Magnesium in PDB 8ugb: Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Udenafil

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

The structure of Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Udenafil 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 Bound to Udenafil (pdb code 8ugb). 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 Bound to Udenafil, PDB code: 8ugb:
Jump to Magnesium binding site number: 1; 2;

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


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 Bound to Udenafil within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:56.1 occ:1.00 OD1 A:ASP600 1.9 85.2 1.0 CG A:ASP600 2.5 80.7 1.0 OD2 A:ASP600 2.6 76.5 1.0 CB A:ASP600 3.9 61.6 1.0 ZN A:ZN902 4.0 130.8 1.0 CD2 A:HIS603 4.2 68.0 1.0 OE2 A:GLU628 4.4 82.7 1.0 NE2 A:HIS603 4.5 70.3 1.0 CE1 A:HIS631 4.6 72.8 1.0 CA A:ASP600 4.7 71.4 1.0 OG1 A:THR669 4.7 88.5 1.0 CD2 A:HIS599 4.7 71.1 1.0 OD1 A:ASP720 4.8 97.0 1.0 ND1 A:HIS631 4.8 60.4 1.0 NE2 A:HIS559 4.8 67.5 1.0 OD2 A:ASP720 4.9 95.8 1.0 CB A:THR669 4.9 78.9 1.0

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


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 Bound to Udenafil within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:47.6 occ:1.00 OD1 B:ASP598 2.6 73.0 1.0 CG B:ASP598 3.4 62.1 1.0 OD2 B:ASP598 3.5 60.0 1.0 ZN B:ZN902 3.6 110.8 1.0 CD2 B:HIS601 4.2 68.7 1.0 O B:HIS597 4.4 83.0 1.0 CD2 B:HIS597 4.4 67.6 1.0 CE1 B:HIS629 4.4 66.7 1.0 OE2 B:GLU626 4.5 78.3 1.0 ND1 B:HIS629 4.6 59.5 1.0 OG1 B:THR667 4.7 88.7 1.0 NE2 B:HIS601 4.8 68.6 1.0 OD2 B:ASP718 4.8 91.3 1.0 OD1 B:ASP718 4.8 82.9 1.0 CB B:ASP598 4.9 53.8 1.0 NE2 B:HIS557 5.0 65.0 1.0 CB B:THR667 5.0 70.8 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