Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Bovine Phosphodiesterase 6 (pdb code 8ufi). 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, PDB code: 8ufi:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Bovine Phosphodiesterase 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:182.0 occ:1.00 OD2 A:ASP600 1.9 103.5 1.0 OD1 A:ASP720 2.0 142.0 1.0 NE2 A:HIS563 2.3 113.2 1.0 NE2 A:HIS599 2.3 109.6 1.0 CG A:ASP720 2.9 134.4 1.0 CD2 A:HIS599 2.9 103.7 1.0 CG A:ASP600 3.1 107.0 1.0 CE1 A:HIS563 3.2 111.8 1.0 OD2 A:ASP720 3.3 135.6 1.0 CD2 A:HIS563 3.3 108.3 1.0 CE1 A:HIS599 3.5 109.7 1.0 OD1 A:ASP600 3.8 113.3 1.0 MG A:MG903 3.8 78.5 1.0 CB A:ASP600 4.2 97.0 1.0 CG A:HIS599 4.2 95.4 1.0 CB A:ASP720 4.3 124.4 1.0 CD2 A:HIS559 4.3 110.0 1.0 ND1 A:HIS563 4.4 103.8 1.0 ND1 A:HIS599 4.4 99.1 1.0 CG A:HIS563 4.4 99.9 1.0 NE2 A:HIS559 4.5 106.7 1.0 O A:ASP720 4.7 123.3 1.0 CA A:ASP720 4.8 119.6 1.0 CG2 A:VAL567 4.8 103.6 1.0

Zinc 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 Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Bovine Phosphodiesterase 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:172.1 occ:1.00 CE1 B:HIS597 1.0 121.9 1.0 ND1 B:HIS597 1.7 114.9 1.0 NE2 B:HIS597 2.3 127.2 1.0 NE2 B:HIS561 2.3 114.5 1.0 OD2 B:ASP598 2.6 116.0 1.0 CG B:HIS597 2.9 106.6 1.0 CD2 B:HIS561 3.0 109.6 1.0 CG B:ASP598 3.0 118.1 1.0 CD2 B:HIS597 3.2 121.3 1.0 CE1 B:HIS561 3.2 110.6 1.0 OD1 B:ASP718 3.3 133.8 1.0 CB B:ASP598 3.4 107.7 1.0 CG2 B:VAL565 3.7 114.5 1.0 OD1 B:ASP598 3.9 116.8 1.0 CG B:HIS561 4.1 104.1 1.0 ND1 B:HIS561 4.1 107.8 1.0 CB B:HIS597 4.2 96.9 1.0 CG B:ASP718 4.3 133.5 1.0 N B:ASP598 4.4 107.4 1.0 CD2 B:HIS557 4.4 121.2 1.0 CA B:ASP598 4.5 103.6 1.0 C B:HIS597 4.6 106.0 1.0 MG B:MG903 4.6 155.2 1.0 O B:HIS561 4.7 119.9 1.0 CB B:VAL565 4.8 103.2 1.0 OD2 B:ASP718 4.9 135.4 1.0 NE2 B:HIS557 4.9 120.2 1.0 CG1 B:VAL565 5.0 105.3 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