Zinc in PDB 5vem: Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5)

The structure of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), PDB code: 5vem 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)	44.94 / 2.60
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	109.411, 109.411, 134.820, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.7

The binding sites of Zinc atom in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) (pdb code 5vem). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), PDB code: 5vem:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:26.8 occ:1.00 OD2 A:ASP238 1.9 21.0 1.0 OG1 A:THR72 2.0 23.3 1.0 OD1 A:ASP36 2.0 28.9 1.0 NE2 A:HIS239 2.1 25.4 1.0 CG A:ASP36 2.6 25.7 1.0 OD2 A:ASP36 2.7 25.4 1.0 CG A:ASP238 2.8 23.1 1.0 HA A:THR72 2.8 28.5 1.0 CD2 A:HIS239 2.9 22.6 1.0 CB A:THR72 3.0 21.8 1.0 HG23 A:THR72 3.0 32.4 1.0 CE1 A:HIS239 3.1 25.8 1.0 HD2 A:HIS239 3.1 27.1 1.0 OD1 A:ASP238 3.1 28.3 1.0 CA A:THR72 3.3 23.8 1.0 HE1 A:HIS239 3.3 31.0 1.0 CG2 A:THR72 3.4 27.0 1.0 HG21 A:THR72 3.7 32.4 1.0 HE1 A:HIS76 3.7 29.8 1.0 HB A:THR72 3.8 26.2 1.0 H A:GLY37 3.9 30.3 1.0 N A:THR72 3.9 21.8 1.0 CG A:HIS239 4.0 24.8 1.0 H A:THR72 4.0 26.1 1.0 CB A:ASP36 4.0 25.9 1.0 ND1 A:HIS239 4.0 24.4 1.0 HE1 A:HIS339 4.0 29.1 1.0 HA A:ASP36 4.1 30.2 1.0 CB A:ASP238 4.1 21.5 1.0 HB2 A:ASP238 4.1 25.8 1.0 OD1 A:ASP191 4.2 25.2 1.0 HB2 A:ASP191 4.2 35.5 1.0 O A:HOH622 4.2 25.6 1.0 N A:GLY37 4.3 25.3 1.0 HG22 A:THR72 4.3 32.4 1.0 CE1 A:HIS339 4.4 24.3 1.0 CG A:ASP191 4.4 30.4 1.0 HB3 A:ASP238 4.5 25.8 1.0 HB3 A:ASP36 4.5 31.1 1.0 CA A:ASP36 4.5 25.2 1.0 ZN A:ZN502 4.5 30.9 1.0 CE1 A:HIS76 4.5 24.9 1.0 HB2 A:ASP36 4.6 31.1 1.0 HH A:TYR186 4.6 31.5 1.0 NE2 A:HIS339 4.6 22.6 1.0 C A:ASP36 4.7 26.0 1.0 C A:THR72 4.7 27.7 1.0 HD1 A:HIS76 4.7 26.4 1.0 C A:LYS71 4.7 24.8 1.0 CB A:ASP191 4.7 29.6 1.0 HA2 A:GLY37 4.7 29.2 1.0 HD1 A:HIS239 4.8 29.3 1.0 OD2 A:ASP191 4.8 36.7 1.0 O A:HOH667 4.9 31.9 1.0 HA3 A:GLY37 4.9 29.2 1.0 HB3 A:ASP191 4.9 35.5 1.0 H A:ASP238 4.9 26.5 1.0 CA A:GLY37 4.9 24.4 1.0 HE1 A:TYR186 5.0 32.3 1.0 ND1 A:HIS76 5.0 22.0 1.0

Zinc binding site 2 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:30.9 occ:1.00 O A:HOH667 1.8 31.9 1.0 NE2 A:HIS339 2.0 22.6 1.0 NE2 A:HIS195 2.1 29.1 1.0 OD1 A:ASP191 2.1 25.2 1.0 OD2 A:ASP191 2.5 36.7 1.0 CG A:ASP191 2.6 30.4 1.0 CE1 A:HIS339 2.9 24.3 1.0 CD2 A:HIS195 2.9 27.3 1.0 CD2 A:HIS339 3.0 23.8 1.0 HE1 A:HIS339 3.0 29.1 1.0 HD2 A:HIS195 3.0 32.8 1.0 CE1 A:HIS195 3.1 26.2 1.0 HD2 A:HIS339 3.3 28.5 1.0 HE1 A:HIS195 3.4 31.5 1.0 HE1 A:HIS239 3.5 31.0 1.0 HE1 A:MET241 3.6 33.1 1.0 O A:HOH622 3.8 25.6 1.0 CE1 A:HIS239 4.0 25.8 1.0 ND1 A:HIS339 4.0 20.9 1.0 CB A:ASP191 4.1 29.6 1.0 NE2 A:HIS239 4.1 25.4 1.0 CG A:HIS339 4.1 20.9 1.0 CG A:HIS195 4.1 31.2 1.0 ND1 A:HIS195 4.2 28.0 1.0 HB2 A:ASP191 4.4 35.5 1.0 OG1 A:THR72 4.4 23.3 1.0 CE A:MET241 4.5 27.6 1.0 ZN A:ZN501 4.5 26.8 1.0 OD1 A:ASP36 4.5 28.9 1.0 HB3 A:ASP191 4.6 35.5 1.0 HD1 A:HIS339 4.8 25.0 1.0 HE2 A:MET241 4.8 33.1 1.0 O A:ASP191 4.9 26.5 1.0 HA A:ASP191 4.9 34.7 1.0 CA A:ASP191 5.0 28.9 1.0 HD1 A:HIS195 5.0 33.6 1.0

Zinc binding site 3 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:90.5 occ:1.00 OD1 A:ASP192 2.1 49.0 1.0 NE2 A:HIS196 2.4 42.0 1.0 HD2 A:HIS196 2.9 50.0 1.0 O A:HOH676 3.0 26.9 1.0 CD2 A:HIS196 3.0 41.7 1.0 CG A:ASP192 3.1 39.9 1.0 OD2 A:ASP192 3.5 54.8 1.0 CE1 A:HIS196 3.6 46.6 1.0 HE1 A:HIS196 4.0 55.9 1.0 HA A:ASP192 4.1 39.3 1.0 CG A:HIS196 4.3 35.9 1.0 CB A:ASP192 4.3 34.9 1.0 O A:ASP192 4.5 35.3 1.0 ND1 A:HIS196 4.6 43.6 1.0 HB2 A:ASP192 4.6 41.9 1.0 CA A:ASP192 4.6 32.8 1.0 C A:ASP192 4.9 29.1 1.0 HB2 A:HIS195 5.0 40.6 1.0

Zinc binding site 4 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:24.3 occ:1.00 OD2 B:ASP238 2.0 19.6 1.0 OD2 B:ASP36 2.0 20.2 1.0 NE2 B:HIS239 2.1 33.0 1.0 OG1 B:THR72 2.1 26.1 1.0 HA B:THR72 2.6 27.1 1.0 CG B:ASP36 2.6 27.1 1.0 OD1 B:ASP36 2.7 33.0 1.0 CG B:ASP238 2.8 24.3 1.0 HG23 B:THR72 2.9 35.9 1.0 CD2 B:HIS239 2.9 23.3 1.0 CB B:THR72 3.0 25.9 1.0 CE1 B:HIS239 3.0 25.4 1.0 HD2 B:HIS239 3.1 27.9 1.0 OD1 B:ASP238 3.2 29.2 1.0 CA B:THR72 3.2 22.6 1.0 HE1 B:HIS239 3.3 30.5 1.0 CG2 B:THR72 3.4 29.9 1.0 HE1 B:HIS76 3.7 25.7 1.0 HG21 B:THR72 3.7 35.9 1.0 N B:THR72 3.8 24.2 1.0 HB B:THR72 3.9 31.1 1.0 H B:GLY37 3.9 32.9 1.0 CG B:HIS239 4.0 23.4 1.0 ND1 B:HIS239 4.0 24.3 1.0 H B:THR72 4.0 29.1 1.0 HE1 B:HIS339 4.0 27.3 1.0 CB B:ASP36 4.1 25.0 1.0 HA B:ASP36 4.1 24.6 1.0 CB B:ASP238 4.1 17.6 1.0 O B:HOH613 4.2 24.7 1.0 HB2 B:ASP238 4.2 21.1 1.0 OD1 B:ASP191 4.2 25.2 1.0 HB2 B:ASP191 4.2 28.0 1.0 HG22 B:THR72 4.2 35.9 1.0 N B:GLY37 4.2 27.4 1.0 CE1 B:HIS339 4.3 22.7 1.0 CG B:ASP191 4.4 29.7 1.0 HH B:TYR186 4.5 25.9 1.0 CA B:ASP36 4.5 20.5 1.0 CE1 B:HIS76 4.5 21.4 1.0 HB3 B:ASP238 4.5 21.1 1.0 C B:THR72 4.5 22.6 1.0 HB3 B:ASP36 4.5 30.0 1.0 HD1 B:HIS76 4.6 26.1 1.0 C B:LYS71 4.6 22.0 1.0 HB2 B:ASP36 4.6 30.0 1.0 NE2 B:HIS339 4.6 19.6 1.0 ZN B:ZN502 4.6 27.7 1.0 C B:ASP36 4.7 22.3 1.0 HA2 B:GLY37 4.7 26.1 1.0 CB B:ASP191 4.7 23.4 1.0 HD1 B:HIS239 4.7 29.2 1.0 OD2 B:ASP191 4.8 30.9 1.0 O B:THR72 4.9 25.4 1.0 HA3 B:GLY37 4.9 26.1 1.0 HB3 B:ASP191 4.9 28.0 1.0 CA B:GLY37 4.9 21.7 1.0 ND1 B:HIS76 4.9 21.7 1.0 O B:LYS71 5.0 19.9 1.0 H B:ASP238 5.0 20.9 1.0

Zinc binding site 5 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:27.7 occ:1.00 NE2 B:HIS339 2.0 19.6 1.0 NE2 B:HIS195 2.1 21.0 1.0 OD1 B:ASP191 2.2 25.2 1.0 OD2 B:ASP191 2.4 30.9 1.0 CG B:ASP191 2.6 29.7 1.0 CE1 B:HIS339 2.9 22.7 1.0 CD2 B:HIS195 3.0 24.8 1.0 HE1 B:HIS339 3.0 27.3 1.0 HD2 B:HIS195 3.1 29.8 1.0 CD2 B:HIS339 3.2 22.9 1.0 CE1 B:HIS195 3.2 26.8 1.0 HD2 B:HIS339 3.4 27.5 1.0 HE1 B:HIS195 3.4 32.2 1.0 O B:HOH613 3.5 24.7 1.0 HE1 B:HIS239 3.6 30.5 1.0 HE1 B:MET241 3.8 34.7 1.0 ND1 B:HIS339 4.1 21.6 1.0 CB B:ASP191 4.1 23.4 1.0 CG B:HIS195 4.2 28.4 1.0 CE1 B:HIS239 4.2 25.4 1.0 CG B:HIS339 4.2 23.1 1.0 ND1 B:HIS195 4.2 26.7 1.0 OG1 B:THR72 4.3 26.1 1.0 NE2 B:HIS239 4.3 33.0 1.0 HB2 B:ASP191 4.5 28.0 1.0 HB3 B:ASP191 4.6 28.0 1.0 OD2 B:ASP36 4.6 20.2 1.0 ZN B:ZN501 4.6 24.3 1.0 CE B:MET241 4.8 28.9 1.0 HD1 B:HIS339 4.8 25.9 1.0 O B:ASP191 4.8 26.2 1.0 HA B:ASP191 5.0 29.3 1.0 C B:ASP191 5.0 25.3 1.0

Zinc binding site 6 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:0.3 occ:1.00 OD1 B:ASP192 2.1 44.9 1.0 NE2 B:HIS196 2.3 45.1 1.0 HD2 B:HIS196 2.7 49.6 1.0 CD2 B:HIS196 2.8 41.4 1.0 CG B:ASP192 3.1 40.7 1.0 O B:HOH671 3.1 30.7 1.0 CE1 B:HIS196 3.5 46.9 1.0 OD2 B:ASP192 3.6 60.0 1.0 HE1 B:HIS196 3.9 56.3 1.0 HA B:ASP192 3.9 34.3 1.0 CG B:HIS196 4.1 38.3 1.0 O B:ASP192 4.2 30.9 1.0 CB B:ASP192 4.3 32.4 1.0 ND1 B:HIS196 4.4 56.0 1.0 CA B:ASP192 4.5 28.6 1.0 HB2 B:HIS195 4.5 30.8 1.0 HB2 B:ASP192 4.6 38.9 1.0 C B:ASP192 4.7 27.9 1.0 HB3 B:HIS195 4.9 30.8 1.0

Zinc binding site 7 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:46.6 occ:1.00 OD2 C:ASP238 1.9 49.9 1.0 OD1 C:ASP36 2.0 50.0 1.0 OG1 C:THR72 2.2 53.2 1.0 NE2 C:HIS239 2.3 50.8 1.0 CG C:ASP36 2.6 48.8 1.0 OD2 C:ASP36 2.7 51.1 1.0 HG23 C:THR72 2.8 55.0 1.0 CG C:ASP238 2.8 49.6 1.0 HA C:THR72 2.8 50.4 1.0 CE1 C:HIS239 3.1 50.6 1.0 CB C:THR72 3.1 42.0 1.0 OD1 C:ASP238 3.1 47.9 1.0 CD2 C:HIS239 3.1 44.8 1.0 HE1 C:HIS239 3.3 60.8 1.0 CG2 C:THR72 3.3 45.8 1.0 HD2 C:HIS239 3.3 53.8 1.0 CA C:THR72 3.4 42.0 1.0 HG21 C:THR72 3.6 55.0 1.0 HE1 C:HIS76 3.7 54.6 1.0 H C:GLY37 3.8 60.5 1.0 HA C:ASP36 3.9 62.8 1.0 HB C:THR72 4.0 50.4 1.0 CB C:ASP36 4.0 49.9 1.0 N C:THR72 4.0 46.6 1.0 ND1 C:HIS239 4.1 45.2 1.0 CB C:ASP238 4.1 45.9 1.0 CG C:HIS239 4.1 40.8 1.0 HG22 C:THR72 4.2 55.0 1.0 N C:GLY37 4.2 50.4 1.0 HE1 C:HIS339 4.2 48.9 1.0 HB2 C:ASP238 4.2 55.1 1.0 HB2 C:ASP191 4.2 57.3 1.0 H C:THR72 4.2 55.9 1.0 HH C:TYR186 4.3 65.2 1.0 OD1 C:ASP191 4.3 46.2 1.0 CA C:ASP36 4.4 52.4 1.0 HB3 C:ASP238 4.5 55.1 1.0 CE1 C:HIS339 4.5 40.7 1.0 CE1 C:HIS76 4.5 45.5 1.0 HB3 C:ASP36 4.5 59.8 1.0 CG C:ASP191 4.5 54.3 1.0 HB2 C:ASP36 4.5 59.8 1.0 C C:ASP36 4.6 50.7 1.0 ZN C:ZN502 4.6 51.6 1.0 HD1 C:HIS76 4.6 55.6 1.0 C C:THR72 4.7 48.4 1.0 NE2 C:HIS339 4.7 42.8 1.0 HA2 C:GLY37 4.7 49.1 1.0 O C:HOH607 4.7 39.5 1.0 CB C:ASP191 4.8 47.7 1.0 HD1 C:HIS239 4.8 54.2 1.0 C C:LYS71 4.8 46.5 1.0 H C:ASP238 4.9 47.0 1.0 CA C:GLY37 4.9 40.9 1.0 HA3 C:GLY37 4.9 49.1 1.0 HE1 C:TYR186 4.9 62.0 1.0 ND1 C:HIS76 4.9 46.4 1.0 HB3 C:ASP191 5.0 57.3 1.0 OD2 C:ASP191 5.0 57.1 1.0

Zinc binding site 8 out of 9 in the Human 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 Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:51.6 occ:1.00 NE2 C:HIS339 2.1 42.8 1.0 NE2 C:HIS195 2.2 46.9 1.0 OD1 C:ASP191 2.4 46.2 1.0 OD2 C:ASP191 2.6 57.1 1.0 CG C:ASP191 2.8 54.3 1.0 CE1 C:HIS339 2.8 40.7 1.0 HE1 C:HIS339 2.8 48.9 1.0 CD2 C:HIS195 3.1 53.4 1.0 HD2 C:HIS195 3.2 64.1 1.0 O C:HOH607 3.3 39.5 1.0 CE1 C:HIS195 3.3 51.9 1.0 CD2 C:HIS339 3.3 48.8 1.0 HE1 C:HIS195 3.5 62.3 1.0 HD2 C:HIS339 3.6 58.5 1.0 HE1 C:HIS239 3.8 60.8 1.0 ND1 C:HIS339 4.0 40.6 1.0 HE1 C:MET241 4.1 61.6 1.0 OG1 C:THR72 4.2 53.2 1.0 CB C:ASP191 4.3 47.7 1.0 CG C:HIS195 4.3 51.3 1.0 CG C:HIS339 4.3 45.1 1.0 CE1 C:HIS239 4.3 50.6 1.0 ND1 C:HIS195 4.3 51.4 1.0 NE2 C:HIS239 4.4 50.8 1.0 OD1 C:ASP36 4.5 50.0 1.0 HB2 C:ASP191 4.6 57.3 1.0 ZN C:ZN501 4.6 46.6 1.0 HB3 C:ASP191 4.7 57.3 1.0 HD1 C:HIS339 4.8 48.8 1.0

Zinc binding site 9 out of 9 in the Human 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 9 of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:0.4 occ:1.00 OD1 C:ASP192 2.2 81.1 1.0 HE2 C:HIS196 2.2 77.8 1.0 OD2 C:ASP192 2.4 72.0 1.0 HD2 C:HIS196 2.5 78.7 1.0 CG C:ASP192 2.5 69.1 1.0 NE2 C:HIS196 2.6 64.9 1.0 CD2 C:HIS196 2.7 65.5 1.0 O C:HOH611 2.9 50.2 1.0 CE1 C:HIS196 3.8 66.8 1.0 CG C:HIS196 4.0 58.1 1.0 CB C:ASP192 4.0 63.6 1.0 O C:ASP192 4.2 60.1 1.0 HA C:ASP192 4.3 75.8 1.0 HE1 C:HIS196 4.3 80.1 1.0 ND1 C:HIS196 4.5 67.9 1.0 HB3 C:ASP192 4.5 76.3 1.0 HB2 C:ASP192 4.5 76.3 1.0 C C:ASP192 4.5 60.8 1.0 CA C:ASP192 4.5 63.2 1.0 HB2 C:HIS196 4.9 62.0 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