASP358 4.2 52.2 1.0 ND1 B:HIS362 4.3 48.0 1.0 CG B:HIS362 4.4 48.1 1.0 CB B:THR238 4.5 46.4 1.0 CE B:MET408 4.9 49.9 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