Magnesium in PDB 6b98: PDE2 in Complex with Compound 1

All present enzymatic activity of PDE2 in Complex with Compound 1:
3.1.4.17;

The structure of PDE2 in Complex with Compound 1, PDB code: 6b98 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.09 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.034, 94.186, 102.526, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24

The structure of PDE2 in Complex with Compound 1 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the PDE2 in Complex with Compound 1 (pdb code 6b98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PDE2 in Complex with Compound 1, PDB code: 6b98:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the PDE2 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE2 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:36.7 occ:1.00 O A:HOH1110 2.0 28.5 1.0 O A:HOH1165 2.1 34.7 1.0 OD1 A:ASP697 2.1 21.2 1.0 O A:HOH1121 2.2 28.9 1.0 O A:HOH1127 2.4 30.4 1.0 O A:HOH1160 2.6 27.7 1.0 CG A:ASP697 3.1 19.4 1.0 OD2 A:ASP697 3.4 18.6 1.0 ZN A:ZN1001 3.9 30.9 1.0 O A:HOH1174 4.1 32.8 1.0 O A:HOH1183 4.1 39.4 1.0 NE2 A:HIS730 4.2 23.9 1.0 OG1 A:THR768 4.2 26.4 1.0 O A:HIS696 4.2 21.1 1.0 CD2 A:HIS696 4.3 24.8 1.0 OE2 A:GLU727 4.3 35.3 1.0 O A:HOH1205 4.3 57.2 1.0 CD2 A:HIS656 4.4 23.4 1.0 CD2 A:HIS700 4.4 22.7 1.0 CD2 A:HIS730 4.4 24.7 1.0 CB A:ASP697 4.4 19.5 1.0 NE2 A:HIS656 4.5 23.1 1.0 CB A:THR768 4.6 28.4 1.0 OD2 A:ASP808 4.6 37.8 1.0 O A:THR768 4.7 28.5 1.0 NE2 A:HIS700 4.7 22.7 1.0 NE2 A:HIS696 4.7 25.0 1.0 CA A:ASP697 4.8 19.0 1.0

Magnesium binding site 2 out of 2 in the PDE2 in Complex with Compound 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE2 in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:31.5 occ:1.00 O B:HOH1151 1.9 27.3 1.0 OD1 B:ASP697 2.1 22.1 1.0 O B:HOH1143 2.2 37.5 1.0 O B:HOH1188 2.2 34.5 1.0 O B:HOH1102 2.3 28.5 1.0 O B:HOH1145 2.3 23.6 1.0 CG B:ASP697 3.1 25.4 1.0 OD2 B:ASP697 3.4 24.0 1.0 ZN B:ZN1001 3.9 30.1 1.0 O B:HOH1161 3.9 39.0 1.0 NE2 B:HIS730 4.2 22.0 1.0 OG1 B:THR768 4.3 26.3 1.0 NE2 B:HIS656 4.3 24.4 1.0 CD2 B:HIS700 4.3 22.3 1.0 CD2 B:HIS656 4.3 24.4 1.0 O B:HIS696 4.4 21.0 1.0 CD2 B:HIS696 4.4 23.2 1.0 CB B:ASP697 4.5 20.8 1.0 OE2 B:GLU727 4.5 34.8 1.0 CD2 B:HIS730 4.5 22.4 1.0 NE2 B:HIS700 4.6 21.9 1.0 OD2 B:ASP808 4.7 35.5 1.0 CB B:THR768 4.7 28.2 1.0 O B:THR768 4.9 29.5 1.0 CA B:ASP697 4.9 19.6 1.0 NE2 B:HIS696 4.9 23.3 1.0

A.B.Forster, P.Abeywickrema, J.Bunda, C.D.Cox, T.D.Cabalu, M.Egbertson, J.Fay, K.Getty, D.Hall, M.Kornienko, J.Lu, G.Parthasarathy, J.Reid, S.Sharma, W.D.Shipe, S.M.Smith, S.Soisson, S.J.Stachel, H.P.Su, D.Wang, R.Berger. The Identification of A Novel Lead Class For Phosphodiesterase 2 Inhibition By Fragment-Based Drug Design. Bioorg. Med. Chem. Lett. V. 27 5167 2017.
ISSN: ESSN 1464-3405
PubMed: 29113762
DOI: 10.1016/J.BMCL.2017.10.054