Calcium in PDB 7oo5: Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades

All present enzymatic activity of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades:
1.11.1.14;

The structure of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades, PDB code: 7oo5 was solved by A.Romero, F.J.Ruiz-Duenas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.56 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.126, 74.95, 82.768, 90, 90, 90
R / Rfree (%)	23.2 / 26.9

The structure of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades (pdb code 7oo5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades, PDB code: 7oo5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:33.6 occ:1.00 O A:HOH527 2.3 31.5 1.0 O A:GLY62 2.3 29.6 1.0 OD1 A:ASP49 2.3 30.4 1.0 OD1 A:ASP64 2.5 36.6 1.0 OG A:SER66 2.6 37.0 1.0 O A:ASP49 2.6 32.9 1.0 O A:HOH509 2.7 32.8 1.0 CG A:ASP49 3.3 32.3 1.0 CB A:SER66 3.4 37.0 1.0 C A:ASP49 3.5 32.1 1.0 C A:GLY62 3.5 34.3 1.0 CG A:ASP64 3.6 37.9 1.0 CA A:ASP49 3.8 29.6 1.0 N A:SER66 3.9 34.2 1.0 OD2 A:ASP49 4.0 31.9 1.0 OD2 A:ASP64 4.1 33.7 1.0 N A:GLY62 4.1 38.0 1.0 CA A:SER66 4.2 34.8 1.0 O A:HOH537 4.2 37.3 1.0 CB A:ASP49 4.2 31.4 1.0 N A:ILE67 4.2 35.2 1.0 N A:ASP64 4.3 34.6 1.0 CA A:GLY62 4.3 35.9 1.0 O A:GLY52 4.3 37.3 1.0 N A:GLY65 4.5 34.7 1.0 N A:ALA50 4.6 31.8 1.0 N A:ALA63 4.6 34.3 1.0 C A:SER66 4.6 38.9 1.0 OE1 A:GLU74 4.7 42.9 1.0 CA A:GLY52 4.8 40.9 1.0 CB A:ASP64 4.8 33.5 1.0 C A:GLY65 4.9 28.6 1.0 OE2 A:GLU74 4.9 35.9 1.0 CA A:ASP64 4.9 36.9 1.0 CA A:ALA63 4.9 31.1 1.0 N A:GLY52 4.9 38.2 1.0 CA A:ALA50 4.9 32.9 1.0 O A:HOH522 5.0 37.4 1.0 CB A:ALA135 5.0 42.7 1.0 C A:GLY61 5.0 38.9 1.0 C A:ASP64 5.0 36.7 1.0 C A:GLY52 5.0 39.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:33.9 occ:1.00 OD2 A:ASP189 2.3 31.4 1.0 O A:LEU194 2.4 32.5 1.0 O A:THR191 2.5 37.9 1.0 OD1 A:ASP196 2.5 37.0 1.0 O A:SER172 2.5 36.0 1.0 OG A:SER172 2.6 34.5 1.0 OG1 A:THR191 2.6 37.2 1.0 OD1 A:ASP189 2.9 37.4 1.0 CG A:ASP189 3.0 35.1 1.0 C A:THR191 3.3 39.0 1.0 C A:SER172 3.4 37.0 1.0 CG A:ASP196 3.5 43.2 1.0 C A:LEU194 3.6 37.6 1.0 CB A:SER172 3.7 36.4 1.0 CA A:SER172 3.8 33.3 1.0 CB A:THR191 3.8 38.3 1.0 OD2 A:ASP196 3.9 39.8 1.0 CA A:THR191 4.0 38.1 1.0 N A:ASP196 4.0 41.2 1.0 N A:PRO192 4.2 39.5 1.0 N A:THR191 4.3 41.2 1.0 CA A:LEU194 4.4 43.0 1.0 CA A:PRO192 4.4 37.9 1.0 N A:LEU194 4.5 35.7 1.0 CB A:LEU194 4.5 39.5 1.0 CB A:GLN198 4.5 38.0 1.0 O A:ASP196 4.5 36.8 1.0 CB A:ASP189 4.5 31.1 1.0 N A:PHE195 4.6 40.3 1.0 N A:ILE173 4.6 33.4 1.0 CB A:ASP196 4.7 37.0 1.0 CA A:PHE195 4.7 36.5 1.0 CA A:ASP196 4.7 41.5 1.0 O A:HOH552 4.8 35.4 1.0 C A:ASP196 4.8 40.5 1.0 CG2 A:ILE173 4.9 35.3 1.0 C A:PRO192 4.9 38.1 1.0 C A:PHE195 4.9 40.6 1.0 CG2 A:THR191 5.0 40.3 1.0

M.I.Sanchez-Ruiz, I.Ayuso-Fernandez, J.Rencoret, A.M.Gonzalez-Ramirez, D.Linde, I.Davo-Siguero, A.Romero, A.Gutierrez, A.T.Martinez, F.J.Ruiz-Duenas. Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities. Antioxidants V. 10 2021.
ISSN: ESSN 2076-3921
PubMed: 34573078
DOI: 10.3390/ANTIOX10091446