Manganese 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:

Calcium	(Ca)	1 atom
Magnesium	(Mg)	4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Catalytic Domain of Human PDE3A, PDB code: 7l27:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn1101 b:24.6 occ:1.00 OD2 A:ASP837 2.1 24.5 1.0 O A:HOH1222 2.1 24.1 1.0 NE2 A:HIS836 2.2 23.4 1.0 NE2 A:HIS756 2.2 21.4 1.0 OD1 A:ASP950 2.2 23.2 1.0 O A:HOH1289 2.5 35.5 1.0 CD2 A:HIS836 3.1 23.8 1.0 CD2 A:HIS756 3.1 24.8 1.0 CG A:ASP950 3.1 24.7 1.0 CG A:ASP837 3.1 24.1 1.0 CE1 A:HIS836 3.2 23.0 1.0 CE1 A:HIS756 3.3 25.0 1.0 OD2 A:ASP950 3.3 27.6 1.0 OD1 A:ASP837 3.6 24.9 1.0 MG A:MG1102 3.9 18.8 1.0 CD2 A:HIS752 4.1 25.4 1.0 CG A:HIS836 4.2 21.9 1.0 ND1 A:HIS836 4.3 22.8 1.0 CG A:HIS756 4.3 23.1 1.0 O A:HOH1261 4.3 32.2 1.0 O A:HOH1320 4.3 30.1 1.0 ND1 A:HIS756 4.3 24.2 1.0 CB A:ASP837 4.3 22.9 1.0 CB A:ASP950 4.5 23.6 1.0 NE2 A:HIS752 4.6 29.4 1.0 CG2 A:VAL760 4.6 21.9 1.0 O A:HOH1254 4.6 22.1 1.0 O A:ASP950 4.9 26.8 1.0 CA A:ASP950 4.9 23.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn1101 b:27.1 occ:1.00 OD2 B:ASP837 2.1 26.8 1.0 NE2 B:HIS756 2.2 21.1 1.0 O B:HOH1210 2.2 25.9 1.0 OD1 B:ASP950 2.2 24.5 1.0 CE1 B:HIS836 2.2 23.1 1.0 O B:HOH1290 2.4 43.1 1.0 CD2 B:HIS756 3.1 26.3 1.0 CG B:ASP837 3.1 27.2 1.0 CG B:ASP950 3.1 26.0 1.0 ND1 B:HIS836 3.2 26.9 1.0 NE2 B:HIS836 3.2 25.8 1.0 CE1 B:HIS756 3.2 28.1 1.0 OD2 B:ASP950 3.4 28.1 1.0 OD1 B:ASP837 3.6 27.6 1.0 MG B:MG1102 3.8 20.3 1.0 O B:HOH1292 4.2 31.1 1.0 CD2 B:HIS752 4.2 25.5 1.0 O B:HOH1248 4.3 34.6 1.0 CG B:HIS756 4.3 24.7 1.0 ND1 B:HIS756 4.3 24.6 1.0 CB B:ASP837 4.3 25.1 1.0 CG B:HIS836 4.4 24.7 1.0 CD2 B:HIS836 4.4 21.0 1.0 CB B:ASP950 4.5 26.1 1.0 CG2 B:VAL760 4.6 24.8 1.0 O B:HOH1244 4.6 25.8 1.0 NE2 B:HIS752 4.8 27.7 1.0 O B:ASP950 4.9 30.6 1.0 CA B:ASP950 4.9 26.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn1101 b:26.1 occ:1.00 OD2 C:ASP837 2.0 24.8 1.0 O C:HOH1227 2.1 26.1 1.0 NE2 C:HIS756 2.2 21.0 1.0 CE1 C:HIS836 2.2 19.5 1.0 OD1 C:ASP950 2.3 23.3 1.0 O C:HOH1324 2.5 37.2 1.0 CD2 C:HIS756 3.1 24.1 1.0 CG C:ASP837 3.1 22.3 1.0 CG C:ASP950 3.1 25.0 1.0 ND1 C:HIS836 3.1 25.6 1.0 NE2 C:HIS836 3.2 21.3 1.0 CE1 C:HIS756 3.3 26.1 1.0 OD2 C:ASP950 3.3 26.8 1.0 OD1 C:ASP837 3.6 25.1 1.0 MG C:MG1102 3.9 19.2 1.0 CD2 C:HIS752 4.1 23.0 1.0 O C:HOH1279 4.2 30.4 1.0 O C:HOH1330 4.3 28.8 1.0 CG C:HIS756 4.3 22.9 1.0 CG C:HIS836 4.3 21.6 1.0 CD2 C:HIS836 4.3 19.1 1.0 CB C:ASP837 4.3 21.1 1.0 ND1 C:HIS756 4.3 23.9 1.0 NE2 C:HIS752 4.5 24.4 1.0 CB C:ASP950 4.5 24.2 1.0 CG2 C:VAL760 4.6 23.7 1.0 O C:HOH1239 4.6 20.8 1.0 CA C:ASP950 4.9 23.5 1.0 O C:ASP950 5.0 28.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn1101 b:21.2 occ:1.00 O D:HOH1228 2.1 23.0 1.0 NE2 D:HIS756 2.2 16.0 1.0 CE1 D:HIS836 2.2 19.8 1.0 OD1 D:ASP950 2.2 19.6 1.0 OD2 D:ASP837 2.3 22.8 1.0 O D:HOH1348 2.3 30.8 1.0 CD2 D:HIS756 3.1 18.9 1.0 CG D:ASP950 3.1 20.1 1.0 ND1 D:HIS836 3.2 23.3 1.0 NE2 D:HIS836 3.2 21.9 1.0 CE1 D:HIS756 3.2 19.7 1.0 CG D:ASP837 3.3 19.7 1.0 OD2 D:ASP950 3.4 23.9 1.0 MG D:MG1102 3.9 15.7 1.0 OD1 D:ASP837 3.9 22.6 1.0 O D:HOH1364 4.2 24.1 1.0 O D:HOH1272 4.2 25.9 1.0 ND1 D:HIS752 4.2 25.0 1.0 CG D:HIS756 4.3 17.0 1.0 ND1 D:HIS756 4.3 18.3 1.0 CB D:ASP837 4.3 19.9 1.0 CG D:HIS836 4.3 20.0 1.0 CD2 D:HIS836 4.4 17.6 1.0 CE1 D:HIS752 4.5 20.2 1.0 CB D:ASP950 4.5 19.7 1.0 CG2 D:VAL760 4.6 17.4 1.0 O D:HOH1258 4.7 19.5 1.0 CA D:ASP950 4.9 18.5 1.0 O D:ASP950 4.9 22.2 1.0

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