Zinc in PDB 8cqm: Broad-Range Phospholipase C From Listeria Monocytogenes

All present enzymatic activity of Broad-Range Phospholipase C From Listeria Monocytogenes:
3.1.4.3;

The structure of Broad-Range Phospholipase C From Listeria Monocytogenes, PDB code: 8cqm was solved by N.Petrisic, M.Podobnik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.46 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.909, 82.922, 140.815, 90, 90, 90
R / Rfree (%)	17.4 / 20.9

The structure of Broad-Range Phospholipase C From Listeria Monocytogenes also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Broad-Range Phospholipase C From Listeria Monocytogenes (pdb code 8cqm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Broad-Range Phospholipase C From Listeria Monocytogenes, PDB code: 8cqm:

Zinc binding site 1 out of 1 in the Broad-Range Phospholipase C From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Broad-Range Phospholipase C From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:39.6 occ:0.43 OD2 A:ASP122 1.8 34.4 1.0 NE2 A:HIS118 2.2 31.9 1.0 ND1 A:HIS69 2.3 36.0 1.0 O1 A:GOL301 2.6 38.6 1.0 CG A:HIS69 2.8 35.3 1.0 CE1 A:HIS69 2.8 37.0 1.0 CG A:ASP122 2.9 26.8 1.0 C1 A:GOL301 3.0 39.9 1.0 CE1 A:HIS118 3.1 36.3 1.0 CD2 A:HIS118 3.3 27.4 1.0 CB A:HIS69 3.3 28.6 1.0 OD1 A:ASP122 3.5 23.7 1.0 C2 A:GOL301 3.5 40.0 1.0 NE2 A:HIS69 3.6 41.2 1.0 CD2 A:HIS69 3.6 39.4 1.0 CB A:ASP122 4.1 20.3 1.0 FE A:FE304 4.2 32.3 0.9 ND1 A:HIS118 4.2 34.0 1.0 O2 A:GOL301 4.2 26.8 1.0 CA A:HIS69 4.3 29.9 1.0 CG A:HIS118 4.3 28.8 1.0 CE1 A:HIS128 4.6 22.4 1.0 O A:ALA54 4.7 53.9 1.0 NE2 A:HIS14 4.8 28.6 1.0 C3 A:GOL301 4.8 40.7 1.0 O A:HIS69 5.0 23.5 1.0 ND1 A:HIS128 5.0 21.6 1.0

N.Petrisic, M.Podobnik. Structural Basis For the Unique Molecular Properties of Broad-Range Phospholipase C From Listeria Monocytogenes Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-42134-4