Magnesium in PDB 7l27: Crystal Structure of the Catalytic Domain of Human PDE3A

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE3A:
3.1.4.17;

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A, PDB code: 7l27 was solved by S.W.Horner, C.Garvie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.85 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.37, 58.79, 157.66, 90, 90.69, 90
R / Rfree (%)	19.4 / 22

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Human PDE3A (pdb code 7l27). 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 the Catalytic Domain of Human PDE3A, PDB code: 7l27:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A


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 the Catalytic Domain of Human PDE3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:18.8 occ:1.00 O A:HOH1320 2.1 30.1 1.0 O A:HOH1222 2.1 24.1 1.0 O A:HOH1275 2.2 25.0 1.0 O A:HOH1284 2.2 21.7 1.0 OD1 A:ASP837 2.2 24.9 1.0 O A:HOH1254 2.2 22.1 1.0 CG A:ASP837 3.2 24.1 1.0 OD2 A:ASP837 3.6 24.5 1.0 MN A:MN1101 3.9 24.6 1.0 OE2 A:GLU866 4.1 25.8 1.0 NE2 A:HIS869 4.1 22.6 1.0 O A:HOH1289 4.2 35.5 1.0 OG1 A:THR908 4.3 21.6 1.0 CD2 A:HIS836 4.3 23.8 1.0 O A:HIS836 4.4 22.5 1.0 CD2 A:HIS869 4.4 22.1 1.0 OD2 A:ASP950 4.4 27.6 1.0 O A:HOH1264 4.5 33.1 1.0 CD2 A:HIS840 4.5 26.0 1.0 CD2 A:HIS752 4.6 25.4 1.0 CB A:ASP837 4.6 22.9 1.0 NE2 A:HIS752 4.7 29.4 1.0 NE2 A:HIS836 4.7 23.4 1.0 CG A:GLU866 4.8 22.5 1.0 NE2 A:HIS840 4.9 25.8 1.0 CB A:THR908 4.9 20.9 1.0 CD A:GLU866 4.9 27.0 1.0 O A:THR908 4.9 23.9 1.0 CA A:ASP837 5.0 20.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A


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 the Catalytic Domain of Human PDE3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1102 b:20.3 occ:1.00 O B:HOH1292 2.1 31.1 1.0 O B:HOH1210 2.1 25.9 1.0 OD1 B:ASP837 2.2 27.6 1.0 O B:HOH1287 2.2 24.7 1.0 O B:HOH1244 2.2 25.8 1.0 O B:HOH1269 2.2 28.4 1.0 CG B:ASP837 3.2 27.2 1.0 OD2 B:ASP837 3.5 26.8 1.0 MN B:MN1101 3.8 27.1 1.0 CE1 B:HIS869 4.1 23.4 1.0 O B:HOH1290 4.1 43.1 1.0 OE2 B:GLU866 4.1 25.0 1.0 OG1 B:THR908 4.4 22.9 1.0 O B:HIS836 4.4 23.7 1.0 ND1 B:HIS869 4.4 24.4 1.0 ND1 B:HIS836 4.4 26.9 1.0 OD2 B:ASP950 4.4 28.1 1.0 CD2 B:HIS840 4.5 26.2 1.0 O B:HOH1229 4.5 40.8 1.0 CB B:ASP837 4.6 25.1 1.0 CD2 B:HIS752 4.6 25.5 1.0 CE1 B:HIS836 4.7 23.1 1.0 CG B:GLU866 4.8 25.0 1.0 NE2 B:HIS752 4.8 27.7 1.0 NE2 B:HIS840 4.8 28.6 1.0 O B:THR908 4.9 26.0 1.0 CB B:THR908 4.9 23.4 1.0 CD B:GLU866 4.9 26.8 1.0 CA B:ASP837 5.0 23.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A


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 the Catalytic Domain of Human PDE3A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1102 b:19.2 occ:1.00 O C:HOH1227 2.1 26.1 1.0 OD1 C:ASP837 2.1 25.1 1.0 O C:HOH1283 2.2 21.6 1.0 O C:HOH1330 2.2 28.8 1.0 O C:HOH1303 2.2 26.1 1.0 O C:HOH1239 2.2 20.8 1.0 CG C:ASP837 3.2 22.3 1.0 OD2 C:ASP837 3.6 24.8 1.0 MN C:MN1101 3.9 26.1 1.0 OE2 C:GLU866 4.1 23.9 1.0 NE2 C:HIS869 4.1 21.5 1.0 O C:HOH1352 4.1 49.5 1.0 O C:HOH1324 4.2 37.2 1.0 OG1 C:THR908 4.3 24.9 1.0 O C:HIS836 4.4 23.6 1.0 ND1 C:HIS836 4.4 25.6 1.0 CD2 C:HIS869 4.4 21.4 1.0 OD2 C:ASP950 4.5 26.8 1.0 O C:HOH1331 4.6 28.5 1.0 CD2 C:HIS840 4.6 22.8 1.0 CB C:ASP837 4.6 21.1 1.0 CD2 C:HIS752 4.6 23.0 1.0 CE1 C:HIS836 4.7 19.5 1.0 NE2 C:HIS752 4.7 24.4 1.0 CG C:GLU866 4.7 22.5 1.0 CB C:THR908 4.8 23.4 1.0 CD C:GLU866 4.9 25.5 1.0 NE2 C:HIS840 4.9 23.9 1.0 O C:THR908 4.9 23.1 1.0 CA C:ASP837 5.0 20.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A


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 the Catalytic Domain of Human PDE3A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1102 b:15.7 occ:1.00 O D:HOH1364 2.1 24.1 1.0 O D:HOH1228 2.2 23.0 1.0 O D:HOH1267 2.2 21.3 1.0 O D:HOH1277 2.2 21.8 1.0 O D:HOH1258 2.2 19.5 1.0 OD1 D:ASP837 2.4 22.6 1.0 CG D:ASP837 3.2 19.7 1.0 OD2 D:ASP837 3.4 22.8 1.0 MN D:MN1101 3.9 21.2 1.0 O D:HOH1348 4.1 30.8 1.0 OE2 D:GLU866 4.1 23.0 1.0 NE2 D:HIS869 4.1 18.5 1.0 O D:HOH1367 4.2 45.0 1.0 OG1 D:THR908 4.3 21.7 1.0 CD2 D:HIS869 4.4 19.2 1.0 O D:HIS836 4.4 20.6 1.0 ND1 D:HIS836 4.4 23.3 1.0 OD2 D:ASP950 4.4 23.9 1.0 O D:HOH1317 4.6 31.2 1.0 CD2 D:HIS840 4.6 19.1 1.0 CE1 D:HIS752 4.6 20.2 1.0 CB D:ASP837 4.6 19.9 1.0 ND1 D:HIS752 4.6 25.0 1.0 CE1 D:HIS836 4.7 19.8 1.0 CG D:GLU866 4.7 20.3 1.0 CB D:THR908 4.8 18.9 1.0 CD D:GLU866 4.8 24.4 1.0 NE2 D:HIS840 4.9 19.4 1.0 O D:THR908 4.9 22.1 1.0 CA D:ASP837 5.0 17.3 1.0

C.W.Garvie, S.W.Horner. Structure of PDE3A-SLFN12 Complex Reveals Requirements For Activation of SLFN12 Rnase To Be Published.