Zinc in PDB 5ven: Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)

The structure of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), PDB code: 5ven was solved by A.Gorelik, A.Randriamihaja, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 1.69
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.403, 82.403, 301.010, 90.00, 90.00, 120.00
R / Rfree (%)	12.9 / 16.4

The binding sites of Zinc atom in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) (pdb code 5ven). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), PDB code: 5ven:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:8.2 occ:1.00 O A:HOH887 2.0 22.6 1.0 NE2 A:HIS195 2.0 5.1 1.0 NE2 A:HIS339 2.0 6.2 1.0 OD1 A:ASP191 2.1 7.1 1.0 O A:HOH612 2.4 31.8 1.0 CG A:ASP191 2.7 7.8 1.0 OD2 A:ASP191 2.8 9.0 1.0 CE1 A:HIS195 3.0 6.3 1.0 CD2 A:HIS339 3.0 7.1 1.0 CD2 A:HIS195 3.0 6.8 1.0 CE1 A:HIS339 3.0 7.1 1.0 HE1 A:HIS195 3.2 7.5 1.0 HD2 A:HIS339 3.2 8.6 1.0 HD2 A:HIS195 3.2 8.1 1.0 HE1 A:HIS339 3.2 8.5 1.0 O A:HOH897 3.3 30.4 1.0 HE1 A:HIS239 3.3 7.9 1.0 HE1 A:MET241 3.4 10.7 1.0 CE1 A:HIS239 3.9 6.6 1.0 O A:HOH883 4.0 39.6 1.0 O A:HOH752 4.0 4.5 1.0 O A:HOH769 4.1 32.0 1.0 ND1 A:HIS195 4.1 7.2 1.0 CG A:HIS195 4.1 5.5 1.0 ND1 A:HIS339 4.2 6.1 1.0 CG A:HIS339 4.2 5.0 1.0 O A:HOH823 4.2 29.2 1.0 CB A:ASP191 4.2 5.9 1.0 NE2 A:HIS239 4.3 6.0 1.0 CE A:MET241 4.3 8.9 1.0 HB2 A:ASP191 4.4 7.1 1.0 ZN A:ZN502 4.5 7.9 1.0 HE2 A:MET241 4.5 10.7 1.0 OD1 A:ASP36 4.6 6.5 1.0 OG1 A:THR72 4.7 6.5 1.0 HB3 A:ASP191 4.7 7.1 1.0 O A:ASP191 4.8 6.7 1.0 HD1 A:HIS195 4.9 8.7 1.0 HE3 A:MET241 4.9 10.7 1.0 HA A:ASP191 4.9 7.0 1.0 HD1 A:HIS339 4.9 7.3 1.0

Zinc binding site 2 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:7.9 occ:1.00 OG1 A:THR72 1.9 6.5 1.0 OD2 A:ASP238 2.0 6.8 1.0 OD1 A:ASP36 2.0 6.5 1.0 NE2 A:HIS239 2.0 6.0 1.0 O A:HOH612 2.6 31.8 1.0 CG A:ASP36 2.6 6.3 1.0 OD2 A:ASP36 2.6 10.2 1.0 CG A:ASP238 2.9 5.6 1.0 CE1 A:HIS239 3.0 6.6 1.0 CD2 A:HIS239 3.0 5.3 1.0 HA A:THR72 3.1 6.3 1.0 CB A:THR72 3.1 5.2 1.0 OD1 A:ASP238 3.1 5.1 1.0 HG23 A:THR72 3.1 7.2 1.0 HD2 A:HIS239 3.2 6.3 1.0 HE1 A:HIS239 3.2 7.9 1.0 CG2 A:THR72 3.5 6.0 1.0 CA A:THR72 3.5 5.2 1.0 O A:HOH823 3.7 29.2 1.0 HG21 A:THR72 3.7 7.2 1.0 HB A:THR72 3.9 6.2 1.0 HE1 A:HIS339 3.9 8.5 1.0 H A:GLY37 3.9 7.3 1.0 HE1 A:HIS76 3.9 6.9 1.0 N A:THR72 4.0 6.8 1.0 CB A:ASP36 4.1 4.1 1.0 ND1 A:HIS239 4.1 5.1 1.0 H A:THR72 4.1 8.1 1.0 CG A:HIS239 4.1 6.3 1.0 OD1 A:ASP191 4.1 7.1 1.0 O A:HOH752 4.2 4.5 1.0 HA A:ASP36 4.2 4.8 1.0 CB A:ASP238 4.2 6.1 1.0 HB2 A:ASP238 4.3 7.4 1.0 CE1 A:HIS339 4.3 7.1 1.0 N A:GLY37 4.3 6.1 1.0 HH A:TYR186 4.3 9.7 1.0 O A:HOH887 4.3 22.6 1.0 HB2 A:ASP191 4.3 7.1 1.0 HG22 A:THR72 4.4 7.2 1.0 CG A:ASP191 4.4 7.8 1.0 ZN A:ZN501 4.5 8.2 1.0 HB3 A:ASP36 4.5 5.0 1.0 CA A:ASP36 4.6 4.0 1.0 HB2 A:ASP36 4.6 5.0 1.0 NE2 A:HIS339 4.6 6.2 1.0 HB3 A:ASP238 4.6 7.4 1.0 CE1 A:HIS76 4.7 5.7 1.0 HA2 A:GLY37 4.7 7.9 1.0 C A:ASP36 4.8 3.0 1.0 C A:LYS71 4.8 6.6 1.0 HD1 A:HIS239 4.8 6.1 1.0 HD1 A:HIS76 4.8 6.9 1.0 CB A:ASP191 4.9 5.9 1.0 C A:THR72 4.9 5.7 1.0 HA3 A:GLY37 4.9 7.9 1.0 CA A:GLY37 4.9 6.6 1.0 OD2 A:ASP191 4.9 9.0 1.0 HE1 A:TYR186 5.0 7.8 1.0 HA A:LYS71 5.0 9.5 1.0

Zinc binding site 3 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:11.9 occ:0.59 OE2 A:GLU159 1.9 19.5 1.0 OD2 A:ASP192 1.9 19.8 1.0 O A:HOH882 2.1 22.6 1.0 CG A:ASP192 2.7 18.2 1.0 CD A:GLU159 2.7 20.2 1.0 OD1 A:ASP192 2.8 19.0 1.0 OE1 A:GLU159 2.9 22.4 1.0 HB3 A:GLU188 3.3 8.1 1.0 HG2 A:GLU188 3.4 8.1 1.0 O A:HOH753 3.9 20.5 1.0 CB A:GLU188 4.0 6.8 1.0 O A:HOH719 4.0 20.9 1.0 CB A:ASP192 4.1 13.1 1.0 CG A:GLU159 4.2 18.1 1.0 CG A:GLU188 4.2 6.8 1.0 HB2 A:GLU188 4.2 8.1 1.0 HG3 A:GLU159 4.3 21.7 1.0 HB2 A:ASP192 4.3 15.8 1.0 HB3 A:ASP192 4.4 15.8 1.0 HG2 A:GLU159 4.5 21.7 1.0 HG3 A:GLU188 4.6 8.1 1.0 O A:HOH769 4.7 32.0 1.0 HA A:ASP192 5.0 10.1 1.0

Zinc binding site 4 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:22.7 occ:0.35 OD1 A:ASP196 2.1 26.4 1.0 O A:HOH899 2.2 49.4 1.0 OD2 A:ASP196 2.2 29.0 1.0 O A:HOH885 2.3 50.9 1.0 CG A:ASP196 2.4 23.8 1.0 O A:HOH875 2.9 39.0 1.0 CB A:ASP196 3.9 13.3 1.0 HB3 A:ASP196 4.2 15.9 1.0 O A:ASP192 4.3 9.3 1.0 HB2 A:ASP196 4.3 15.9 1.0 HA A:ASP196 4.4 11.6 1.0 HB3 A:ASP192 4.6 15.8 1.0 CA A:ASP196 4.7 9.7 1.0 O A:HOH895 4.8 47.5 1.0 H A:ASP196 4.8 9.7 1.0 N A:ASP196 5.0 8.0 1.0 O A:HOH854 5.0 44.0 1.0

Zinc binding site 5 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:13.1 occ:1.00 NE2 B:HIS195 2.0 10.9 1.0 NE2 B:HIS339 2.1 6.9 1.0 O B:HOH879 2.1 20.7 1.0 OD1 B:ASP191 2.1 14.1 1.0 O B:HOH605 2.5 37.5 1.0 CG B:ASP191 2.7 12.3 1.0 OD2 B:ASP191 2.7 13.0 1.0 CE1 B:HIS195 3.0 10.1 1.0 CD2 B:HIS339 3.0 8.4 1.0 CD2 B:HIS195 3.0 11.3 1.0 CE1 B:HIS339 3.1 8.6 1.0 HD2 B:HIS339 3.1 10.1 1.0 HE1 B:HIS195 3.2 12.2 1.0 HD2 B:HIS195 3.2 13.6 1.0 O B:HOH883 3.2 31.6 1.0 HE1 B:HIS239 3.3 10.4 1.0 HE1 B:HIS339 3.3 10.3 1.0 HE1 B:MET241 3.4 15.2 1.0 CE1 B:HIS239 3.9 8.6 1.0 O B:HOH777 4.0 40.9 1.0 O B:HOH651 4.1 10.5 1.0 ND1 B:HIS195 4.1 11.5 1.0 CG B:HIS195 4.1 10.1 1.0 CG B:HIS339 4.2 8.2 1.0 ND1 B:HIS339 4.2 8.7 1.0 CB B:ASP191 4.2 9.8 1.0 O B:HOH877 4.2 41.0 1.0 NE2 B:HIS239 4.3 8.9 1.0 CE B:MET241 4.4 12.7 1.0 HB2 B:ASP191 4.5 11.7 1.0 ZN B:ZN502 4.5 13.4 1.0 HE2 B:MET241 4.6 15.2 1.0 OD1 B:ASP36 4.6 13.0 1.0 OG1 B:THR72 4.6 9.9 1.0 HB3 B:ASP191 4.7 11.7 1.0 HA B:ASP191 4.9 11.3 1.0 HD1 B:HIS195 4.9 13.8 1.0 O B:ASP191 4.9 11.7 1.0 HE3 B:MET241 5.0 15.2 1.0 HD1 B:HIS339 5.0 10.5 1.0 CA B:ASP191 5.0 9.5 1.0

Zinc binding site 6 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:13.4 occ:1.00 OD2 B:ASP238 2.0 12.4 1.0 OD1 B:ASP36 2.0 13.0 1.0 OG1 B:THR72 2.1 9.9 1.0 NE2 B:HIS239 2.1 8.9 1.0 O B:HOH605 2.4 37.5 1.0 CG B:ASP36 2.6 12.7 1.0 OD2 B:ASP36 2.6 13.7 1.0 CG B:ASP238 2.9 12.0 1.0 HA B:THR72 3.0 11.3 1.0 CE1 B:HIS239 3.0 8.6 1.0 CD2 B:HIS239 3.0 10.8 1.0 CB B:THR72 3.1 9.2 1.0 HG23 B:THR72 3.1 13.0 1.0 OD1 B:ASP238 3.1 12.8 1.0 HD2 B:HIS239 3.2 13.0 1.0 HE1 B:HIS239 3.2 10.4 1.0 CA B:THR72 3.5 9.4 1.0 CG2 B:THR72 3.5 10.8 1.0 O B:HOH777 3.7 40.9 1.0 HG21 B:THR72 3.8 13.0 1.0 HE1 B:HIS339 3.9 10.3 1.0 HE1 B:HIS76 3.9 15.1 1.0 HB B:THR72 3.9 11.1 1.0 H B:GLY37 4.0 12.5 1.0 N B:THR72 4.0 11.4 1.0 CB B:ASP36 4.0 12.5 1.0 H B:THR72 4.0 13.7 1.0 OD1 B:ASP191 4.1 14.1 1.0 ND1 B:HIS239 4.1 10.6 1.0 O B:HOH651 4.2 10.5 1.0 CG B:HIS239 4.2 8.8 1.0 HA B:ASP36 4.2 13.4 1.0 CE1 B:HIS339 4.3 8.6 1.0 HH B:TYR186 4.3 19.7 1.0 CB B:ASP238 4.3 10.8 1.0 N B:GLY37 4.3 10.4 1.0 O B:HOH879 4.3 20.7 1.0 HB2 B:ASP238 4.4 13.0 1.0 HB2 B:ASP191 4.4 11.7 1.0 HG22 B:THR72 4.4 13.0 1.0 CG B:ASP191 4.4 12.3 1.0 HB3 B:ASP36 4.5 15.0 1.0 ZN B:ZN501 4.5 13.1 1.0 CA B:ASP36 4.5 11.2 1.0 NE2 B:HIS339 4.5 6.9 1.0 HB2 B:ASP36 4.6 15.0 1.0 HB3 B:ASP238 4.7 13.0 1.0 CE1 B:HIS76 4.7 12.6 1.0 C B:ASP36 4.7 9.7 1.0 HD1 B:HIS76 4.7 15.1 1.0 HA2 B:GLY37 4.8 11.2 1.0 C B:LYS71 4.8 9.7 1.0 C B:THR72 4.9 10.4 1.0 HD1 B:HIS239 4.9 12.7 1.0 CB B:ASP191 4.9 9.8 1.0 HA3 B:GLY37 4.9 11.2 1.0 HE1 B:TYR186 4.9 17.0 1.0 OD2 B:ASP191 4.9 13.0 1.0 CA B:GLY37 5.0 9.3 1.0

Zinc binding site 7 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:26.5 occ:0.68 OE2 B:GLU159 1.9 32.7 1.0 OD2 B:ASP192 2.1 29.6 1.0 O B:HOH880 2.4 32.4 1.0 O B:HOH893 2.6 47.1 1.0 CG B:ASP192 2.7 27.4 1.0 OD1 B:ASP192 2.7 31.7 1.0 O B:HOH825 2.7 49.3 1.0 CD B:GLU159 2.8 31.7 1.0 OE1 B:GLU159 2.9 33.6 1.0 HB3 B:GLU188 3.3 19.8 1.0 HG2 B:GLU188 3.4 21.0 1.0 O B:HOH730 3.9 29.0 1.0 CB B:GLU188 4.0 16.5 1.0 O B:HOH694 4.0 28.9 1.0 CB B:ASP192 4.1 20.1 1.0 CG B:GLU188 4.2 17.5 1.0 HB2 B:GLU188 4.2 19.8 1.0 CG B:GLU159 4.2 28.2 1.0 HG3 B:GLU159 4.4 33.8 1.0 HB3 B:ASP192 4.5 24.1 1.0 HB2 B:ASP192 4.5 24.1 1.0 HG2 B:GLU159 4.5 33.8 1.0 HG3 B:GLU188 4.6 21.0 1.0 HA B:ASP192 4.9 19.3 1.0

Zinc binding site 8 out of 8 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:68.4 occ:0.47 O B:HOH631 2.1 55.8 1.0 OD1 B:ASP196 2.3 31.3 1.0 OD2 B:ASP196 2.6 35.0 1.0 CG B:ASP196 2.8 29.4 1.0 O B:ASP192 4.1 17.4 1.0 CB B:ASP196 4.3 20.0 1.0 HB3 B:ASP192 4.5 24.1 1.0 HB3 B:ASP196 4.7 24.0 1.0 HB2 B:HIS195 4.7 11.7 1.0 HB2 B:ASP196 4.7 24.0 1.0 HA B:ASP196 4.7 17.7 1.0 O B:HOH862 4.8 43.1 1.0 H B:ASP196 4.9 16.4 1.0 HA B:ASP192 4.9 19.3 1.0 C B:ASP192 4.9 16.5 1.0 CA B:ASP196 4.9 14.8 1.0

A.Gorelik, A.Randriamihaja, K.Illes, B.Nagar. A Key Tyrosine Substitution Restricts Nucleotide Hydrolysis By the Ectoenzyme NPP5. Febs J. V. 284 3718 2017.
ISSN: ISSN 1742-4658
PubMed: 28898552
DOI: 10.1111/FEBS.14266