Magnesium in PDB 7eg4: Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex

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

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

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Nauclefine-Induced PDE3A-SLFN12 Complex (pdb code 7eg4). 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 Nauclefine-Induced PDE3A-SLFN12 Complex, PDB code: 7eg4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Nauclefine-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 Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1202 b:30.5 occ:1.00 OD2 C:ASP837 1.9 41.8 1.0 NE2 C:HIS836 2.1 38.2 1.0 OD1 C:ASP950 2.1 38.6 1.0 NE2 C:HIS756 2.3 43.9 1.0 CD2 C:HIS836 3.0 38.2 1.0 CG C:ASP837 3.1 41.8 1.0 CE1 C:HIS836 3.2 38.2 1.0 CG C:ASP950 3.2 38.6 1.0 CE1 C:HIS756 3.2 43.9 1.0 CD2 C:HIS756 3.2 43.9 1.0 OD2 C:ASP950 3.6 38.6 1.0 OD1 C:ASP837 3.6 41.8 1.0 CG C:HIS836 4.1 38.2 1.0 ND1 C:HIS836 4.2 38.2 1.0 CB C:ASP837 4.3 41.8 1.0 ND1 C:HIS756 4.3 43.9 1.0 CG C:HIS756 4.4 43.9 1.0 CD2 C:HIS752 4.5 46.0 1.0 CB C:ASP950 4.5 38.6 1.0 CG2 C:VAL760 4.7 43.6 1.0 MG C:MG1203 4.8 38.3 1.0 NE2 C:HIS752 4.9 46.0 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Nauclefine-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 Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1203 b:38.3 occ:1.00 OD1 C:ASP837 3.1 41.8 1.0 OE2 C:GLU866 3.9 35.3 1.0 NE2 C:HIS869 4.0 34.9 1.0 CG C:ASP837 4.1 41.8 1.0 CD C:GLU866 4.2 35.3 1.0 CD2 C:HIS869 4.2 34.9 1.0 NE2 C:HIS840 4.4 44.0 1.0 CD2 C:HIS840 4.5 44.0 1.0 O C:THR908 4.5 33.5 1.0 OD2 C:ASP837 4.5 41.8 1.0 CG C:GLU866 4.6 35.3 1.0 O C:HIS836 4.7 38.2 1.0 OE1 C:GLU866 4.7 35.3 1.0 OG1 C:THR908 4.7 33.5 1.0 MG C:MG1202 4.8 30.5 1.0 CB C:LEU865 4.9 34.3 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Nauclefine-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 Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:30.5 occ:1.00 OD2 A:ASP837 1.9 41.8 1.0 NE2 A:HIS836 2.1 38.2 1.0 OD1 A:ASP950 2.1 38.6 1.0 NE2 A:HIS756 2.3 43.9 1.0 CD2 A:HIS836 3.0 38.2 1.0 CG A:ASP837 3.1 41.8 1.0 CE1 A:HIS836 3.2 38.2 1.0 CG A:ASP950 3.2 38.6 1.0 CE1 A:HIS756 3.2 43.9 1.0 CD2 A:HIS756 3.2 43.9 1.0 OD2 A:ASP950 3.6 38.6 1.0 OD1 A:ASP837 3.6 41.8 1.0 CG A:HIS836 4.1 38.2 1.0 ND1 A:HIS836 4.2 38.2 1.0 CB A:ASP837 4.3 41.8 1.0 ND1 A:HIS756 4.3 43.9 1.0 CG A:HIS756 4.4 43.9 1.0 CD2 A:HIS752 4.5 46.0 1.0 CB A:ASP950 4.5 38.6 1.0 CG2 A:VAL760 4.7 43.6 1.0 MG A:MG1203 4.8 38.3 1.0 NE2 A:HIS752 4.9 46.0 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Nauclefine-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 Nauclefine-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:38.3 occ:1.00 OD1 A:ASP837 3.1 41.8 1.0 OE2 A:GLU866 3.9 35.3 1.0 NE2 A:HIS869 4.0 34.9 1.0 CG A:ASP837 4.1 41.8 1.0 CD2 A:HIS869 4.2 34.9 1.0 CD A:GLU866 4.2 35.3 1.0 NE2 A:HIS840 4.4 44.0 1.0 CD2 A:HIS840 4.5 44.0 1.0 O A:THR908 4.5 33.5 1.0 OD2 A:ASP837 4.5 41.8 1.0 CG A:GLU866 4.6 35.3 1.0 O A:HIS836 4.7 38.2 1.0 OE1 A:GLU866 4.7 35.3 1.0 OG1 A:THR908 4.7 33.5 1.0 MG A:MG1202 4.8 30.5 1.0 CB A:LEU865 4.9 34.3 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