Magnesium in PDB 8ufi: Cryo-Em Structure of Bovine Phosphodiesterase 6

All present enzymatic activity of Cryo-Em Structure of Bovine Phosphodiesterase 6:
3.1.4.35;

The structure of Cryo-Em Structure of Bovine Phosphodiesterase 6 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Bovine Phosphodiesterase 6 (pdb code 8ufi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Bovine Phosphodiesterase 6, PDB code: 8ufi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Bovine Phosphodiesterase 6


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 Bovine Phosphodiesterase 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:78.5 occ:1.00 OD1 A:ASP600 2.1 113.3 1.0 CG A:ASP600 2.9 107.0 1.0 OD2 A:ASP600 3.1 103.5 1.0 ZN A:ZN902 3.8 182.0 1.0 OE2 A:GLU628 3.9 120.8 1.0 CE1 A:HIS631 3.9 100.7 1.0 ND1 A:HIS631 4.2 96.1 1.0 CD2 A:HIS603 4.3 99.3 1.0 CB A:ASP600 4.4 97.0 1.0 O A:HIS599 4.4 114.1 1.0 CD A:GLU628 4.5 117.3 1.0 CD2 A:HIS599 4.5 103.7 1.0 NE2 A:HIS603 4.6 99.9 1.0 CG A:GLU628 4.6 109.5 1.0 OG1 A:THR669 4.6 121.0 1.0 CA A:ASP600 4.8 96.0 1.0 NE2 A:HIS599 4.9 109.6 1.0 OD2 A:ASP720 4.9 135.6 1.0 CD2 A:HIS559 4.9 110.0 1.0 OD1 A:ASP720 5.0 142.0 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Bovine Phosphodiesterase 6


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 Bovine Phosphodiesterase 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:155.2 occ:1.00 OD1 B:ASP598 2.3 116.8 1.0 OD2 B:ASP598 2.8 116.0 1.0 CG B:ASP598 2.9 118.1 1.0 CE1 B:HIS629 4.0 108.2 1.0 NE2 B:HIS597 4.0 127.2 1.0 OE2 B:GLU626 4.2 120.1 1.0 ND1 B:HIS629 4.3 105.8 1.0 CB B:ASP598 4.4 107.7 1.0 CD2 B:HIS601 4.4 105.5 1.0 CE1 B:HIS597 4.5 121.9 1.0 NE2 B:HIS601 4.6 112.2 1.0 ZN B:ZN902 4.6 172.1 1.0 CD B:GLU626 4.7 113.8 1.0 OG1 B:THR667 4.7 115.3 1.0 CD2 B:HIS597 4.7 121.3 1.0 O B:HIS597 4.8 115.5 1.0 CG B:GLU626 4.8 107.0 1.0 OD2 B:ASP718 4.8 135.4 1.0 CD2 B:HIS557 5.0 121.2 1.0 NE2 B:HIS557 5.0 120.2 1.0

C.Aplin, R.A.Cerione. Probing the Mechanism By Which the Retinal G Protein Transducin Activates Its Biological Effector PDE6. J.Biol.Chem. 05608 2023.
ISSN: ESSN 1083-351X
PubMed: 38159849
DOI: 10.1016/J.JBC.2023.105608