Zinc in PDB 4gty: Crystal Structure of Mouse ENPP1 in Complex with Gmp

All present enzymatic activity of Crystal Structure of Mouse ENPP1 in Complex with Gmp:
3.1.4.39;

The structure of Crystal Structure of Mouse ENPP1 in Complex with Gmp, PDB code: 4gty was solved by K.Kato, H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.05 / 3.19
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	104.863, 104.863, 174.831, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 28.1

The structure of Crystal Structure of Mouse ENPP1 in Complex with Gmp also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Mouse ENPP1 in Complex with Gmp (pdb code 4gty). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Mouse ENPP1 in Complex with Gmp, PDB code: 4gty:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Mouse ENPP1 in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mouse ENPP1 in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1010 b:90.1 occ:1.00 OG1 A:THR238 1.9 74.9 1.0 NE2 A:HIS406 1.9 72.1 1.0 OD1 A:ASP200 2.0 58.6 1.0 O2P A:5GP1009 2.2 94.7 1.0 OD2 A:ASP405 2.2 72.1 1.0 CE1 A:HIS406 2.6 71.1 1.0 CG A:ASP200 2.7 59.9 1.0 OD2 A:ASP200 2.7 60.3 1.0 CD2 A:HIS406 3.0 71.3 1.0 CB A:THR238 3.2 75.3 1.0 CG A:ASP405 3.3 71.7 1.0 P A:5GP1009 3.5 93.5 1.0 OD1 A:ASP358 3.5 86.5 1.0 CA A:THR238 3.5 75.5 1.0 ND1 A:HIS406 3.7 70.1 1.0 ZN A:ZN1011 3.7 72.3 1.0 N A:THR238 3.8 76.4 1.0 O3P A:5GP1009 3.8 92.8 1.0 OD1 A:ASP405 3.8 71.7 1.0 CG A:HIS406 3.9 70.4 1.0 CG A:ASP358 3.9 87.7 1.0 CG2 A:THR238 3.9 74.8 1.0 CE1 A:HIS517 4.1 76.8 1.0 CB A:ASP200 4.2 61.2 1.0 NE2 A:HIS517 4.2 75.8 1.0 C5' A:5GP1009 4.2 67.4 1.0 N A:GLY201 4.4 62.9 1.0 O5' A:5GP1009 4.4 67.3 1.0 OD2 A:ASP358 4.4 90.0 1.0 CB A:ASP358 4.5 86.3 1.0 CB A:ASP405 4.6 70.8 1.0 C A:LYS237 4.6 77.1 1.0 O1P A:5GP1009 4.7 93.2 1.0 CA A:ASP200 4.8 62.2 1.0 ND1 A:HIS517 4.8 77.0 1.0 C A:ASP200 4.8 62.8 1.0 CA A:GLY201 4.9 63.4 1.0 C A:THR238 5.0 76.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mouse ENPP1 in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mouse ENPP1 in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1011 b:72.3 occ:1.00 NE2 A:HIS517 2.1 75.8 1.0 OD2 A:ASP358 2.1 90.0 1.0 OD1 A:ASP358 2.2 86.5 1.0 O2P A:5GP1009 2.2 94.7 1.0 NE2 A:HIS362 2.2 74.0 1.0 O1P A:5GP1009 2.4 93.2 1.0 CG A:ASP358 2.4 87.7 1.0 P A:5GP1009 2.6 93.5 1.0 CE1 A:HIS517 2.9 76.8 1.0 CD2 A:HIS362 3.1 74.3 1.0 CE1 A:HIS362 3.2 74.6 1.0 CD2 A:HIS517 3.2 75.5 1.0 ZN A:ZN1010 3.7 90.1 1.0 O5' A:5GP1009 3.8 67.3 1.0 O3P A:5GP1009 3.9 92.8 1.0 CB A:ASP358 3.9 86.3 1.0 CE1 A:HIS406 4.0 71.1 1.0 NE2 A:HIS406 4.0 72.1 1.0 ND1 A:HIS517 4.0 77.0 1.0 CG A:HIS517 4.3 76.5 1.0 CG A:HIS362 4.3 75.0 1.0 ND1 A:HIS362 4.3 75.1 1.0 C5' A:5GP1009 4.4 67.4 1.0 OG1 A:THR238 4.4 74.9 1.0 OD1 A:ASP200 4.5 58.6 1.0 CE A:MET408 4.7 94.8 1.0 CA A:ASP358 4.9 85.5 1.0 O A:ASP358 4.9 86.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mouse ENPP1 in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mouse ENPP1 in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:89.4 occ:1.00 OG1 B:THR238 1.8 82.2 1.0 NE2 B:HIS406 1.9 82.0 1.0 OD1 B:ASP200 2.0 61.6 1.0 O2P B:5GP1005 2.2 0.2 1.0 OD2 B:ASP405 2.2 86.9 1.0 CE1 B:HIS406 2.6 81.3 1.0 CG B:ASP200 2.7 63.5 1.0 OD2 B:ASP200 2.7 64.5 1.0 CD2 B:HIS406 3.0 80.5 1.0 CB B:THR238 3.0 81.3 1.0 CG B:ASP405 3.4 85.2 1.0 CA B:THR238 3.4 79.3 1.0 P B:5GP1005 3.6 0.7 1.0 ND1 B:HIS406 3.7 79.6 1.0 CG2 B:THR238 3.7 80.1 1.0 OD2 B:ASP358 3.7 86.3 1.0 N B:THR238 3.8 82.2 1.0 ZN B:ZN1007 3.8 87.8 1.0 OD1 B:ASP405 3.9 85.4 1.0 CG B:HIS406 3.9 78.8 1.0 CG B:ASP358 3.9 87.3 1.0 O3P B:5GP1005 4.0 99.7 1.0 CE1 B:HIS517 4.1 77.9 1.0 CB B:ASP200 4.1 65.3 1.0 N B:GLY201 4.2 67.8 1.0 NE2 B:HIS517 4.3 77.1 1.0 OD1 B:ASP358 4.4 88.8 1.0 C5' B:5GP1005 4.4 77.0 1.0 O5' B:5GP1005 4.4 76.6 1.0 CB B:ASP358 4.5 86.2 1.0 CB B:ASP405 4.6 81.8 1.0 CA B:ASP200 4.7 66.3 1.0 C B:LYS237 4.7 83.1 1.0 O1P B:5GP1005 4.7 0.2 1.0 C B:ASP200 4.7 66.9 1.0 CA B:GLY201 4.8 69.8 1.0 C B:THR238 4.9 77.0 1.0 ND1 B:HIS517 4.9 77.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mouse ENPP1 in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mouse ENPP1 in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1007 b:87.8 occ:1.00 NE2 B:HIS517 2.0 77.1 1.0 OD2 B:ASP358 2.1 86.3 1.0 O2P B:5GP1005 2.1 0.2 1.0 NE2 B:HIS362 2.2 74.2 1.0 OD1 B:ASP358 2.4 88.8 1.0 O1P B:5GP1005 2.4 0.2 1.0 CG B:ASP358 2.5 87.3 1.0 P B:5GP1005 2.5 0.7 1.0 CE1 B:HIS517 2.7 77.9 1.0 CE1 B:HIS362 3.1 75.5 1.0 CD2 B:HIS362 3.2 75.7 1.0 CD2 B:HIS517 3.2 76.6 1.0 O5' B:5GP1005 3.4 76.6 1.0 ZN B:ZN1006 3.8 89.4 1.0 CE1 B:HIS406 3.9 81.3 1.0 NE2 B:HIS406 3.9 82.0 1.0 O3P B:5GP1005 3.9 99.7 1.0 ND1 B:HIS517 4.0 77.8 1.0 CB B:ASP358 4.0 86.2 1.0 CG B:HIS517 4.2 77.3 1.0 ND1 B:HIS362 4.3 77.5 1.0 OG1 B:THR238 4.3 82.2 1.0 CG B:HIS362 4.3 78.2 1.0 C5' B:5GP1005 4.4 77.0 1.0 OD1 B:ASP200 4.5 61.6 1.0 CE B:MET408 4.6 86.4 1.0 O B:ASP358 4.9 87.5 1.0 CA B:ASP358 4.9 85.8 1.0

K.Kato, H.Nishimasu, S.Okudaira, E.Mihara, R.Ishitani, J.Takagi, J.Aoki, O.Nureki. Crystal Structure of ENPP1, An Extracellular Glycoprotein Involved in Bone Mineralization and Insulin Signaling. Proc.Natl.Acad.Sci.Usa V. 109 16876 2012.
ISSN: ISSN 0027-8424
PubMed: 23027977
DOI: 10.1073/PNAS.1208017109