Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Udenafil, PDB code: 8ugb:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn902 b:130.8 occ:1.00 OD1 A:ASP720 2.0 97.0 1.0 OD2 A:ASP600 2.0 76.5 1.0 NE2 A:HIS599 2.3 78.3 1.0 NE2 A:HIS563 2.3 61.8 1.0 CD2 A:HIS599 2.6 71.1 1.0 CG A:ASP600 3.1 80.7 1.0 CE1 A:HIS563 3.2 68.7 1.0 CG A:ASP720 3.2 91.0 1.0 CD2 A:HIS563 3.4 65.5 1.0 CE1 A:HIS599 3.6 79.3 1.0 OD2 A:ASP720 3.8 95.8 1.0 CG A:HIS599 3.9 60.5 1.0 OD1 A:ASP600 4.0 85.2 1.0 MG A:MG903 4.0 56.1 1.0 CB A:ASP600 4.0 61.6 1.0 CB A:ASP720 4.3 82.1 1.0 CG2 A:VAL567 4.3 70.0 1.0 ND1 A:HIS563 4.3 66.4 1.0 ND1 A:HIS599 4.4 69.1 1.0 CG A:HIS563 4.5 60.1 1.0 CD2 A:HIS559 4.5 75.2 1.0 CA A:ASP720 4.6 79.3 1.0 NE2 A:HIS559 4.6 67.5 1.0 O A:ASP720 4.7 88.1 1.0 N A:ASP600 4.9 79.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn902 b:110.8 occ:1.00 OD2 B:ASP598 2.2 60.0 1.0 NE2 B:HIS597 2.3 72.5 1.0 NE2 B:HIS561 2.3 52.8 1.0 OD1 B:ASP718 2.5 82.9 1.0 CD2 B:HIS597 2.6 67.6 1.0 CG B:ASP598 3.1 62.1 1.0 CE1 B:HIS561 3.2 57.7 1.0 CD2 B:HIS561 3.3 62.6 1.0 OD1 B:ASP598 3.5 73.0 1.0 CG B:ASP718 3.5 85.7 1.0 MG B:MG903 3.6 47.6 1.0 CE1 B:HIS597 3.6 72.2 1.0 CG B:HIS597 3.9 53.0 1.0 OD2 B:ASP718 4.1 91.3 1.0 CD2 B:HIS557 4.3 73.7 1.0 CB B:ASP598 4.3 53.8 1.0 ND1 B:HIS597 4.4 61.0 1.0 ND1 B:HIS561 4.4 55.8 1.0 CG2 B:VAL565 4.4 69.2 1.0 CG B:HIS561 4.4 55.0 1.0 CB B:ASP718 4.6 75.3 1.0 NE2 B:HIS557 4.7 65.0 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