Iron 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:

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the Broad-Range Phospholipase C From Listeria Monocytogenes (pdb code 8cqm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Broad-Range Phospholipase C From Listeria Monocytogenes, PDB code: 8cqm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Broad-Range Phospholipase C From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Broad-Range Phospholipase C From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:27.0 occ:1.00 O3 A:GOL301 2.0 30.9 1.0 NE2 A:HIS128 2.1 23.4 1.0 OE2 A:GLU146 2.1 24.8 1.0 NE2 A:HIS142 2.2 25.1 1.0 O2 A:GOL301 2.4 26.8 1.0 OE1 A:GLU146 2.5 24.6 1.0 CD A:GLU146 2.6 26.1 1.0 CE1 A:HIS128 2.9 22.4 1.0 C3 A:GOL301 3.1 40.7 1.0 CE1 A:HIS142 3.2 24.1 1.0 C2 A:GOL301 3.2 40.0 1.0 CD2 A:HIS128 3.2 20.8 1.0 CD2 A:HIS142 3.2 22.3 1.0 CG A:GLU146 4.0 22.7 1.0 N A:TRP1 4.1 26.6 1.0 ND1 A:HIS128 4.1 21.6 1.0 FE A:FE304 4.1 32.3 0.9 CG A:HIS128 4.3 24.6 1.0 ND1 A:HIS142 4.3 26.6 1.0 CG A:HIS142 4.4 25.3 1.0 NE2 A:GLN125 4.4 21.6 1.0 C1 A:GOL301 4.6 39.9 1.0 O A:TRP1 4.6 40.9 1.0 CA A:TRP1 4.9 28.4 1.0 O1 A:GOL301 4.9 38.6 1.0 OD1 A:ASP122 5.0 23.7 1.0 CB A:GLU146 5.0 22.3 1.0

Iron binding site 2 out of 4 in the Broad-Range Phospholipase C From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Broad-Range Phospholipase C From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe304 b:32.3 occ:0.88 OD1 A:ASP122 2.2 23.7 1.0 NE2 A:HIS14 2.2 28.6 1.0 N A:TRP1 2.3 26.6 1.0 O2 A:GOL301 2.4 26.8 1.0 O A:TRP1 2.5 40.9 1.0 O1 A:GOL301 2.7 38.6 1.0 CE1 A:HIS14 3.0 27.6 1.0 CA A:TRP1 3.2 28.4 1.0 C A:TRP1 3.2 31.6 1.0 CG A:ASP122 3.3 26.8 1.0 CD2 A:HIS14 3.4 26.6 1.0 C2 A:GOL301 3.4 40.0 1.0 C1 A:GOL301 3.6 39.9 1.0 OD2 A:ASP122 3.7 34.4 1.0 CB A:TRP1 3.9 29.5 1.0 FE A:FE303 4.1 27.0 1.0 OE2 A:GLU146 4.2 24.8 1.0 ZN A:ZN302 4.2 39.6 0.4 CE1 A:HIS128 4.2 22.4 1.0 ND1 A:HIS14 4.2 25.7 1.0 NE2 A:HIS128 4.2 23.4 1.0 CG A:HIS14 4.4 26.0 1.0 CE1 A:HIS118 4.4 36.3 1.0 CB A:ASP122 4.5 20.3 1.0 CA A:ASP122 4.6 17.5 1.0 CD A:GLU146 4.7 26.1 1.0 C3 A:GOL301 4.7 40.7 1.0 OE1 A:GLU146 4.7 24.6 1.0 NE2 A:HIS118 4.8 31.9 1.0 CG A:TRP1 4.8 31.9 1.0 O3 A:GOL301 4.8 30.9 1.0 ND1 A:HIS128 5.0 21.6 1.0

Iron binding site 3 out of 4 in the Broad-Range Phospholipase C From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Broad-Range Phospholipase C From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:26.6 occ:1.00 OE2 B:GLU146 2.1 24.7 1.0 O3 B:GOL301 2.1 25.1 1.0 NE2 B:HIS142 2.2 29.0 1.0 NE2 B:HIS128 2.2 24.8 1.0 OE1 B:GLU146 2.3 25.5 1.0 O2 B:GOL301 2.4 22.6 1.0 CD B:GLU146 2.5 23.7 1.0 CE1 B:HIS142 3.1 28.8 1.0 CE1 B:HIS128 3.1 25.2 1.0 C3 B:GOL301 3.2 31.3 1.0 CD2 B:HIS128 3.3 22.4 1.0 CD2 B:HIS142 3.3 24.5 1.0 C2 B:GOL301 3.3 35.8 1.0 CG B:GLU146 3.9 21.6 1.0 N B:TRP1 4.0 23.3 1.0 FE B:FE303 4.2 29.7 1.0 ND1 B:HIS142 4.3 26.6 1.0 NE2 B:GLN125 4.3 21.2 1.0 ND1 B:HIS128 4.3 24.6 1.0 CG B:HIS142 4.4 28.1 1.0 CG B:HIS128 4.4 21.7 1.0 C1 B:GOL301 4.7 34.6 1.0 O B:TRP1 4.7 27.5 1.0 OD1 B:ASP122 4.8 23.8 1.0 CA B:TRP1 4.9 22.4 1.0 CB B:GLU146 4.9 22.0 1.0 C B:TRP1 4.9 26.4 1.0 O1 B:GOL301 5.0 30.1 1.0

Iron binding site 4 out of 4 in the Broad-Range Phospholipase C From Listeria Monocytogenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Broad-Range Phospholipase C From Listeria Monocytogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:29.7 occ:0.96 O1 B:GOL301 2.2 30.1 1.0 OD1 B:ASP122 2.2 23.8 1.0 NE2 B:HIS14 2.3 21.8 1.0 O2 B:GOL301 2.3 22.6 1.0 O B:TRP1 2.4 27.5 1.0 N B:TRP1 2.4 23.3 1.0 C2 B:GOL301 3.1 35.8 1.0 C B:TRP1 3.2 26.4 1.0 C1 B:GOL301 3.2 34.6 1.0 CG B:ASP122 3.2 27.6 1.0 CA B:TRP1 3.2 22.4 1.0 CE1 B:HIS14 3.2 25.5 1.0 CD2 B:HIS14 3.3 23.5 1.0 OD2 B:ASP122 3.6 30.6 1.0 CB B:TRP1 3.9 24.2 1.0 FE B:FE302 4.2 26.6 1.0 OE2 B:GLU146 4.2 24.7 1.0 CE1 B:HIS118 4.2 32.9 1.0 NE2 B:HIS128 4.3 24.8 1.0 CE1 B:HIS128 4.4 25.2 1.0 ND1 B:HIS14 4.4 22.5 1.0 CG B:HIS14 4.5 23.9 1.0 C3 B:GOL301 4.5 31.3 1.0 CB B:ASP122 4.5 21.2 1.0 OE1 B:GLU146 4.6 25.5 1.0 CA B:ASP122 4.6 19.4 1.0 CD B:GLU146 4.6 23.7 1.0 O3 B:GOL301 4.7 25.1 1.0 CG B:TRP1 4.8 24.3 1.0 NE2 B:HIS118 4.8 32.0 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