Magnesium in PDB 7eg0: Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex

All present enzymatic activity of Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex:
3.1.4.17;

The structure of Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex (pdb code 7eg0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex, PDB code: 7eg0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:41.9 occ:1.00 OD1 A:ASP950 2.0 49.7 1.0 OD2 A:ASP837 2.0 49.1 1.0 NE2 A:HIS836 2.2 46.7 1.0 OD2 A:ASP950 2.4 49.7 1.0 CG A:ASP950 2.5 49.7 1.0 NE2 A:HIS756 2.6 50.6 1.0 CD2 A:HIS836 2.9 46.7 1.0 CG A:ASP837 2.9 49.1 1.0 OD1 A:ASP837 3.1 49.1 1.0 CE1 A:HIS836 3.4 46.7 1.0 CE1 A:HIS756 3.5 50.6 1.0 CD2 A:HIS756 3.6 50.6 1.0 CB A:ASP950 4.0 49.7 1.0 CG A:HIS836 4.1 46.7 1.0 MG A:MG1203 4.2 34.0 1.0 CD2 A:HIS752 4.3 52.1 1.0 ND1 A:HIS836 4.3 46.7 1.0 CB A:ASP837 4.3 49.1 1.0 ND1 A:HIS756 4.7 50.6 1.0 NE2 A:HIS752 4.7 52.1 1.0 CG A:HIS756 4.8 50.6 1.0 CA A:ASP950 4.8 49.7 1.0 O A:ASP950 4.9 49.7 1.0 CG2 A:VAL760 4.9 48.4 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:34.0 occ:1.00 OD1 A:ASP837 2.8 49.1 1.0 OE2 A:GLU866 3.9 42.5 1.0 CG A:ASP837 4.0 49.1 1.0 NE2 A:HIS869 4.1 42.8 1.0 O A:THR908 4.2 40.8 1.0 MG A:MG1202 4.2 41.9 1.0 CD2 A:HIS869 4.3 42.8 1.0 OG1 A:THR908 4.3 40.8 1.0 CD A:GLU866 4.3 42.5 1.0 O A:HIS836 4.5 46.7 1.0 OD2 A:ASP950 4.5 49.7 1.0 OD2 A:ASP837 4.5 49.1 1.0 CG A:GLU866 4.7 42.5 1.0 NE2 A:HIS840 4.8 52.0 1.0 CD2 A:HIS840 4.9 52.0 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1202 b:41.9 occ:1.00 OD1 C:ASP950 2.0 49.7 1.0 OD2 C:ASP837 2.0 49.1 1.0 NE2 C:HIS836 2.2 46.7 1.0 OD2 C:ASP950 2.4 49.7 1.0 CG C:ASP950 2.5 49.7 1.0 NE2 C:HIS756 2.6 50.6 1.0 CD2 C:HIS836 2.9 46.7 1.0 CG C:ASP837 2.9 49.1 1.0 OD1 C:ASP837 3.1 49.1 1.0 CE1 C:HIS836 3.4 46.7 1.0 CE1 C:HIS756 3.5 50.6 1.0 CD2 C:HIS756 3.6 50.6 1.0 CB C:ASP950 4.0 49.7 1.0 CG C:HIS836 4.1 46.7 1.0 MG C:MG1203 4.2 34.0 1.0 CD2 C:HIS752 4.3 52.1 1.0 ND1 C:HIS836 4.3 46.7 1.0 CB C:ASP837 4.3 49.1 1.0 ND1 C:HIS756 4.7 50.6 1.0 NE2 C:HIS752 4.7 52.1 1.0 CG C:HIS756 4.8 50.6 1.0 CA C:ASP950 4.8 49.7 1.0 O C:ASP950 4.9 49.7 1.0 CG2 C:VAL760 4.9 48.4 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1203 b:34.0 occ:1.00 OD1 C:ASP837 2.8 49.1 1.0 OE2 C:GLU866 3.9 42.5 1.0 CG C:ASP837 4.0 49.1 1.0 NE2 C:HIS869 4.2 42.8 1.0 O C:THR908 4.2 40.8 1.0 MG C:MG1202 4.2 41.9 1.0 CD2 C:HIS869 4.3 42.8 1.0 OG1 C:THR908 4.3 40.8 1.0 CD C:GLU866 4.3 42.5 1.0 O C:HIS836 4.5 46.7 1.0 OD2 C:ASP950 4.5 49.7 1.0 OD2 C:ASP837 4.5 49.1 1.0 CG C:GLU866 4.7 42.5 1.0 NE2 C:HIS840 4.8 52.0 1.0 CD2 C:HIS840 4.9 52.0 1.0

J.Chen, N.Liu, L.Dianrong, W.Yuanxun, S.Yuxing, W.Qingcui, H.Yinpin, H.W.Wang, H.Niu, Q.Xiangbing, X.D.Wang. Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex Nat Commun 2021.
ISSN: ESSN 2041-1723