Zinc in PDB 8ugs: Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp

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

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


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 Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:93.1 occ:1.00 OD2 A:ASP600 2.1 51.3 1.0 NE2 A:HIS599 2.3 56.9 1.0 NE2 A:HIS563 2.3 57.5 1.0 OD1 A:ASP720 2.3 86.9 1.0 O2A A:PCG904 2.4 84.7 1.0 OD2 A:ASP720 2.8 86.7 1.0 CG A:ASP720 2.8 81.0 1.0 CE1 A:HIS563 3.0 55.1 1.0 CD2 A:HIS599 3.0 52.9 1.0 CG A:ASP600 3.2 57.9 1.0 CE1 A:HIS599 3.5 52.0 1.0 CD2 A:HIS563 3.5 57.0 1.0 PA A:PCG904 3.5 92.2 1.0 O1A A:PCG904 3.9 85.0 1.0 OD1 A:ASP600 3.9 58.6 1.0 O5' A:PCG904 4.0 86.3 1.0 ND1 A:HIS563 4.2 46.9 1.0 CB A:ASP720 4.2 70.9 1.0 CG A:HIS599 4.2 47.1 1.0 MG A:MG903 4.2 33.9 1.0 CB A:ASP600 4.3 54.0 1.0 ND1 A:HIS599 4.4 45.8 1.0 CG A:HIS563 4.5 50.9 1.0 CG2 A:VAL567 4.5 56.6 1.0 CD2 A:HIS559 4.6 68.3 1.0 CA A:ASP720 4.7 71.5 1.0 C5' A:PCG904 4.7 84.8 1.0 NE2 A:HIS559 4.8 65.0 1.0 O A:ASP720 4.9 77.8 1.0 CG2 A:THR669 4.9 63.3 1.0 O3' A:PCG904 4.9 89.6 1.0

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


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 Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:141.3 occ:1.00 NE2 B:HIS597 1.4 74.2 1.0 CD2 B:HIS597 1.6 64.3 1.0 CE1 B:HIS597 1.9 78.9 1.0 CG B:HIS597 2.2 64.2 1.0 OD2 B:ASP598 2.3 67.3 1.0 NE2 B:HIS561 2.3 64.7 1.0 ND1 B:HIS597 2.3 78.9 1.0 CG B:ASP598 2.4 64.9 1.0 OD1 B:ASP598 3.0 63.0 1.0 CB B:ASP598 3.0 51.1 1.0 CE1 B:HIS561 3.1 52.4 1.0 CD2 B:HIS561 3.3 69.3 1.0 C B:HIS597 3.5 60.7 1.0 CB B:HIS597 3.5 49.7 1.0 N B:ASP598 3.5 61.5 1.0 O B:HIS597 3.6 65.8 1.0 CA B:ASP598 3.8 51.6 1.0 OD1 B:ASP718 3.9 74.2 1.0 O2A B:PCG904 4.0 83.0 1.0 CA B:HIS597 4.1 46.4 1.0 MG B:MG903 4.1 20.4 1.0 ND1 B:HIS561 4.3 39.6 1.0 CG B:HIS561 4.4 58.1 1.0 O1A B:PCG904 4.4 80.8 1.0 CG B:ASP718 4.6 74.7 1.0 CG2 B:VAL565 4.7 59.8 1.0 PA B:PCG904 4.7 88.7 1.0 OD2 B:ASP718 4.8 77.0 1.0 O5' B:PCG904 5.0 71.2 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