Calcium in PDB 8qx0: Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion

All present enzymatic activity of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion:
1.11.1.13;

The structure of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion, PDB code: 8qx0 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)	62.28 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.63, 39.811, 63.56, 90, 101.5, 90
R / Rfree (%)	17.8 / 19.9

The structure of Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Iron	(Fe)	1 atom

The binding sites of Calcium atom in the Ligninolytic Manganese Peroxidase Ape-MNP1 From Agaricales Mushrooms in Complex with A Manganese Ion (pdb code 8qx0). 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 in Complex with A Manganese Ion, PDB code: 8qx0:
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 in Complex with A Manganese Ion


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 in Complex with A Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:7.1 occ:1.00 OD1 A:ASP47 2.3 7.5 1.0 O A:HOH549 2.4 8.8 1.0 O A:GLY59 2.4 7.0 1.0 OD1 A:ASP61 2.4 6.6 1.0 O A:HOH536 2.4 7.5 1.0 OG A:SER63 2.4 7.1 1.0 O A:ASP47 2.4 7.8 1.0 C A:ASP47 3.4 7.3 1.0 CG A:ASP47 3.4 7.0 1.0 CG A:ASP61 3.5 7.1 1.0 CB A:SER63 3.6 8.0 1.0 C A:GLY59 3.6 7.3 1.0 CA A:ASP47 3.7 6.4 1.0 N A:SER63 3.9 7.4 1.0 OD2 A:ASP61 4.0 8.2 1.0 CB A:ASP47 4.2 6.8 1.0 N A:GLY59 4.2 8.8 1.0 OD2 A:ASP47 4.2 8.3 1.0 N A:ASP61 4.2 7.7 1.0 O A:HOH559 4.2 9.0 1.0 CA A:SER63 4.2 8.0 1.0 CA A:GLY59 4.3 7.9 1.0 N A:ILE64 4.3 8.2 1.0 N A:ALA48 4.5 7.2 1.0 N A:GLY62 4.6 6.5 1.0 OE2 A:GLU71 4.6 8.8 1.0 CB A:ALA50 4.6 8.6 1.0 N A:ALA60 4.7 7.3 1.0 O A:ALA50 4.7 9.4 1.0 CB A:ASP61 4.7 7.9 1.0 C A:SER63 4.7 7.6 1.0 O A:HIS46 4.7 8.0 1.0 OE1 A:GLU71 4.8 8.9 1.0 CA A:ASP61 4.8 7.4 1.0 CA A:ALA48 4.9 7.5 1.0 CA A:ALA60 4.9 7.5 1.0 C A:GLY62 5.0 7.8 1.0 C A:GLY58 5.0 9.6 1.0 C A:ASP61 5.0 7.3 1.0

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


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 in Complex with A Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:9.1 occ:1.00 O A:SER172 2.4 9.3 1.0 OD1 A:ASP196 2.4 10.4 1.0 O A:THR191 2.4 9.0 1.0 O A:ILE194 2.5 9.6 1.0 OD2 A:ASP189 2.5 9.4 1.0 OG1 A:THR191 2.5 10.8 1.0 OG A:SER172 2.5 8.8 1.0 OD1 A:ASP189 2.7 9.3 1.0 CG A:ASP189 2.9 8.3 1.0 C A:THR191 3.3 8.6 1.0 C A:SER172 3.3 8.3 1.0 CG A:ASP196 3.4 11.1 1.0 CB A:THR191 3.5 11.3 1.0 CB A:SER172 3.6 8.9 1.0 CA A:SER172 3.6 8.5 1.0 C A:ILE194 3.7 7.8 1.0 OD2 A:ASP196 3.8 11.3 1.0 CA A:THR191 3.9 8.9 1.0 N A:ASP196 4.1 10.3 1.0 N A:THR191 4.1 9.2 1.0 N A:PRO192 4.2 8.8 1.0 CB A:ASP189 4.4 9.0 1.0 N A:ILE194 4.4 9.8 1.0 CA A:ILE194 4.5 10.2 1.0 CA A:PRO192 4.5 9.3 1.0 O A:ASP196 4.5 11.1 1.0 N A:VAL173 4.5 8.4 1.0 O A:HOH632 4.6 11.2 1.0 CB A:ILE194 4.6 11.1 1.0 CB A:ASP196 4.6 10.1 1.0 N A:PHE195 4.7 9.2 1.0 CA A:ASP196 4.7 9.9 1.0 C A:ASP196 4.8 10.0 1.0 CG1 A:VAL173 4.8 9.6 1.0 CB A:GLN198 4.8 9.8 1.0 CA A:PHE195 4.8 9.7 1.0 CG2 A:THR191 4.8 11.9 1.0 C A:PRO192 5.0 9.7 1.0 C A:PHE195 5.0 9.7 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