Zinc in PDB 9cxi: Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp

All present enzymatic activity of Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp:
3.1.4.35;

The structure of Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp (pdb code 9cxi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp, PDB code: 9cxi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:108.2 occ:1.00 OD2 A:ASP723 2.0 77.7 1.0 NE2 A:HIS602 2.0 55.9 1.0 OD1 A:ASP723 2.0 80.9 1.0 OD1 A:ASP603 2.1 76.5 1.0 NE2 A:HIS566 2.1 52.4 1.0 OD2 A:ASP603 2.3 69.8 1.0 CG A:ASP723 2.3 71.9 1.0 CG A:ASP603 2.3 67.8 1.0 CD2 A:HIS602 2.6 56.7 1.0 MG A:MG902 2.9 55.0 1.0 CE1 A:HIS566 3.0 48.2 1.0 CE1 A:HIS602 3.1 52.3 1.0 CD2 A:HIS566 3.2 55.8 1.0 CB A:ASP603 3.7 49.3 1.0 CG A:HIS602 3.7 47.3 1.0 CB A:ASP723 3.8 53.5 1.0 ND1 A:HIS602 4.0 56.5 1.0 ND1 A:HIS566 4.1 45.0 1.0 CG A:HIS566 4.2 48.4 1.0 CG2 A:VAL570 4.5 44.1 1.0 CG2 A:THR672 4.5 66.8 1.0 CA A:ASP723 4.6 57.6 1.0 CA A:ASP603 4.7 43.5 1.0 CD2 A:HIS562 4.7 57.9 1.0 N A:ASP603 4.7 53.3 1.0 NE2 A:HIS562 4.9 48.9 1.0

Zinc binding site 2 out of 2 in the Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of PDE6C in Complex with the Rod Inhibitory P Gamma Subunit in the Absence of Added Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:116.4 occ:1.00 OD2 B:ASP603 2.0 50.5 1.0 OD1 B:ASP723 2.0 77.9 1.0 NE2 B:HIS566 2.0 48.7 1.0 NE2 B:HIS602 2.0 60.2 1.0 CE1 B:HIS566 2.8 43.5 1.0 CD2 B:HIS602 3.0 52.9 1.0 CE1 B:HIS602 3.0 49.9 1.0 CD2 B:HIS566 3.1 45.3 1.0 CG B:ASP723 3.2 75.4 1.0 CG B:ASP603 3.2 51.9 1.0 OD2 B:ASP723 3.8 84.8 1.0 ND1 B:HIS566 3.9 41.6 1.0 OD1 B:ASP603 3.9 60.4 1.0 CG B:HIS566 4.0 41.6 1.0 CG2 B:VAL570 4.1 47.2 1.0 ND1 B:HIS602 4.1 45.6 1.0 CG B:HIS602 4.1 41.7 1.0 MG B:MG902 4.3 30.7 1.0 CB B:ASP603 4.3 37.8 1.0 CB B:ASP723 4.3 62.4 1.0 O B:ASP723 4.4 72.8 1.0 CA B:ASP723 4.6 51.4 1.0 CD2 B:HIS562 4.6 57.3 1.0 NE2 B:HIS562 4.8 52.2 1.0 C B:ASP723 5.0 61.3 1.0

S.Singh, D.Srivastava, K.Boyd, N.Artemyev. Structural and Functional Dynamics of Human Cone Cgmp-Phosphodiesterase Important For Photopic Vision Proc.Natl.Acad.Sci.Usa 2025.
ISSN: ESSN 1091-6490