Magnesium in PDB 4jib: Crystal Structure of of PDE2-Inhibitor Complex

All present enzymatic activity of Crystal Structure of of PDE2-Inhibitor Complex:
3.1.4.17;

The structure of Crystal Structure of of PDE2-Inhibitor Complex, PDB code: 4jib was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.72
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.880, 74.132, 91.802, 109.67, 88.72, 88.97
R / Rfree (%)	18.8 / 24

The structure of Crystal Structure of of PDE2-Inhibitor Complex also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of of PDE2-Inhibitor Complex (pdb code 4jib). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of of PDE2-Inhibitor Complex, PDB code: 4jib:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


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 of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:12.2 occ:1.00 OD1 A:ASP697 2.0 9.9 1.0 O A:HOH1454 2.1 13.1 1.0 O A:HOH1216 2.1 11.2 1.0 O A:HOH1269 2.1 9.0 1.0 O A:HOH1445 2.2 11.1 1.0 O A:HOH1465 2.2 11.4 1.0 CG A:ASP697 3.1 12.1 1.0 OD2 A:ASP697 3.5 9.0 1.0 ZN A:ZN1001 3.9 16.0 1.0 O A:HOH1120 4.1 12.2 1.0 NE2 A:HIS730 4.1 12.2 1.0 OG1 A:THR768 4.2 13.7 1.0 OE2 A:GLU727 4.2 19.3 1.0 CD2 A:HIS696 4.2 10.0 1.0 O A:HOH1124 4.3 19.4 1.0 CD2 A:HIS730 4.3 9.1 1.0 O A:HIS696 4.3 10.9 1.0 CB A:ASP697 4.4 10.2 1.0 O A:THR768 4.5 14.6 1.0 OD2 A:ASP808 4.6 20.2 1.0 CB A:THR768 4.6 13.9 1.0 CD2 A:HIS700 4.6 15.2 1.0 O A:HOH1448 4.6 32.3 1.0 NE2 A:HIS656 4.6 17.0 1.0 CD2 A:HIS656 4.7 12.7 1.0 NE2 A:HIS696 4.7 8.9 1.0 CA A:ASP697 4.8 9.6 1.0 NE2 A:HIS700 4.9 13.0 1.0 CG A:GLU727 4.9 11.9 1.0 CD A:GLU727 5.0 17.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


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 of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:12.6 occ:1.00 OD1 B:ASP697 2.1 9.0 1.0 O B:HOH1457 2.1 11.1 1.0 O B:HOH1442 2.1 12.9 1.0 O B:HOH1450 2.2 11.7 1.0 O B:HOH1456 2.2 13.1 1.0 O B:HOH1284 2.2 12.8 1.0 CG B:ASP697 3.1 11.2 1.0 OD2 B:ASP697 3.5 11.4 1.0 O B:HOH1262 3.7 28.0 1.0 ZN B:ZN1001 3.9 16.7 1.0 NE2 B:HIS730 4.0 11.4 1.0 OE2 B:GLU727 4.1 17.7 1.0 OG1 B:THR768 4.1 11.2 1.0 O B:HOH1103 4.1 14.5 1.0 O B:HIS696 4.2 11.1 1.0 CD2 B:HIS696 4.2 11.2 1.0 CD2 B:HIS730 4.2 9.6 1.0 O B:HOH1149 4.3 21.9 1.0 O B:HOH1298 4.5 27.3 1.0 CB B:ASP697 4.5 11.1 1.0 CD2 B:HIS700 4.5 15.7 1.0 O B:THR768 4.6 13.7 1.0 OD2 B:ASP808 4.6 19.3 1.0 CB B:THR768 4.6 12.9 1.0 CE1 B:HIS656 4.6 11.6 1.0 NE2 B:HIS696 4.7 10.3 1.0 CA B:ASP697 4.8 11.1 1.0 NE2 B:HIS700 4.8 15.8 1.0 ND1 B:HIS656 4.8 16.9 1.0 CG B:GLU727 4.9 11.4 1.0 CD B:GLU727 4.9 13.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:13.8 occ:1.00 O C:HOH1410 2.1 11.8 1.0 O C:HOH1424 2.1 13.1 1.0 OD1 C:ASP697 2.1 9.6 1.0 O C:HOH1122 2.1 13.6 1.0 O C:HOH1415 2.1 11.6 1.0 O C:HOH1425 2.2 12.8 1.0 CG C:ASP697 3.2 11.7 1.0 OD2 C:ASP697 3.5 11.9 1.0 ZN C:ZN1001 3.9 17.2 1.0 CE1 C:HIS730 4.0 11.3 1.0 OE2 C:GLU727 4.0 17.7 1.0 O C:HOH1140 4.1 19.4 1.0 OG1 C:THR768 4.2 13.3 1.0 O C:HOH1107 4.2 15.0 1.0 CD2 C:HIS696 4.2 13.0 1.0 O C:HIS696 4.3 11.7 1.0 CD2 C:HIS700 4.4 15.7 1.0 ND1 C:HIS730 4.4 15.0 1.0 CB C:ASP697 4.5 12.1 1.0 O C:THR768 4.5 13.5 1.0 OD2 C:ASP808 4.5 23.0 1.0 NE2 C:HIS656 4.6 17.1 1.0 CB C:THR768 4.6 13.6 1.0 NE2 C:HIS700 4.6 16.7 1.0 CD2 C:HIS656 4.7 16.2 1.0 NE2 C:HIS696 4.7 12.3 1.0 O C:HOH1224 4.8 24.7 1.0 CA C:ASP697 4.8 12.1 1.0 CG C:GLU727 4.8 13.3 1.0 CD C:GLU727 4.8 17.7 1.0 O C:HOH1137 4.9 20.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of of PDE2-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of of PDE2-Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:14.9 occ:1.00 O D:HOH1176 2.0 16.9 1.0 OD1 D:ASP697 2.1 12.7 1.0 O D:HOH1436 2.1 14.2 1.0 O D:HOH1429 2.1 13.1 1.0 O D:HOH1446 2.1 11.1 1.0 O D:HOH1459 2.2 13.8 1.0 CG D:ASP697 3.1 12.1 1.0 OD2 D:ASP697 3.4 12.8 1.0 ZN D:ZN1001 3.9 18.1 1.0 OE2 D:GLU727 4.1 18.9 1.0 O D:HOH1120 4.1 17.1 1.0 CD2 D:HIS696 4.2 14.5 1.0 O D:HOH1130 4.2 18.7 1.0 NE2 D:HIS730 4.2 13.1 1.0 OG1 D:THR768 4.2 12.9 1.0 O D:HIS696 4.3 13.7 1.0 CD2 D:HIS700 4.4 17.1 1.0 CD2 D:HIS730 4.4 11.0 1.0 O D:THR768 4.5 13.8 1.0 CB D:ASP697 4.5 12.4 1.0 OD2 D:ASP808 4.5 22.3 1.0 CB D:THR768 4.5 11.8 1.0 NE2 D:HIS656 4.6 15.0 1.0 NE2 D:HIS696 4.6 11.1 1.0 NE2 D:HIS700 4.6 16.5 1.0 CD2 D:HIS656 4.7 15.5 1.0 CA D:ASP697 4.8 11.9 1.0 O D:HOH1250 4.9 32.7 1.0 CG D:GLU727 4.9 11.5 1.0 CD D:GLU727 4.9 15.2 1.0

M.S.Plummer, J.Cornicelli, H.Roark, D.J.Skalitzky, C.J.Stankovic, S.Bove, J.Pandit, A.Goodman, J.Hicks, A.Shahripour, D.Beidler, X.K.Lu, B.Sanchez, C.Whitehead, R.Sarver, T.Braden, R.Gowan, X.Q.Shen, K.Welch, A.Ogden, N.Sadagopan, H.Baum, H.Miller, C.Banotai, C.Spessard, S.Lightle. Discovery of Potent, Selective, Bioavailable Phosphodiesterase 2 (PDE2) Inhibitors Active in An Osteoarthritis Pain Model, Part I: Transformation of Selective Pyrazolodiazepinone Phosphodiesterase 4 (PDE4) Inhibitors Into Selective PDE2 Inhibitors. Bioorg.Med.Chem.Lett. V. 23 3438 2013.
ISSN: ISSN 0960-894X
PubMed: 23582272
DOI: 10.1016/J.BMCL.2013.03.072