Zinc in PDB 5veo: Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), Inactive (T72A), in Complex with Amp

The structure of Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), Inactive (T72A), in Complex with Amp, PDB code: 5veo 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)	32.98 / 1.53
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.239, 84.239, 295.796, 90.00, 90.00, 120.00
R / Rfree (%)	11.5 / 14.5

The binding sites of Zinc atom in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), Inactive (T72A), in Complex with Amp (pdb code 5veo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), Inactive (T72A), in Complex with Amp, PDB code: 5veo:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), Inactive (T72A), in Complex with Amp


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), Inactive (T72A), in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:7.0 occ:1.00 O2P A:AMP524 2.0 7.9 1.0 NE2 A:HIS195 2.0 5.4 1.0 NE2 A:HIS339 2.1 4.9 1.0 OD1 A:ASP191 2.1 8.8 1.0 OD2 A:ASP191 2.5 10.1 1.0 CG A:ASP191 2.6 5.1 1.0 CE1 A:HIS195 3.0 5.8 1.0 CE1 A:HIS339 3.0 6.6 1.0 P A:AMP524 3.0 8.0 1.0 CD2 A:HIS195 3.0 5.0 1.0 CD2 A:HIS339 3.1 6.2 1.0 O3P A:AMP524 3.1 8.4 1.0 HE1 A:HIS195 3.1 7.0 1.0 HE1 A:HIS339 3.2 7.9 1.0 HD2 A:HIS195 3.2 6.1 1.0 HD2 A:HIS339 3.3 7.4 1.0 HE1 A:HIS239 3.5 4.9 1.0 HE1 A:MET241 3.5 8.0 1.0 H5'1 A:AMP524 3.8 13.9 1.0 O A:HOH768 3.8 20.3 1.0 O1P A:AMP524 4.0 9.2 1.0 ND1 A:HIS195 4.1 6.7 1.0 CE1 A:HIS239 4.1 4.1 1.0 ND1 A:HIS339 4.1 5.9 1.0 CB A:ASP191 4.1 6.2 1.0 ZN A:ZN502 4.1 6.8 1.0 CG A:HIS195 4.1 5.2 1.0 O5' A:AMP524 4.2 10.5 1.0 CG A:HIS339 4.2 4.3 1.0 NE2 A:HIS239 4.2 4.7 1.0 HB2 A:ASP191 4.4 7.4 1.0 CE A:MET241 4.5 6.7 1.0 C5' A:AMP524 4.5 11.6 1.0 OD1 A:ASP36 4.6 5.5 1.0 HB3 A:ASP191 4.6 7.4 1.0 HE2 A:MET241 4.7 8.0 1.0 HA A:ASP191 4.8 7.2 1.0 HD1 A:HIS195 4.8 8.0 1.0 O A:ASP191 4.9 7.6 1.0 HD1 A:HIS339 4.9 7.1 1.0 CA A:ASP191 5.0 6.0 1.0

Zinc binding site 2 out of 3 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), Inactive (T72A), in Complex with Amp


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), Inactive (T72A), in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:6.8 occ:1.00 O3P A:AMP524 1.8 8.4 1.0 OD1 A:ASP36 1.9 5.5 1.0 OD2 A:ASP238 2.0 5.6 1.0 NE2 A:HIS239 2.1 4.7 1.0 CG A:ASP36 2.7 4.7 1.0 HB2 A:ALA72 2.7 9.6 1.0 OD2 A:ASP36 2.8 6.3 1.0 CG A:ASP238 2.8 4.6 1.0 OD1 A:ASP238 3.0 5.0 1.0 CD2 A:HIS239 3.0 6.4 1.0 CE1 A:HIS239 3.0 4.1 1.0 HD2 A:HIS239 3.2 7.7 1.0 HE1 A:HIS239 3.2 4.9 1.0 P A:AMP524 3.3 8.0 1.0 HA A:ALA72 3.6 8.4 1.0 CB A:ALA72 3.6 8.0 1.0 OD1 A:ASP191 3.7 8.8 1.0 H A:GLY37 3.8 6.8 1.0 HE1 A:HIS339 3.8 7.9 1.0 H5'1 A:AMP524 3.8 13.9 1.0 H A:ALA72 3.9 6.3 1.0 CA A:ALA72 3.9 7.0 1.0 O1P A:AMP524 3.9 9.2 1.0 HE1 A:HIS76 4.0 7.1 1.0 H5'2 A:AMP524 4.0 13.9 1.0 HB1 A:ALA72 4.0 9.6 1.0 HB2 A:ASP191 4.0 7.4 1.0 CG A:ASP191 4.0 5.1 1.0 N A:ALA72 4.0 5.2 1.0 ND1 A:HIS239 4.1 6.1 1.0 CE1 A:HIS339 4.1 6.6 1.0 CB A:ASP36 4.1 6.5 1.0 N A:GLY37 4.1 5.7 1.0 CG A:HIS239 4.1 6.7 1.0 ZN A:ZN501 4.1 7.0 1.0 O5' A:AMP524 4.2 10.5 1.0 CB A:ASP238 4.2 6.7 1.0 O2P A:AMP524 4.2 7.9 1.0 C5' A:AMP524 4.2 11.6 1.0 HA A:ASP36 4.2 5.8 1.0 HB2 A:ASP238 4.3 8.0 1.0 HB3 A:ALA72 4.3 9.6 1.0 NE2 A:HIS339 4.3 4.9 1.0 HA2 A:GLY37 4.4 6.5 1.0 OD2 A:ASP191 4.5 10.1 1.0 HH A:TYR186 4.5 12.9 1.0 HB3 A:ASP36 4.5 7.8 1.0 CB A:ASP191 4.5 6.2 1.0 CA A:ASP36 4.5 4.8 1.0 C A:ASP36 4.6 3.8 1.0 HA3 A:GLY37 4.6 6.5 1.0 HB3 A:ASP238 4.6 8.0 1.0 HB2 A:ASP36 4.6 7.8 1.0 CA A:GLY37 4.7 5.4 1.0 HA A:LYS71 4.7 8.3 1.0 C A:LYS71 4.8 5.0 1.0 HB3 A:ASP191 4.8 7.4 1.0 HD1 A:HIS239 4.8 7.3 1.0 CE1 A:HIS76 4.8 5.9 1.0 ND1 A:HIS339 4.9 5.9 1.0 H A:ASP238 5.0 8.2 1.0

Zinc binding site 3 out of 3 in the Murine Ectonucleotide Pyrophosphatase / Phosphodiesterase 5 (ENPP5, NPP5), Inactive (T72A), in Complex with Amp


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), Inactive (T72A), in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:34.5 occ:0.54 HO3' A:AMP524 1.5 24.8 1.0 OE2 A:GLU159 2.1 36.7 1.0 O3' A:AMP524 2.2 20.7 1.0 O A:HOH948 2.4 53.9 1.0 O A:HOH603 2.4 52.8 1.0 HO2' A:AMP524 2.4 26.8 1.0 O A:HOH607 2.5 36.3 1.0 OD1 A:ASP192 2.6 36.6 1.0 OD2 A:ASP192 2.8 37.0 1.0 O2' A:AMP524 2.9 22.3 1.0 CD A:GLU159 3.0 36.2 1.0 CG A:ASP192 3.0 30.7 1.0 OE1 A:GLU159 3.3 39.1 1.0 HG2 A:GLU188 3.3 13.4 1.0 C3' A:AMP524 3.3 12.7 1.0 HB3 A:GLU188 3.4 11.2 1.0 C2' A:AMP524 3.6 14.9 1.0 O A:HOH672 3.7 32.2 1.0 H3' A:AMP524 3.8 15.3 1.0 CG A:GLU188 4.1 11.2 1.0 CB A:GLU188 4.1 9.3 1.0 H2' A:AMP524 4.3 17.9 1.0 H4' A:AMP524 4.4 12.6 1.0 HB2 A:GLU188 4.4 11.2 1.0 CG A:GLU159 4.4 28.0 1.0 HG3 A:GLU188 4.4 13.4 1.0 O A:HOH967 4.5 52.7 1.0 HG3 A:GLU159 4.5 33.6 1.0 C4' A:AMP524 4.5 10.5 1.0 CB A:ASP192 4.6 13.9 1.0 H1' A:AMP524 4.6 19.6 1.0 C1' A:AMP524 4.7 16.3 1.0 HG2 A:GLU159 4.8 33.6 1.0 HB3 A:ASP192 4.9 16.7 1.0 HA A:ASP192 4.9 11.0 1.0 HB2 A:ASP192 5.0 16.7 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