Zinc in PDB 8ghr: Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2

The structure of Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2 (pdb code 8ghr). 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 Human ENPP1 in Complex with Variable Heavy Domain VH27.2, PDB code: 8ghr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1301 b:40.9 occ:1.00 O2P A:AMP1303 1.9 15.6 1.0 OD1 A:ASP376 2.0 13.9 1.0 OD2 A:ASP376 2.2 13.9 1.0 NE2 A:HIS380 2.3 13.0 1.0 NE2 A:HIS535 2.3 13.8 1.0 CG A:ASP376 2.4 13.9 1.0 CD2 A:HIS535 3.1 13.8 1.0 P A:AMP1303 3.2 15.6 1.0 CD2 A:HIS380 3.2 13.0 1.0 CE1 A:HIS380 3.3 13.0 1.0 CE1 A:HIS535 3.3 13.8 1.0 CE1 A:HIS424 3.5 29.3 1.0 O3P A:AMP1303 3.5 15.6 1.0 NE2 A:HIS424 3.9 29.3 1.0 CB A:ASP376 3.9 13.9 1.0 O5' A:AMP1303 4.0 15.6 1.0 CG A:HIS535 4.2 13.8 1.0 CE A:MET426 4.3 13.3 1.0 ND1 A:HIS535 4.3 13.8 1.0 O1P A:AMP1303 4.3 15.6 1.0 ND1 A:HIS380 4.4 13.0 1.0 CG A:HIS380 4.4 13.0 1.0 OD1 A:ASP218 4.5 12.5 1.0 ND1 A:HIS424 4.6 29.3 1.0 ZN A:ZN1302 4.7 33.7 1.0 O A:HOH1402 4.7 29.3 1.0 O A:ASP376 4.7 13.9 1.0 CA A:ASP376 4.7 13.9 1.0 C A:ASP376 4.9 13.9 1.0

Zinc binding site 2 out of 4 in the Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:33.7 occ:1.00 OD1 A:ASP218 2.0 12.5 1.0 O3P A:AMP1303 2.1 15.6 1.0 OD2 A:ASP423 2.2 14.9 1.0 NE2 A:HIS424 2.3 29.3 1.0 CG A:ASP218 2.7 12.5 1.0 OD2 A:ASP218 2.8 12.5 1.0 CD2 A:HIS424 2.9 29.3 1.0 CG A:ASP423 3.2 14.9 1.0 CE1 A:HIS424 3.5 29.3 1.0 OD1 A:ASP423 3.5 14.9 1.0 P A:AMP1303 3.6 15.6 1.0 CB A:ALA256 3.9 8.3 1.0 CA A:ALA256 4.0 8.3 1.0 CB A:ASP218 4.1 12.5 1.0 CG A:HIS424 4.2 29.3 1.0 O5' A:AMP1303 4.3 15.6 1.0 ND1 A:HIS424 4.4 29.3 1.0 O2P A:AMP1303 4.4 15.6 1.0 N A:GLY219 4.4 11.6 1.0 CA A:ASP218 4.5 12.5 1.0 CB A:ASP423 4.5 14.9 1.0 O1P A:AMP1303 4.5 15.6 1.0 NE2 A:HIS260 4.6 10.1 1.0 N A:ALA256 4.6 8.3 1.0 OD1 A:ASP376 4.7 13.9 1.0 ZN A:ZN1301 4.7 40.9 1.0 C5' A:AMP1303 4.8 15.6 1.0 CG A:ASP376 4.8 13.9 1.0 CD2 A:HIS260 4.8 10.1 1.0 C A:ASP218 4.9 12.5 1.0 OH A:TYR371 4.9 9.8 1.0 OD2 A:ASP376 5.0 13.9 1.0 C A:LYS255 5.0 8.4 1.0

Zinc binding site 3 out of 4 in the Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:37.6 occ:1.00 O2P B:AMP1303 1.9 13.4 1.0 OD1 B:ASP376 2.0 11.9 1.0 OD2 B:ASP376 2.2 11.9 1.0 NE2 B:HIS380 2.3 11.8 1.0 NE2 B:HIS535 2.3 10.1 1.0 CG B:ASP376 2.4 11.9 1.0 CD2 B:HIS535 3.1 10.1 1.0 P B:AMP1303 3.2 13.4 1.0 CD2 B:HIS380 3.2 11.8 1.0 CE1 B:HIS380 3.3 11.8 1.0 CE1 B:HIS535 3.3 10.1 1.0 CE1 B:HIS424 3.5 8.0 1.0 O3P B:AMP1303 3.5 13.4 1.0 NE2 B:HIS424 3.9 8.0 1.0 CB B:ASP376 3.9 11.9 1.0 O5' B:AMP1303 3.9 13.4 1.0 CG B:HIS535 4.2 10.1 1.0 CE B:MET426 4.3 10.2 1.0 ND1 B:HIS535 4.3 10.1 1.0 O1P B:AMP1303 4.3 13.4 1.0 ND1 B:HIS380 4.4 11.8 1.0 CG B:HIS380 4.4 11.8 1.0 OD1 B:ASP218 4.5 9.3 1.0 ND1 B:HIS424 4.6 8.0 1.0 ZN B:ZN1302 4.7 26.0 1.0 O B:HOH1402 4.7 29.3 1.0 O B:ASP376 4.7 11.9 1.0 CA B:ASP376 4.7 11.9 1.0 C B:ASP376 4.9 11.9 1.0

Zinc binding site 4 out of 4 in the Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human ENPP1 in Complex with Variable Heavy Domain VH27.2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:26.0 occ:1.00 OD1 B:ASP218 2.0 9.3 1.0 O3P B:AMP1303 2.1 13.4 1.0 OD2 B:ASP423 2.2 7.4 1.0 NE2 B:HIS424 2.3 8.0 1.0 CG B:ASP218 2.7 9.3 1.0 OD2 B:ASP218 2.8 9.3 1.0 CD2 B:HIS424 2.9 8.0 1.0 CG B:ASP423 3.2 7.4 1.0 CE1 B:HIS424 3.4 8.0 1.0 OD1 B:ASP423 3.5 7.4 1.0 P B:AMP1303 3.6 13.4 1.0 CB B:ALA256 3.9 6.6 1.0 CA B:ALA256 4.0 6.6 1.0 CB B:ASP218 4.1 9.3 1.0 CG B:HIS424 4.2 8.0 1.0 O5' B:AMP1303 4.3 13.4 1.0 ND1 B:HIS424 4.4 8.0 1.0 O2P B:AMP1303 4.4 13.4 1.0 N B:GLY219 4.4 7.8 1.0 CA B:ASP218 4.5 9.3 1.0 CB B:ASP423 4.5 7.4 1.0 O1P B:AMP1303 4.5 13.4 1.0 NE2 B:HIS260 4.6 10.0 1.0 N B:ALA256 4.6 6.6 1.0 OD1 B:ASP376 4.7 11.9 1.0 ZN B:ZN1301 4.7 37.6 1.0 C5' B:AMP1303 4.8 13.4 1.0 CG B:ASP376 4.8 11.9 1.0 CD2 B:HIS260 4.8 10.0 1.0 C B:ASP218 4.9 9.3 1.0 OH B:TYR371 4.9 9.1 1.0 OD2 B:ASP376 5.0 11.9 1.0 C B:LYS255 5.0 7.3 1.0

P.E.Solomon, C.J.Bracken, J.A.Carozza, H.Wang, E.P.Young, A.Wellner, C.C.Liu, E.A.Sweet-Cordero, L.Li, J.A.Wells. Discovery of Vh Domains That Allosterically Inhibit ENPP1. Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
PubMed: 37400538
DOI: 10.1038/S41589-023-01368-5