Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Ibmx, PDB code: 8ulg:
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 Ibmx


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 Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:111.6 occ:1.00 OD2 A:ASP600 2.3 82.0 1.0 NE2 A:HIS599 2.3 73.2 1.0 NE2 A:HIS563 2.3 63.0 1.0 CD2 A:HIS599 2.8 65.0 1.0 OD1 A:ASP720 3.1 77.7 1.0 CD2 A:HIS563 3.2 61.0 1.0 CE1 A:HIS563 3.3 67.6 1.0 OD2 A:ASP720 3.5 78.1 1.0 CG A:ASP600 3.5 77.9 1.0 CE1 A:HIS599 3.5 68.9 1.0 CG A:ASP720 3.6 75.0 1.0 CG A:HIS599 4.1 52.6 1.0 MG A:MG902 4.2 62.5 1.0 OD1 A:ASP600 4.3 89.0 1.0 CB A:ASP600 4.3 63.0 1.0 CG A:HIS563 4.4 57.3 1.0 ND1 A:HIS599 4.4 57.6 1.0 ND1 A:HIS563 4.4 63.3 1.0 CD2 A:HIS559 4.5 74.2 1.0 NE2 A:HIS559 4.7 70.0 1.0 CG2 A:VAL567 4.8 56.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn903 b:110.1 occ:1.00 OD2 B:ASP598 2.1 63.0 1.0 NE2 B:HIS597 2.3 70.4 1.0 NE2 B:HIS561 2.3 65.6 1.0 OD1 B:ASP718 2.7 81.4 1.0 CD2 B:HIS597 2.9 65.6 1.0 CG B:ASP598 3.2 69.3 1.0 CE1 B:HIS561 3.2 63.7 1.0 CD2 B:HIS561 3.3 64.5 1.0 CE1 B:HIS597 3.5 64.0 1.0 OD1 B:ASP598 3.7 80.5 1.0 CG B:ASP718 3.8 83.7 1.0 MG B:MG902 4.1 44.5 1.0 CG B:HIS597 4.1 54.2 1.0 OD2 B:ASP718 4.3 86.6 1.0 CB B:ASP598 4.4 58.3 1.0 ND1 B:HIS561 4.4 55.2 1.0 ND1 B:HIS597 4.4 52.2 1.0 CG B:HIS561 4.4 52.1 1.0 CD2 B:HIS557 4.5 73.1 1.0 CG2 B:VAL565 4.8 59.9 1.0 CB B:ASP718 4.9 79.2 1.0 NE2 B:HIS557 4.9 68.5 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