Magnesium in PDB 6b97: Crystal Structure of PDE2 in Complex with Complex 9

All present enzymatic activity of Crystal Structure of PDE2 in Complex with Complex 9:
3.1.4.17;

The structure of Crystal Structure of PDE2 in Complex with Complex 9, PDB code: 6b97 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.06 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.270, 96.070, 102.060, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22

The structure of Crystal Structure of PDE2 in Complex with Complex 9 also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE2 in Complex with Complex 9 (pdb code 6b97). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of PDE2 in Complex with Complex 9, PDB code: 6b97:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:18.8 occ:1.00 OD1 A:ASP697 2.0 19.4 1.0 O A:HOH1120 2.0 21.4 1.0 O A:HOH1160 2.1 21.2 1.0 O A:HOH1106 2.1 20.4 1.0 O A:HOH1139 2.1 19.6 1.0 O A:HOH1209 2.1 18.4 1.0 CG A:ASP697 3.0 19.9 1.0 OD2 A:ASP697 3.4 20.4 1.0 ZN A:ZN1001 4.0 25.2 1.0 NE2 A:HIS730 4.1 18.8 1.0 OE2 A:GLU727 4.1 24.7 1.0 O A:HOH1199 4.1 21.0 1.0 OG1 A:THR768 4.2 21.5 1.0 O A:HOH1217 4.3 21.1 1.0 O A:HIS696 4.3 18.6 1.0 CD2 A:HIS696 4.3 22.4 1.0 CD2 A:HIS730 4.3 19.5 1.0 O A:HOH1121 4.4 37.8 1.0 CB A:ASP697 4.4 18.3 1.0 CD2 A:HIS700 4.4 19.7 1.0 CB A:THR768 4.5 24.7 1.0 OD2 A:ASP808 4.5 22.5 1.0 NE2 A:HIS656 4.6 21.1 1.0 NE2 A:HIS696 4.7 21.6 1.0 O A:THR768 4.7 23.4 1.0 CD2 A:HIS656 4.7 20.9 1.0 NE2 A:HIS700 4.8 19.5 1.0 CA A:ASP697 4.8 17.6 1.0 CG A:GLU727 4.9 20.3 1.0 CD A:GLU727 4.9 27.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE2 in Complex with Complex 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of PDE2 in Complex with Complex 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:20.0 occ:1.00 O B:HOH1134 2.0 18.6 1.0 O B:HOH1170 2.1 21.1 1.0 OD1 B:ASP697 2.1 20.3 1.0 O B:HOH1242 2.1 19.9 1.0 O B:HOH1138 2.1 21.1 1.0 O B:HOH1105 2.1 18.6 1.0 CG B:ASP697 3.1 22.0 1.0 OD2 B:ASP697 3.4 21.1 1.0 ZN B:ZN1001 4.0 26.1 1.0 NE2 B:HIS730 4.1 18.1 1.0 O B:HOH1181 4.1 23.3 1.0 OE2 B:GLU727 4.2 26.8 1.0 O B:HOH1187 4.2 23.7 1.0 OG1 B:THR768 4.2 19.9 1.0 CD2 B:HIS696 4.3 20.1 1.0 CD2 B:HIS730 4.3 17.9 1.0 O B:HIS696 4.3 18.1 1.0 CB B:ASP697 4.4 17.8 1.0 O B:HOH1199 4.5 35.1 1.0 CD2 B:HIS700 4.5 22.1 1.0 OD2 B:ASP808 4.5 23.6 1.0 CB B:THR768 4.5 23.3 1.0 NE2 B:HIS656 4.6 20.6 1.0 NE2 B:HIS700 4.7 22.0 1.0 NE2 B:HIS696 4.7 19.6 1.0 O B:THR768 4.7 23.9 1.0 CD2 B:HIS656 4.7 20.8 1.0 CA B:ASP697 4.8 17.4 1.0 CG B:GLU727 4.9 20.7 1.0 CD B:GLU727 4.9 30.6 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