Zinc in PDB 5u7j: PDE2 Catalytic Domain Complexed with Inhibitors

All present enzymatic activity of PDE2 Catalytic Domain Complexed with Inhibitors:
3.1.4.17;

The structure of PDE2 Catalytic Domain Complexed with Inhibitors, PDB code: 5u7j was solved by J.Pandit, K.Parris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.18 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.866, 74.035, 92.411, 109.66, 91.43, 90.92
R / Rfree (%)	19.4 / 22.5

The structure of PDE2 Catalytic Domain Complexed with Inhibitors also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the PDE2 Catalytic Domain Complexed with Inhibitors (pdb code 5u7j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the PDE2 Catalytic Domain Complexed with Inhibitors, PDB code: 5u7j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the PDE2 Catalytic Domain Complexed with Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE2 Catalytic Domain Complexed with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:19.1 occ:1.00 OD2 A:ASP697 2.1 13.2 1.0 NE2 A:HIS660 2.1 13.6 1.0 NE2 A:HIS696 2.1 12.5 1.0 OD1 A:ASP808 2.1 17.7 1.0 O A:HOH1111 2.3 13.5 1.0 O A:HOH1210 2.5 15.7 1.0 CD2 A:HIS696 3.0 12.1 1.0 CG A:ASP808 3.1 20.7 1.0 CD2 A:HIS660 3.1 14.3 1.0 CG A:ASP697 3.1 14.6 1.0 CE1 A:HIS660 3.1 13.2 1.0 CE1 A:HIS696 3.2 12.5 1.0 OD2 A:ASP808 3.3 25.2 1.0 OD1 A:ASP697 3.6 11.7 1.0 MG A:MG1003 3.8 11.8 1.0 CG A:HIS696 4.2 10.8 1.0 CD2 A:HIS656 4.2 18.1 1.0 O A:HOH1261 4.2 12.7 1.0 CG A:HIS660 4.2 12.9 1.0 ND1 A:HIS660 4.3 13.5 1.0 O A:HOH1233 4.3 20.1 1.0 ND1 A:HIS696 4.3 12.2 1.0 CB A:ASP697 4.3 12.4 1.0 NE2 A:HIS656 4.4 18.1 1.0 CB A:ASP808 4.5 14.3 1.0 CG2 A:VAL664 4.7 16.7 1.0 O A:HOH1106 4.7 13.4 1.0 CA A:ASP808 4.9 13.3 1.0 O A:ASP808 5.0 15.1 1.0 O A:HOH1338 5.0 35.4 1.0

Zinc binding site 2 out of 4 in the PDE2 Catalytic Domain Complexed with Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE2 Catalytic Domain Complexed with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:19.3 occ:1.00 OD2 B:ASP697 2.0 15.4 1.0 NE2 B:HIS696 2.1 14.7 1.0 NE2 B:HIS660 2.2 15.2 1.0 OD1 B:ASP808 2.2 17.9 1.0 O B:HOH1124 2.2 13.6 1.0 O B:HOH1203 2.6 23.2 1.0 CD2 B:HIS696 2.9 14.2 1.0 CG B:ASP697 3.1 11.7 1.0 CG B:ASP808 3.1 19.0 1.0 CD2 B:HIS660 3.1 15.2 1.0 CE1 B:HIS660 3.2 14.9 1.0 CE1 B:HIS696 3.3 14.3 1.0 OD2 B:ASP808 3.3 22.9 1.0 OD1 B:ASP697 3.6 11.9 1.0 MG B:MG1003 3.7 13.9 1.0 CG B:HIS696 4.1 12.7 1.0 CD2 B:HIS656 4.1 17.2 1.0 O B:HOH1260 4.2 24.1 1.0 O B:HOH1225 4.2 15.2 1.0 CB B:ASP697 4.3 10.0 1.0 CG B:HIS660 4.3 13.8 1.0 ND1 B:HIS696 4.3 14.3 1.0 ND1 B:HIS660 4.3 15.6 1.0 NE2 B:HIS656 4.4 17.2 1.0 CB B:ASP808 4.5 14.8 1.0 O B:HOH1106 4.5 18.3 1.0 CG2 B:VAL664 4.8 15.0 1.0 CA B:ASP808 4.9 13.1 1.0

Zinc binding site 3 out of 4 in the PDE2 Catalytic Domain Complexed with Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PDE2 Catalytic Domain Complexed with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:19.8 occ:1.00 OD2 C:ASP697 2.1 16.3 1.0 NE2 C:HIS696 2.1 15.5 1.0 OD1 C:ASP808 2.1 16.6 1.0 NE2 C:HIS660 2.2 17.7 1.0 O C:HOH1122 2.2 17.2 1.0 O C:HOH1133 2.5 21.8 1.0 CD2 C:HIS696 2.9 15.6 1.0 CG C:ASP808 3.1 19.4 1.0 CG C:ASP697 3.1 12.3 1.0 CD2 C:HIS660 3.2 18.7 1.0 CE1 C:HIS660 3.2 17.1 1.0 CE1 C:HIS696 3.2 15.1 1.0 OD2 C:ASP808 3.3 30.2 1.0 OD1 C:ASP697 3.6 10.6 1.0 MG C:MG1003 3.8 13.8 1.0 O C:HOH1207 4.1 10.2 1.0 CG C:HIS696 4.1 14.3 1.0 CD2 C:HIS656 4.1 19.1 1.0 O C:HOH1220 4.3 16.9 1.0 ND1 C:HIS696 4.3 15.5 1.0 CB C:ASP697 4.3 13.1 1.0 CG C:HIS660 4.3 17.3 1.0 ND1 C:HIS660 4.3 18.7 1.0 NE2 C:HIS656 4.4 18.6 1.0 CB C:ASP808 4.4 12.1 1.0 O C:HOH1101 4.7 16.5 1.0 CG2 C:VAL664 4.8 17.8 1.0 CA C:ASP808 4.9 12.2 1.0

Zinc binding site 4 out of 4 in the PDE2 Catalytic Domain Complexed with Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PDE2 Catalytic Domain Complexed with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:20.4 occ:1.00 OD2 D:ASP697 2.1 14.3 1.0 OD1 D:ASP808 2.1 18.5 1.0 NE2 D:HIS660 2.1 16.1 1.0 NE2 D:HIS696 2.1 16.2 1.0 O D:HOH1115 2.2 17.9 1.0 O D:HOH1213 2.6 18.9 1.0 CD2 D:HIS696 3.0 15.8 1.0 CG D:ASP808 3.0 22.9 1.0 CG D:ASP697 3.1 15.9 1.0 CD2 D:HIS660 3.1 17.1 1.0 CE1 D:HIS660 3.1 15.7 1.0 CE1 D:HIS696 3.2 16.7 1.0 OD2 D:ASP808 3.3 33.6 1.0 OD1 D:ASP697 3.6 13.9 1.0 MG D:MG1003 3.8 14.9 1.0 O D:HOH1200 4.1 11.0 1.0 CD2 D:HIS656 4.1 19.4 1.0 CG D:HIS696 4.2 15.4 1.0 CG D:HIS660 4.3 16.0 1.0 ND1 D:HIS660 4.3 16.8 1.0 ND1 D:HIS696 4.3 17.2 1.0 CB D:ASP697 4.3 13.7 1.0 O D:HOH1252 4.3 22.3 1.0 NE2 D:HIS656 4.4 19.3 1.0 CB D:ASP808 4.4 16.7 1.0 O D:HOH1102 4.7 12.8 1.0 O D:HOH1338 4.7 38.9 1.0 CG2 D:VAL664 4.7 14.8 1.0 CA D:ASP808 4.9 15.5 1.0 O D:ASP808 5.0 16.0 1.0

C.J.Helal, E.P.Arnold, T.L.Boyden, C.Chang, T.A.Chappie, K.F.Fennell, M.D.Forman, M.Hajos, J.F.Harms, W.E.Hoffman, J.M.Humphrey, Z.Kang, R.J.Kleiman, B.L.Kormos, C.W.Lee, J.Lu, N.Maklad, L.Mcdowell, S.Mente, R.E.O'connor, J.Pandit, M.Piotrowski, A.W.Schmidt, C.J.Schmidt, H.Ueno, P.R.Verhoest, E.X.Yang. Application of Structure-Based Design and Parallel Chemistry to Identify A Potent, Selective, and Brain Penetrant Phosphodiesterase 2A Inhibitor. J. Med. Chem. V. 60 5673 2017.
ISSN: ISSN 1520-4804
PubMed: 28574706
DOI: 10.1021/ACS.JMEDCHEM.7B00397