Calcium in PDB 6a6q: Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH

All present enzymatic activity of Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH:
1.11.1.14;

The structure of Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH, PDB code: 6a6q was solved by H.Seo, K.-J.Kim, L.T.M.Pham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.72 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.212, 99.621, 48.322, 90.00, 113.86, 90.00
R / Rfree (%)	14.2 / 17.1

The structure of Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH (pdb code 6a6q). 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 Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH, PDB code: 6a6q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:13.7 occ:1.00 OD1 A:ASP48 2.3 15.2 1.0 O A:GLY66 2.4 13.3 1.0 OD1 A:ASP68 2.4 14.7 1.0 O A:HOH595 2.4 15.9 1.0 O A:ASP48 2.4 14.6 1.0 OG A:SER70 2.5 15.8 1.0 O A:HOH526 2.5 15.3 1.0 CG A:ASP48 3.4 15.4 1.0 C A:ASP48 3.4 13.8 1.0 CG A:ASP68 3.5 16.0 1.0 C A:GLY66 3.6 13.2 1.0 CB A:SER70 3.6 15.9 1.0 CA A:ASP48 3.7 13.2 1.0 N A:SER70 3.9 15.2 1.0 OD2 A:ASP68 4.0 16.9 1.0 CB A:ASP48 4.2 13.2 1.0 N A:ASP68 4.2 15.2 1.0 OD2 A:ASP48 4.2 15.1 1.0 N A:GLY66 4.2 15.9 1.0 CA A:SER70 4.3 16.0 1.0 O A:HOH614 4.3 16.4 1.0 CA A:GLY66 4.3 15.1 1.0 N A:ILE71 4.4 14.6 1.0 N A:SER49 4.5 13.7 1.0 N A:GLY69 4.6 15.0 1.0 O A:ALA51 4.6 15.1 1.0 N A:ALA67 4.6 13.7 1.0 OE2 A:GLU78 4.6 17.2 1.0 CB A:ASP68 4.6 16.3 1.0 CB A:ALA51 4.7 16.5 1.0 OE1 A:GLU78 4.7 18.0 1.0 CA A:ALA67 4.8 16.4 1.0 C A:SER70 4.8 15.9 1.0 CA A:ASP68 4.8 15.9 1.0 O A:HIS47 4.9 15.2 1.0 C A:GLY65 4.9 16.2 1.0 C A:ASP68 5.0 16.4 1.0 C A:GLY69 5.0 14.8 1.0 CA A:SER49 5.0 14.0 1.0

Calcium binding site 2 out of 2 in the Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Strcuture of A Lignin Peroxidase Isozyme H8 Variant That Is Stable at Very Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:12.7 occ:1.00 O A:SER177 2.4 13.6 1.0 O A:THR196 2.4 14.9 1.0 OD2 A:ASP194 2.4 13.2 1.0 O A:ILE199 2.4 13.9 1.0 OD1 A:ASP201 2.4 14.2 1.0 OG1 A:THR196 2.5 14.1 1.0 OG A:SER177 2.5 13.6 1.0 OD1 A:ASP194 2.7 14.2 1.0 CG A:ASP194 2.9 14.8 1.0 C A:THR196 3.2 14.7 1.0 C A:SER177 3.4 12.8 1.0 CG A:ASP201 3.4 15.6 1.0 CB A:THR196 3.5 16.0 1.0 CB A:SER177 3.6 13.5 1.0 C A:ILE199 3.7 13.4 1.0 CA A:SER177 3.7 12.7 1.0 OD2 A:ASP201 3.8 18.1 1.0 CA A:THR196 3.8 14.2 1.0 N A:ASP201 4.1 15.3 1.0 N A:PRO197 4.2 14.7 1.0 N A:THR196 4.2 16.5 1.0 N A:ILE199 4.4 14.0 1.0 CB A:ASP194 4.4 13.6 1.0 CA A:ILE199 4.4 13.2 1.0 CA A:PRO197 4.5 15.0 1.0 O A:HOH660 4.6 15.6 1.0 O A:ASP201 4.6 15.5 1.0 CB A:ILE199 4.6 13.7 1.0 N A:VAL178 4.6 11.2 1.0 CB A:GLN203 4.6 15.9 1.0 CB A:ASP201 4.7 14.9 1.0 N A:PHE200 4.7 13.5 1.0 CA A:ASP201 4.8 15.2 1.0 CA A:PHE200 4.8 13.5 1.0 C A:ASP201 4.8 15.1 1.0 CG1 A:VAL178 4.9 15.6 1.0 CG2 A:THR196 4.9 14.7 1.0 C A:PRO197 4.9 14.2 1.0 C A:PHE200 5.0 13.5 1.0

L.T.M.Pham, H.Seo, K.J.Kim, Y.H.Kim. In Silico-Designed Lignin Peroxidase Fromphanerochaete Chrysosporiumshows Enhanced Acid Stability For Depolymerization of Lignin. Biotechnol Biofuels V. 11 325 2018.
ISSN: ESSN 1754-6834
PubMed: 30555531
DOI: 10.1186/S13068-018-1324-4