Calcium in PDB 1b82: Pristine Recomb. Lignin Peroxidase H8

All present enzymatic activity of Pristine Recomb. Lignin Peroxidase H8:
1.11.1.14;

The structure of Pristine Recomb. Lignin Peroxidase H8, PDB code: 1b82 was solved by W.Blodig, W.A.Doyle, A.T.Smith, K.Piontek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.260, 94.420, 228.050, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.4

The structure of Pristine Recomb. Lignin Peroxidase H8 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Pristine Recomb. Lignin Peroxidase H8 (pdb code 1b82). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Pristine Recomb. Lignin Peroxidase H8, PDB code: 1b82:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Pristine Recomb. Lignin Peroxidase H8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pristine Recomb. Lignin Peroxidase H8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1351 b:25.9 occ:1.00 OD1 A:ASP48 2.5 23.8 1.0 O A:HOH558 2.6 27.1 1.0 O A:ASP48 2.6 20.8 1.0 OD1 A:ASP68 2.6 24.9 1.0 O A:HOH455 2.6 24.2 1.0 O A:GLY66 2.6 23.9 1.0 OG A:SER70 2.6 26.2 1.0 C A:ASP48 3.5 23.9 1.0 CG A:ASP68 3.5 28.2 1.0 CG A:ASP48 3.6 25.2 1.0 CB A:SER70 3.6 26.6 1.0 C A:GLY66 3.8 23.1 1.0 CA A:ASP48 3.9 22.3 1.0 N A:SER70 3.9 23.3 1.0 OD2 A:ASP68 3.9 29.1 1.0 N A:ASP68 4.1 25.9 1.0 O A:HOH555 4.3 27.0 1.0 CA A:SER70 4.3 26.1 1.0 N A:GLY66 4.3 26.9 1.0 CB A:ASP48 4.3 23.0 1.0 OD2 A:ASP48 4.4 24.1 1.0 N A:ILE71 4.4 25.6 1.0 CA A:GLY66 4.5 24.5 1.0 O A:ALA51 4.5 28.3 1.0 CB A:ALA51 4.5 24.0 1.0 OE2 A:GLU78 4.6 28.0 1.0 N A:GLY69 4.6 26.9 1.0 N A:SER49 4.6 19.1 1.0 CB A:ASP68 4.7 26.2 1.0 N A:ALA67 4.7 22.9 1.0 OE1 A:GLU78 4.7 27.8 1.0 CA A:ASP68 4.8 26.3 1.0 CA A:ALA67 4.9 21.6 1.0 C A:SER70 4.9 27.2 1.0 O A:HIS47 4.9 22.7 1.0 C A:GLY65 5.0 27.9 1.0 C A:GLY69 5.0 22.5 1.0 C A:ASP68 5.0 26.3 1.0 CA A:SER49 5.0 21.2 1.0

Calcium binding site 2 out of 4 in the Pristine Recomb. Lignin Peroxidase H8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pristine Recomb. Lignin Peroxidase H8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1352 b:13.4 occ:1.00 O A:THR196 2.5 14.2 1.0 O A:SER177 2.5 13.0 1.0 OD2 A:ASP194 2.5 12.8 1.0 OD1 A:ASP201 2.5 13.9 1.0 O A:ILE199 2.5 13.6 1.0 OG A:SER177 2.6 13.4 1.0 OG1 A:THR196 2.6 15.7 1.0 OD1 A:ASP194 2.7 13.2 1.0 CG A:ASP194 3.0 13.9 1.0 C A:THR196 3.4 14.5 1.0 CG A:ASP201 3.4 16.1 1.0 C A:SER177 3.5 13.6 1.0 CB A:THR196 3.6 16.3 1.0 CB A:SER177 3.7 14.2 1.0 CA A:SER177 3.7 11.6 1.0 C A:ILE199 3.7 18.1 1.0 OD2 A:ASP201 3.8 14.0 1.0 CA A:THR196 3.9 14.4 1.0 N A:ASP201 4.1 13.8 1.0 N A:THR196 4.3 12.9 1.0 N A:PRO197 4.3 13.0 1.0 N A:ILE199 4.4 17.5 1.0 CA A:ILE199 4.5 19.0 1.0 CB A:ASP194 4.5 13.2 1.0 O A:ASP201 4.5 14.8 1.0 CA A:PRO197 4.5 14.9 1.0 CB A:ILE199 4.6 20.1 1.0 O A:HOH372 4.6 16.3 1.0 CB A:GLN203 4.6 13.6 1.0 CB A:ASP201 4.6 12.8 1.0 N A:VAL178 4.6 12.2 1.0 N A:PHE200 4.7 14.1 1.0 CA A:ASP201 4.7 13.6 1.0 C A:ASP201 4.8 11.8 1.0 CA A:PHE200 4.8 15.2 1.0 CG1 A:VAL178 4.8 11.2 1.0 CG2 A:THR196 4.9 16.6 1.0 N A:GLN203 4.9 13.5 1.0 C A:PHE200 4.9 15.1 1.0 C A:PRO197 5.0 15.7 1.0

Calcium binding site 3 out of 4 in the Pristine Recomb. Lignin Peroxidase H8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pristine Recomb. Lignin Peroxidase H8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2351 b:16.8 occ:1.00 O B:HOH569 2.4 14.8 1.0 OD1 B:ASP48 2.5 15.2 1.0 O B:ASP48 2.5 13.3 1.0 OD1 B:ASP68 2.5 16.7 1.0 O B:GLY66 2.6 14.2 1.0 OG B:SER70 2.6 14.5 1.0 O B:HOH570 2.6 15.4 1.0 C B:ASP48 3.4 15.6 1.0 CG B:ASP48 3.5 15.5 1.0 CG B:ASP68 3.5 18.5 1.0 CB B:SER70 3.7 16.6 1.0 C B:GLY66 3.7 16.9 1.0 CA B:ASP48 3.8 14.7 1.0 OD2 B:ASP68 3.9 17.5 1.0 N B:SER70 3.9 15.4 1.0 N B:ASP68 4.1 17.0 1.0 O B:HOH429 4.2 18.4 1.0 CB B:ASP48 4.2 15.7 1.0 OD2 B:ASP48 4.3 15.8 1.0 N B:GLY66 4.3 17.6 1.0 CA B:SER70 4.3 16.6 1.0 CA B:GLY66 4.4 16.2 1.0 N B:ILE71 4.5 16.9 1.0 O B:ALA51 4.5 18.7 1.0 N B:SER49 4.6 14.8 1.0 N B:GLY69 4.6 17.0 1.0 OE2 B:GLU78 4.6 19.0 1.0 CB B:ALA51 4.6 19.1 1.0 N B:ALA67 4.7 15.1 1.0 CB B:ASP68 4.7 17.9 1.0 OE1 B:GLU78 4.7 19.3 1.0 CA B:ALA67 4.8 15.6 1.0 CA B:ASP68 4.8 17.6 1.0 C B:SER70 4.9 18.4 1.0 O B:HIS47 4.9 16.6 1.0 C B:ASP68 5.0 16.8 1.0 CA B:SER49 5.0 15.0 1.0 C B:GLY69 5.0 15.2 1.0 C B:GLY65 5.0 19.1 1.0 C B:ALA67 5.0 15.5 1.0

Calcium binding site 4 out of 4 in the Pristine Recomb. Lignin Peroxidase H8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pristine Recomb. Lignin Peroxidase H8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2352 b:14.5 occ:1.00 O B:THR196 2.4 14.0 1.0 O B:SER177 2.5 12.3 1.0 OD1 B:ASP201 2.5 15.2 1.0 OD2 B:ASP194 2.5 14.1 1.0 O B:ILE199 2.5 14.2 1.0 OG B:SER177 2.6 12.5 1.0 OG1 B:THR196 2.6 14.1 1.0 OD1 B:ASP194 2.8 12.9 1.0 CG B:ASP194 3.0 15.3 1.0 C B:THR196 3.3 15.8 1.0 CG B:ASP201 3.4 17.9 1.0 C B:SER177 3.4 11.3 1.0 CB B:THR196 3.6 14.8 1.0 CB B:SER177 3.7 14.3 1.0 CA B:SER177 3.7 11.5 1.0 C B:ILE199 3.7 13.9 1.0 OD2 B:ASP201 3.8 14.8 1.0 CA B:THR196 3.9 13.7 1.0 N B:ASP201 4.1 15.0 1.0 N B:PRO197 4.2 16.6 1.0 N B:THR196 4.3 12.8 1.0 N B:ILE199 4.4 15.4 1.0 CA B:PRO197 4.5 15.4 1.0 O B:ASP201 4.5 14.8 1.0 CA B:ILE199 4.5 14.0 1.0 CB B:ASP194 4.5 13.6 1.0 CB B:ILE199 4.6 16.6 1.0 N B:VAL178 4.6 12.4 1.0 O B:HOH462 4.6 15.7 1.0 CB B:ASP201 4.6 14.9 1.0 CB B:GLN203 4.6 14.7 1.0 N B:PHE200 4.7 12.6 1.0 CA B:ASP201 4.8 15.7 1.0 CA B:PHE200 4.8 12.5 1.0 C B:ASP201 4.8 15.1 1.0 CG1 B:VAL178 4.8 14.5 1.0 CG2 B:THR196 4.9 15.0 1.0 C B:PHE200 4.9 15.3 1.0 C B:PRO197 4.9 14.7 1.0 N B:GLN203 5.0 14.7 1.0

W.Blodig, A.T.Smith, W.A.Doyle, K.Piontek. Crystal Structures of Pristine and Oxidatively Processed Lignin Peroxidase Expressed in Escherichia Coli and of the W171F Variant That Eliminates the Redox Active Tryptophan 171. Implications For the Reaction Mechanism. J.Mol.Biol. V. 305 851 2001.
ISSN: ISSN 0022-2836
PubMed: 11162097
DOI: 10.1006/JMBI.2000.4346