Magnesium in PDB 8ulg: Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Ibmx

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

The structure of Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Ibmx 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 Ibmx (pdb code 8ulg). 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 Ibmx, PDB code: 8ulg:
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 Ibmx


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 Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:62.5 occ:1.00 CE1 A:HIS631 3.9 63.4 1.0 CB A:ASP600 4.1 63.0 1.0 ND1 A:HIS631 4.2 54.3 1.0 ZN A:ZN903 4.2 111.6 1.0 OD2 A:ASP600 4.4 82.0 1.0 O A:HIS599 4.4 83.8 1.0 CD2 A:HIS603 4.5 60.0 1.0 OE2 A:GLU628 4.5 80.5 1.0 OG1 A:THR669 4.6 71.1 1.0 NE2 A:HIS603 4.6 59.8 1.0 CD2 A:HIS599 4.7 65.0 1.0 CG A:ASP600 4.7 77.9 1.0 CA A:ASP600 4.8 64.3 1.0 CD A:GLU628 4.9 78.6 1.0 OD2 A:ASP720 4.9 78.1 1.0

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


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 Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:44.5 occ:1.00 OD1 B:ASP598 2.4 80.5 1.0 CG B:ASP598 3.4 69.3 1.0 OD2 B:ASP598 3.7 63.0 1.0 CE1 B:HIS629 3.9 65.9 1.0 ZN B:ZN903 4.1 110.1 1.0 OE2 B:GLU626 4.2 85.2 1.0 ND1 B:HIS629 4.3 59.9 1.0 O B:HIS597 4.3 68.5 1.0 OG1 B:THR667 4.4 83.2 1.0 CD2 B:HIS601 4.5 66.8 1.0 CD B:GLU626 4.8 82.2 1.0 CD2 B:HIS597 4.8 65.6 1.0 CB B:ASP598 4.8 58.3 1.0 CG B:GLU626 4.8 68.9 1.0 NE2 B:HIS601 4.8 66.9 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