Zinc in PDB 4b56: Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)

All present enzymatic activity of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1):
3.1.4.1; 3.6.1.9;

The structure of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1), PDB code: 4b56 was solved by S.Jansen, A.Perrakis, C.Ulens, C.Winkler, M.Andries, R.P.Joosten, M.Van Acker, F.P.Luyten, W.H.Moolenaar, M.Bollen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.470 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.385, 105.412, 245.258, 90.00, 90.00, 90.00
R / Rfree (%)	20.02 / 23.35

The structure of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) (pdb code 4b56). 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 Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1), PDB code: 4b56:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:90.4 occ:1.00 O4 A:PO41007 2.0 0.5 1.0 NE2 A:HIS362 2.0 88.2 1.0 NE2 A:HIS517 2.1 86.8 1.0 OD2 A:ASP358 2.1 85.2 1.0 OD1 A:ASP358 2.7 84.6 1.0 P A:PO41007 2.7 0.4 1.0 CG A:ASP358 2.7 84.9 1.0 O2 A:PO41007 2.9 0.7 1.0 CE1 A:HIS362 2.9 87.7 1.0 O1 A:PO41007 3.0 0.7 1.0 CD2 A:HIS517 3.1 86.0 1.0 CE1 A:HIS517 3.1 88.8 1.0 CD2 A:HIS362 3.1 88.6 1.0 CE1 A:HIS406 4.0 87.4 1.0 ND1 A:HIS362 4.1 86.0 1.0 NE2 A:HIS406 4.1 89.0 1.0 O3 A:PO41007 4.1 0.9 1.0 CG A:HIS362 4.2 87.0 1.0 ND1 A:HIS517 4.2 86.8 1.0 CG A:HIS517 4.2 84.4 1.0 CB A:ASP358 4.3 84.9 1.0 OG1 A:THR238 4.3 86.6 1.0 ZN A:ZN1002 4.5 89.4 1.0 OD1 A:ASP200 4.7 0.4 1.0 O A:ASP358 4.9 86.2 1.0 SD A:MET408 5.0 90.6 1.0

Zinc binding site 2 out of 4 in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:89.4 occ:1.00 OD2 A:ASP405 1.7 81.9 1.0 OD1 A:ASP200 1.9 0.4 1.0 OG1 A:THR238 2.0 86.6 1.0 NE2 A:HIS406 2.2 89.0 1.0 CG A:ASP200 2.6 99.1 1.0 CG A:ASP405 2.7 82.3 1.0 OD2 A:ASP200 2.8 0.2 1.0 CB A:THR238 2.9 85.6 1.0 CD2 A:HIS406 3.0 89.1 1.0 CG2 A:THR238 3.2 85.3 1.0 OD1 A:ASP405 3.2 77.5 1.0 CE1 A:HIS406 3.2 87.4 1.0 O2 A:PO41007 3.2 0.7 1.0 CA A:THR238 3.3 83.9 1.0 OD2 A:ASP358 3.5 85.2 1.0 N A:THR238 3.9 82.5 1.0 CB A:ASP405 4.1 82.5 1.0 CG A:HIS406 4.1 86.2 1.0 CB A:ASP200 4.1 96.5 1.0 O1 A:PO41007 4.1 0.7 1.0 ND1 A:HIS406 4.1 85.9 1.0 N A:GLY201 4.2 90.3 1.0 P A:PO41007 4.3 0.4 1.0 CE1 A:HIS517 4.3 88.8 1.0 CG A:ASP358 4.4 84.9 1.0 ZN A:ZN1001 4.5 90.4 1.0 CE1 A:HIS242 4.5 95.7 1.0 CA A:ASP200 4.5 92.5 1.0 C A:THR238 4.6 85.5 1.0 NE2 A:HIS517 4.7 86.8 1.0 C A:LYS237 4.7 80.7 1.0 ND1 A:HIS242 4.8 95.7 1.0 C A:ASP200 4.8 90.8 1.0 CB A:ASP358 4.9 84.9 1.0 O A:THR238 4.9 85.0 1.0

Zinc binding site 3 out of 4 in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:96.4 occ:1.00 O3 B:PO41007 2.0 0.7 1.0 NE2 B:HIS362 2.0 91.7 1.0 NE2 B:HIS517 2.1 93.2 1.0 OD2 B:ASP358 2.2 77.7 1.0 OD1 B:ASP358 2.7 79.5 1.0 CG B:ASP358 2.8 79.6 1.0 P B:PO41007 2.8 0.6 1.0 CE1 B:HIS362 2.9 91.0 1.0 O1 B:PO41007 3.1 1.0 1.0 CD2 B:HIS362 3.1 90.5 1.0 CE1 B:HIS517 3.1 93.6 1.0 CD2 B:HIS517 3.1 88.6 1.0 O2 B:PO41007 3.2 0.3 1.0 CE1 B:HIS406 4.0 94.1 1.0 ND1 B:HIS362 4.0 90.1 1.0 NE2 B:HIS406 4.1 96.4 1.0 CG B:HIS362 4.2 89.6 1.0 O4 B:PO41007 4.2 0.4 1.0 ND1 B:HIS517 4.2 91.3 1.0 OG1 B:THR238 4.2 0.9 1.0 CG B:HIS517 4.3 87.4 1.0 CB B:ASP358 4.3 79.5 1.0 CE B:MET408 4.3 91.8 1.0 ZN B:ZN1002 4.5 95.4 1.0 OD1 B:ASP200 4.7 95.8 1.0 O B:ASP358 4.9 82.0 1.0

Zinc binding site 4 out of 4 in the Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ectonucleotide Pyrophosphatase-Phosphodiesterase-1 (NPP1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:95.4 occ:1.00 OD2 B:ASP405 1.7 89.1 1.0 OG1 B:THR238 1.8 0.9 1.0 OD1 B:ASP200 2.1 95.8 1.0 NE2 B:HIS406 2.3 96.4 1.0 CB B:THR238 2.7 0.8 1.0 CG B:ASP200 2.7 98.2 1.0 OD2 B:ASP200 2.8 0.8 1.0 CG B:ASP405 2.8 92.7 1.0 CD2 B:HIS406 3.0 96.0 1.0 CG2 B:THR238 3.0 0.2 1.0 CA B:THR238 3.2 0.1 1.0 O1 B:PO41007 3.2 1.0 1.0 OD1 B:ASP405 3.3 91.9 1.0 CE1 B:HIS406 3.3 94.1 1.0 OD2 B:ASP358 3.6 77.7 1.0 N B:THR238 3.8 0.7 1.0 O2 B:PO41007 4.0 0.3 1.0 CB B:ASP405 4.0 96.3 1.0 CG B:HIS406 4.1 93.2 1.0 CB B:ASP200 4.2 98.5 1.0 P B:PO41007 4.2 0.6 1.0 ND1 B:HIS406 4.3 93.7 1.0 CE1 B:HIS517 4.3 93.6 1.0 C B:THR238 4.4 0.2 1.0 N B:GLY201 4.4 94.1 1.0 CE1 B:HIS242 4.5 0.3 1.0 CG B:ASP358 4.5 79.6 1.0 ZN B:ZN1001 4.5 96.4 1.0 C B:LYS237 4.6 0.8 1.0 CA B:ASP200 4.7 97.8 1.0 NE2 B:HIS517 4.7 93.2 1.0 ND1 B:HIS242 4.7 0.8 1.0 O B:THR238 4.7 0.1 1.0 C B:ASP200 5.0 95.3 1.0

S.Jansen, A.Perrakis, C.Ulens, C.Winkler, M.Andries, R.P.Joosten, M.Van Acker, F.P.Luyten, W.H.Moolenaar, M.Bollen. Structure of NPP1, An Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification. Structure V. 20 1948 2012.
ISSN: ISSN 0969-2126
PubMed: 23041369
DOI: 10.1016/J.STR.2012.09.001