Zinc in PDB 4htz: Crystal Structure of PDE2 Catalytic Domain in Space Group P1

All present enzymatic activity of Crystal Structure of PDE2 Catalytic Domain in Space Group P1:
3.1.4.17;

The structure of Crystal Structure of PDE2 Catalytic Domain in Space Group P1, PDB code: 4htz was solved by J.Zhu, Q.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.81 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.190, 73.870, 92.610, 109.68, 91.71, 90.91
R / Rfree (%)	18.8 / 24.9

The structure of Crystal Structure of PDE2 Catalytic Domain in Space Group P1 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE2 Catalytic Domain in Space Group P1 (pdb code 4htz). 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 PDE2 Catalytic Domain in Space Group P1, PDB code: 4htz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Space Group P1


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 PDE2 Catalytic Domain in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:15.8 occ:1.00 OD2 A:ASP697 2.1 8.4 1.0 O A:HOH1313 2.1 6.3 1.0 NE2 A:HIS660 2.2 8.9 1.0 OD1 A:ASP808 2.2 16.3 1.0 O A:HOH1169 2.2 24.2 1.0 NE2 A:HIS696 2.2 10.9 1.0 CD2 A:HIS696 3.0 8.2 1.0 CG A:ASP697 3.1 11.6 1.0 CG A:ASP808 3.1 15.5 1.0 CD2 A:HIS660 3.2 8.9 1.0 CE1 A:HIS660 3.2 9.2 1.0 OD2 A:ASP808 3.3 18.3 1.0 CE1 A:HIS696 3.4 11.3 1.0 OD1 A:ASP697 3.5 8.3 1.0 MG A:MG1002 3.8 11.2 1.0 O A:HOH1187 4.2 4.9 1.0 O A:HOH1127 4.2 13.9 1.0 CG A:HIS696 4.2 8.9 1.0 CB A:ASP697 4.3 11.0 1.0 ND1 A:HIS660 4.3 9.4 1.0 CD2 A:HIS656 4.3 12.6 1.0 CG A:HIS660 4.3 9.2 1.0 ND1 A:HIS696 4.4 10.7 1.0 CB A:ASP808 4.5 14.1 1.0 NE2 A:HIS656 4.6 13.4 1.0 O A:HOH1171 4.6 3.5 1.0 CG2 A:VAL664 4.9 9.2 1.0 CA A:ASP808 4.9 15.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Space Group P1


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 PDE2 Catalytic Domain in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:16.0 occ:1.00 OD2 B:ASP697 2.2 10.5 1.0 OD1 B:ASP808 2.2 13.2 1.0 O B:HOH1220 2.2 17.4 1.0 NE2 B:HIS696 2.2 10.0 1.0 NE2 B:HIS660 2.2 10.8 1.0 CD2 B:HIS696 3.0 9.9 1.0 CG B:ASP808 3.1 18.1 1.0 CE1 B:HIS660 3.1 11.1 1.0 CD2 B:HIS660 3.2 10.9 1.0 CG B:ASP697 3.2 11.4 1.0 OD2 B:ASP808 3.2 24.0 1.0 CE1 B:HIS696 3.3 13.3 1.0 O B:HOH1104 3.3 25.1 1.0 MG B:MG1002 3.8 15.1 1.0 OD1 B:ASP697 3.8 10.5 1.0 O B:HOH1221 4.2 10.0 1.0 CG B:HIS696 4.2 16.1 1.0 ND1 B:HIS660 4.2 11.5 1.0 ND1 B:HIS696 4.3 13.9 1.0 CG B:HIS660 4.3 11.4 1.0 O B:HOH1143 4.3 24.5 1.0 CD2 B:HIS656 4.3 19.6 1.0 CB B:ASP697 4.4 12.5 1.0 CB B:ASP808 4.5 14.7 1.0 NE2 B:HIS656 4.6 19.2 1.0 O B:HOH1140 4.6 9.6 1.0 CG2 B:VAL664 4.9 12.3 1.0 CA B:ASP808 4.9 15.8 1.0 O B:ASP808 5.0 15.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Space Group P1


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 PDE2 Catalytic Domain in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:16.4 occ:1.00 OD2 C:ASP697 2.1 14.3 1.0 OD1 C:ASP808 2.1 16.4 1.0 NE2 C:HIS696 2.2 15.2 1.0 NE2 C:HIS660 2.2 11.2 1.0 O C:HOH1261 2.2 8.1 1.0 O C:HOH1248 2.4 20.6 1.0 CD2 C:HIS696 3.0 14.0 1.0 CG C:ASP808 3.0 18.0 1.0 CD2 C:HIS660 3.2 9.1 1.0 CE1 C:HIS660 3.2 8.9 1.0 CG C:ASP697 3.2 13.2 1.0 OD2 C:ASP808 3.2 23.6 1.0 CE1 C:HIS696 3.3 15.7 1.0 OD1 C:ASP697 3.8 12.4 1.0 MG C:MG1002 3.8 12.5 1.0 O C:HOH1204 3.9 16.1 1.0 CG C:HIS696 4.2 21.0 1.0 O C:HOH1205 4.3 20.0 1.0 ND1 C:HIS660 4.3 9.5 1.0 ND1 C:HIS696 4.3 18.8 1.0 CG C:HIS660 4.3 9.6 1.0 CD2 C:HIS656 4.3 13.9 1.0 CB C:ASP697 4.4 12.9 1.0 CB C:ASP808 4.5 14.4 1.0 NE2 C:HIS656 4.6 19.0 1.0 O C:HOH1225 4.8 37.1 1.0 O C:HOH1148 4.8 11.8 1.0 CG2 C:VAL664 4.8 9.7 1.0 CA C:ASP808 4.9 18.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Space Group P1


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 PDE2 Catalytic Domain in Space Group P1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:18.8 occ:1.00 O D:HOH1254 2.0 9.1 1.0 OD2 D:ASP697 2.1 11.1 1.0 NE2 D:HIS696 2.1 11.0 1.0 OD1 D:ASP808 2.2 17.6 1.0 NE2 D:HIS660 2.2 12.2 1.0 O D:HOH1269 2.3 21.2 1.0 CD2 D:HIS696 2.9 10.1 1.0 CG D:ASP808 3.1 16.6 1.0 CG D:ASP697 3.1 10.4 1.0 CD2 D:HIS660 3.2 12.8 1.0 CE1 D:HIS696 3.2 12.3 1.0 CE1 D:HIS660 3.2 15.8 1.0 OD2 D:ASP808 3.3 29.5 1.0 OD1 D:ASP697 3.7 9.7 1.0 MG D:MG1002 3.7 11.7 1.0 O D:HOH1268 4.1 11.0 1.0 CG D:HIS696 4.1 10.2 1.0 O D:HOH1106 4.2 19.5 1.0 ND1 D:HIS696 4.2 16.4 1.0 CD2 D:HIS656 4.3 14.2 1.0 CB D:ASP697 4.3 10.9 1.0 ND1 D:HIS660 4.3 13.5 1.0 CG D:HIS660 4.4 13.4 1.0 CB D:ASP808 4.5 15.8 1.0 NE2 D:HIS656 4.5 17.6 1.0 O D:HOH1147 4.7 6.8 1.0 CG2 D:VAL664 4.9 12.4 1.0 CA D:ASP808 5.0 19.4 1.0

J.Zhu, Q.Yang, D.Dai, Q.Huang. X-Ray Crystal Structure of Phosphodiesterase 2 in Complex with A Highly Selective, Nanomolar Inhibitor Reveals A Binding-Induced Pocket Important For Selectivity. J.Am.Chem.Soc. V. 135 11708 2013.
ISSN: ISSN 0002-7863
PubMed: 23899287
DOI: 10.1021/JA404449G