Calcium in PDB 8qwx: Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms

All present enzymatic activity of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms:
1.11.1.13;

The structure of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms, PDB code: 8qwx was solved by E.Santillana, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.78 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.623, 39.63, 63.493, 90, 101.23, 90
R / Rfree (%)	15.1 / 18.6

The structure of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms (pdb code 8qwx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms, PDB code: 8qwx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:10.7 occ:1.00 OD1 A:ASP47 2.3 10.6 1.0 OD1 A:ASP61 2.4 11.2 1.0 O A:HOH552 2.4 11.4 1.0 O A:ASP47 2.4 10.8 1.0 OG A:SER63 2.4 11.1 1.0 O A:GLY59 2.4 10.7 1.0 O A:HOH559 2.5 11.5 1.0 C A:ASP47 3.3 10.8 1.0 CG A:ASP47 3.4 10.8 1.0 CG A:ASP61 3.5 13.2 1.0 C A:GLY59 3.6 11.6 1.0 CB A:SER63 3.6 11.7 1.0 CA A:ASP47 3.7 10.1 1.0 N A:SER63 3.9 11.2 1.0 OD2 A:ASP61 4.1 13.8 1.0 CB A:ASP47 4.2 10.7 1.0 N A:ASP61 4.2 11.7 1.0 O A:HOH582 4.2 12.1 1.0 OD2 A:ASP47 4.2 12.2 1.0 N A:GLY59 4.2 12.4 1.0 CA A:SER63 4.3 12.3 1.0 CA A:GLY59 4.3 12.6 1.0 N A:ILE64 4.3 12.3 1.0 N A:ALA48 4.5 11.3 1.0 N A:GLY62 4.6 10.6 1.0 CB A:ALA50 4.6 11.9 1.0 OE2 A:GLU71 4.6 12.6 1.0 CB A:ASP61 4.7 13.7 1.0 O A:ALA50 4.7 12.4 1.0 N A:ALA60 4.7 11.4 1.0 O A:HIS46 4.7 11.6 1.0 C A:SER63 4.8 11.9 1.0 OE1 A:GLU71 4.8 14.0 1.0 CA A:ASP61 4.8 12.0 1.0 CA A:ALA60 4.9 12.0 1.0 CA A:ALA48 4.9 11.0 1.0 C A:GLY62 4.9 12.1 1.0 C A:ASP61 5.0 11.8 1.0 C A:GLY58 5.0 12.5 1.0

Calcium binding site 2 out of 2 in the Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:11.8 occ:1.00 O A:SER172 2.4 10.2 1.0 O A:THR191 2.4 11.7 1.0 OD1 A:ASP196 2.5 13.8 1.0 OD2 A:ASP189 2.5 12.1 1.0 OG A:SER172 2.5 11.3 1.0 O A:ILE194 2.5 11.5 1.0 OG1 A:THR191 2.5 14.1 1.0 OD1 A:ASP189 2.7 11.3 1.0 CG A:ASP189 2.9 11.3 1.0 C A:THR191 3.3 12.2 1.0 C A:SER172 3.3 10.6 1.0 CG A:ASP196 3.4 16.2 1.0 CB A:THR191 3.6 14.9 1.0 CB A:SER172 3.6 10.7 1.0 CA A:SER172 3.7 9.6 1.0 C A:ILE194 3.7 12.5 1.0 CA A:THR191 3.9 13.5 1.0 OD2 A:ASP196 3.9 14.6 1.0 N A:ASP196 4.1 13.3 1.0 N A:THR191 4.2 13.6 1.0 N A:PRO192 4.2 12.7 1.0 N A:ILE194 4.4 12.8 1.0 CB A:ASP189 4.4 11.3 1.0 CA A:ILE194 4.5 11.8 1.0 CA A:PRO192 4.5 12.5 1.0 O A:ASP196 4.5 13.9 1.0 N A:VAL173 4.6 10.8 1.0 CB A:ILE194 4.6 13.7 1.0 CB A:ASP196 4.6 14.4 1.0 O A:HOH637 4.6 14.2 1.0 N A:PHE195 4.7 11.5 1.0 CA A:ASP196 4.7 13.4 1.0 C A:ASP196 4.8 14.4 1.0 CB A:GLN198 4.8 13.9 1.0 CA A:PHE195 4.8 12.1 1.0 CG1 A:VAL173 4.8 12.0 1.0 CG2 A:THR191 4.9 15.6 1.0 C A:PRO192 4.9 13.2 1.0 C A:PHE195 5.0 14.0 1.0

M.I.Sanchez-Ruiz, E.Santillana, D.Linde, A.Romero, A.T.Martinez, F.J.Ruiz-Duenas. Structure-Function Characterization of Two Enzymes From Novel Subfamilies of Manganese Peroxidases Secreted By the Lignocellulose-Degrading Agaricales Fungi Agrocybe Pediades and Cyathus Striatus. Biotechnol Biofuels Bioprod V. 17 74 2024.
ISSN: ISSN 2731-3654
PubMed: 38824538
DOI: 10.1186/S13068-024-02517-1