Zinc in PDB 4htx: Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550

All present enzymatic activity of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550:
3.1.4.17;

The structure of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550, PDB code: 4htx 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)	44.16 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.260, 73.820, 92.470, 109.59, 91.93, 90.88
R / Rfree (%)	17.3 / 22.7

The structure of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550 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 Complex with BAY60-7550 (pdb code 4htx). 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 Complex with BAY60-7550, PDB code: 4htx:
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 Complex with BAY60-7550


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 Complex with BAY60-7550 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:18.2 occ:1.00 O A:HOH1297 2.1 15.6 1.0 OD2 A:ASP697 2.1 13.0 1.0 NE2 A:HIS696 2.2 12.0 1.0 OD1 A:ASP808 2.2 15.5 1.0 NE2 A:HIS660 2.3 10.8 1.0 O A:HOH1117 2.4 15.8 1.0 CD2 A:HIS696 3.1 9.4 1.0 CG A:ASP808 3.1 16.2 1.0 CG A:ASP697 3.1 11.4 1.0 CE1 A:HIS696 3.2 17.4 1.0 CD2 A:HIS660 3.2 10.9 1.0 OD2 A:ASP808 3.3 23.1 1.0 CE1 A:HIS660 3.3 11.4 1.0 OD1 A:ASP697 3.6 9.7 1.0 MG A:MG1002 3.8 14.2 1.0 CD2 A:HIS656 4.2 14.2 1.0 O A:HOH1103 4.2 13.8 1.0 CG A:HIS696 4.3 14.0 1.0 ND1 A:HIS696 4.3 9.3 1.0 O A:HOH1110 4.3 16.9 1.0 ND1 A:HIS660 4.4 11.8 1.0 CG A:HIS660 4.4 11.4 1.0 CB A:ASP697 4.4 9.6 1.0 NE2 A:HIS656 4.4 16.3 1.0 CB A:ASP808 4.5 15.8 1.0 O A:HOH1299 4.5 35.3 1.0 O A:HOH1261 4.7 13.3 1.0 CG2 A:VAL664 4.9 11.2 1.0 CA A:ASP808 5.0 14.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550


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 Complex with BAY60-7550 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:19.3 occ:1.00 OD2 B:ASP697 2.1 15.0 1.0 OD1 B:ASP808 2.1 16.0 1.0 NE2 B:HIS696 2.2 14.5 1.0 NE2 B:HIS660 2.2 18.4 1.0 O B:HOH1219 2.2 12.3 1.0 O B:HOH1133 2.5 19.6 1.0 CG B:ASP808 3.0 25.8 1.0 CD2 B:HIS696 3.0 10.4 1.0 CG B:ASP697 3.2 13.6 1.0 CD2 B:HIS660 3.2 20.1 1.0 CE1 B:HIS696 3.2 12.0 1.0 OD2 B:ASP808 3.2 31.9 1.0 CE1 B:HIS660 3.3 13.5 1.0 OD1 B:ASP697 3.7 11.4 1.0 MG B:MG1002 3.8 13.5 1.0 O B:HOH1101 4.0 12.6 1.0 O B:HOH1124 4.1 23.9 1.0 CG B:HIS696 4.2 12.5 1.0 CD2 B:HIS656 4.3 20.5 1.0 ND1 B:HIS696 4.3 9.9 1.0 CB B:ASP697 4.3 10.4 1.0 CG B:HIS660 4.3 19.2 1.0 ND1 B:HIS660 4.3 13.7 1.0 CB B:ASP808 4.4 15.6 1.0 NE2 B:HIS656 4.5 21.8 1.0 O B:HOH1103 4.7 14.4 1.0 CG2 B:VAL664 4.9 10.9 1.0 O B:HOH1137 4.9 39.1 1.0 CA B:ASP808 4.9 17.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550


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 Complex with BAY60-7550 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:23.1 occ:1.00 OD1 C:ASP808 2.0 19.9 1.0 OD2 C:ASP697 2.1 19.3 1.0 NE2 C:HIS696 2.1 15.1 1.0 NE2 C:HIS660 2.3 17.6 1.0 O C:HOH1105 2.3 21.8 1.0 O C:HOH1120 2.4 20.8 1.0 CG C:ASP808 3.0 24.1 1.0 CD2 C:HIS696 3.0 14.9 1.0 CE1 C:HIS696 3.1 18.9 1.0 CG C:ASP697 3.2 18.3 1.0 CD2 C:HIS660 3.2 16.3 1.0 OD2 C:ASP808 3.2 27.3 1.0 CE1 C:HIS660 3.3 15.9 1.0 OD1 C:ASP697 3.7 14.0 1.0 MG C:MG1002 3.8 16.0 1.0 O C:HOH1110 4.2 21.0 1.0 O C:HOH1103 4.2 11.7 1.0 CG C:HIS696 4.2 19.3 1.0 ND1 C:HIS696 4.2 18.9 1.0 CD2 C:HIS656 4.2 18.9 1.0 CG C:HIS660 4.4 22.1 1.0 ND1 C:HIS660 4.4 16.4 1.0 CB C:ASP697 4.4 18.3 1.0 CB C:ASP808 4.4 20.4 1.0 NE2 C:HIS656 4.5 18.7 1.0 O C:HOH1104 4.8 17.2 1.0 CA C:ASP808 4.9 24.7 1.0 CG2 C:VAL664 4.9 18.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550


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 Complex with BAY60-7550 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:23.9 occ:1.00 OD2 D:ASP697 2.1 17.4 1.0 O D:HOH1238 2.1 18.9 1.0 OD1 D:ASP808 2.2 25.2 1.0 NE2 D:HIS696 2.2 16.6 1.0 NE2 D:HIS660 2.2 17.3 1.0 O D:HOH1106 2.3 26.3 1.0 CD2 D:HIS696 3.0 16.0 1.0 CG D:ASP808 3.0 23.1 1.0 CG D:ASP697 3.1 18.4 1.0 CE1 D:HIS660 3.2 14.9 1.0 CD2 D:HIS660 3.2 16.5 1.0 OD2 D:ASP808 3.2 32.9 1.0 CE1 D:HIS696 3.3 16.8 1.0 OD1 D:ASP697 3.6 16.6 1.0 MG D:MG1002 3.8 15.3 1.0 CD2 D:HIS656 4.1 20.5 1.0 O D:HOH1237 4.1 15.4 1.0 CG D:HIS696 4.2 22.4 1.0 NE2 D:HIS656 4.3 23.9 1.0 O D:HOH1158 4.3 23.3 1.0 ND1 D:HIS660 4.3 16.1 1.0 ND1 D:HIS696 4.3 19.7 1.0 CG D:HIS660 4.3 21.2 1.0 CB D:ASP697 4.3 20.2 1.0 CB D:ASP808 4.5 19.7 1.0 O D:HOH1105 4.7 15.5 1.0 CA D:ASP808 4.9 19.6 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