Magnesium in PDB 7eg1: Cryo-Em Structure of Dnmdp-Induced PDE3A-SLFN12 Complex

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

The structure of Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex (pdb code 7eg1). 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 Dnmdp-Induced PDE3A-SLFN12 Complex, PDB code: 7eg1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:10.5 occ:1.00 OD1 A:ASP950 2.0 15.3 1.0 OD2 A:ASP837 2.1 14.6 1.0 NE2 A:HIS836 2.2 13.5 1.0 NE2 A:HIS756 2.3 15.9 1.0 CD2 A:HIS836 2.9 13.5 1.0 CG A:ASP837 3.1 14.6 1.0 CE1 A:HIS756 3.2 15.9 1.0 CG A:ASP950 3.2 15.3 1.0 CE1 A:HIS836 3.3 13.5 1.0 CD2 A:HIS756 3.3 15.9 1.0 OD1 A:ASP837 3.5 14.6 1.0 OD2 A:ASP950 3.7 15.3 1.0 MG A:MG1203 3.9 9.5 1.0 CG A:HIS836 4.0 13.5 1.0 ND1 A:HIS836 4.2 13.5 1.0 ND1 A:HIS756 4.3 15.9 1.0 CG A:HIS756 4.4 15.9 1.0 CB A:ASP950 4.4 15.3 1.0 CB A:ASP837 4.4 14.6 1.0 CG2 A:VAL760 4.5 16.9 1.0 CD2 A:HIS752 4.6 17.6 1.0 CA A:ASP950 4.8 15.3 1.0 O A:ASP950 4.9 15.3 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:9.5 occ:1.00 OD1 A:ASP837 2.3 14.6 1.0 CG A:ASP837 3.4 14.6 1.0 OD2 A:ASP837 3.8 14.6 1.0 OE2 A:GLU866 3.9 11.2 1.0 MG A:MG1202 3.9 10.5 1.0 O A:HIS836 4.1 13.5 1.0 OG1 A:THR908 4.3 9.3 1.0 NE2 A:HIS869 4.4 11.0 1.0 O A:THR908 4.4 9.3 1.0 CD2 A:HIS869 4.5 11.0 1.0 NE2 A:HIS840 4.6 14.4 1.0 CB A:ASP837 4.6 14.6 1.0 CD2 A:HIS840 4.6 14.4 1.0 CD2 A:HIS836 4.7 13.5 1.0 CA A:ASP837 4.9 14.6 1.0 OD1 A:ASP950 4.9 15.3 1.0 OD2 A:ASP950 4.9 15.3 1.0 CD A:GLU866 4.9 11.2 1.0 CD2 A:HIS752 5.0 17.6 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1202 b:10.8 occ:1.00 OD2 C:ASP837 2.0 14.2 1.0 OD1 C:ASP950 2.1 15.4 1.0 NE2 C:HIS836 2.2 13.3 1.0 NE2 C:HIS756 2.2 15.7 1.0 CD2 C:HIS836 2.9 13.3 1.0 CG C:ASP837 3.1 14.2 1.0 CE1 C:HIS756 3.2 15.7 1.0 CD2 C:HIS756 3.2 15.7 1.0 CG C:ASP950 3.2 15.4 1.0 CE1 C:HIS836 3.3 13.3 1.0 OD1 C:ASP837 3.4 14.2 1.0 OD2 C:ASP950 3.8 15.4 1.0 MG C:MG1203 3.9 9.9 1.0 CG C:HIS836 4.1 13.3 1.0 ND1 C:HIS836 4.2 13.3 1.0 ND1 C:HIS756 4.3 15.7 1.0 CG C:HIS756 4.4 15.7 1.0 CB C:ASP837 4.4 14.2 1.0 CB C:ASP950 4.5 15.4 1.0 CG2 C:VAL760 4.6 16.7 1.0 CD2 C:HIS752 4.6 16.5 1.0 CA C:ASP950 4.8 15.4 1.0 O C:ASP950 4.9 15.4 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Dnmdp-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 Dnmdp-Induced PDE3A-SLFN12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1203 b:9.9 occ:1.00 OD1 C:ASP837 2.2 14.2 1.0 CG C:ASP837 3.3 14.2 1.0 OD2 C:ASP837 3.8 14.2 1.0 MG C:MG1202 3.9 10.8 1.0 OE2 C:GLU866 4.0 11.4 1.0 O C:HIS836 4.0 13.3 1.0 NE2 C:HIS869 4.3 10.2 1.0 CD2 C:HIS869 4.4 10.2 1.0 OG1 C:THR908 4.4 9.7 1.0 NE2 C:HIS840 4.4 13.7 1.0 CD2 C:HIS840 4.5 13.7 1.0 CB C:ASP837 4.5 14.2 1.0 O C:THR908 4.5 9.7 1.0 CD2 C:HIS836 4.7 13.3 1.0 CA C:ASP837 4.8 14.2 1.0 CD2 C:HIS752 4.9 16.5 1.0 OD1 C:ASP950 5.0 15.4 1.0 NE2 C:HIS752 5.0 16.5 1.0 CD C:GLU866 5.0 11.4 1.0 C C:HIS836 5.0 13.3 1.0 OD2 C:ASP950 5.0 15.4 1.0

J.Chen, N.Liu, D.R.Li, Y.X.Wang, Y.X.Sun, Q.C.Wu, Y.P.Huang, H.W.Wang, N.Huang, X.B.Qi, X.D.Wang. Cryo-Em Structure of Anagrelide-Induced PDE3A-SLFN12 Complex To Be Published.