Calcium in PDB 1b85: Lignin Peroxidase

All present enzymatic activity of Lignin Peroxidase:
1.11.1.14;

The structure of Lignin Peroxidase, PDB code: 1b85 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)	12.00 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.400, 94.400, 230.990, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 18.1

The structure of Lignin Peroxidase also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Lignin Peroxidase (pdb code 1b85). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Lignin Peroxidase, PDB code: 1b85:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lignin Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1351 b:19.7 occ:1.00 OD1 A:ASP48 2.4 19.7 1.0 O A:HOH565 2.5 20.2 1.0 OD1 A:ASP68 2.5 22.9 1.0 O A:ASP48 2.6 16.1 1.0 OG A:SER70 2.6 19.2 1.0 O A:HOH458 2.6 17.9 1.0 O A:GLY66 2.6 19.4 1.0 C A:ASP48 3.5 19.3 1.0 CG A:ASP48 3.5 19.6 1.0 CG A:ASP68 3.6 23.9 1.0 CB A:SER70 3.6 21.8 1.0 CA A:ASP48 3.8 17.1 1.0 C A:GLY66 3.8 19.5 1.0 N A:SER70 3.9 18.8 1.0 OD2 A:ASP68 4.0 23.4 1.0 N A:ASP68 4.1 20.0 1.0 CB A:ASP48 4.2 16.5 1.0 CA A:SER70 4.3 21.1 1.0 OD2 A:ASP48 4.3 18.1 1.0 O A:HOH562 4.3 21.8 1.0 N A:GLY66 4.4 21.7 1.0 N A:ILE71 4.4 18.9 1.0 CA A:GLY66 4.5 21.8 1.0 CB A:ALA51 4.6 16.9 1.0 N A:GLY69 4.6 20.2 1.0 N A:SER49 4.6 14.2 1.0 OE2 A:GLU78 4.6 21.3 1.0 O A:ALA51 4.6 21.9 1.0 CB A:ASP68 4.7 21.4 1.0 OE1 A:GLU78 4.7 22.0 1.0 N A:ALA67 4.8 18.1 1.0 CA A:ASP68 4.8 21.5 1.0 C A:SER70 4.8 23.2 1.0 CA A:ALA67 4.8 18.6 1.0 O A:HIS47 4.9 17.4 1.0 C A:ASP68 5.0 22.1 1.0 C A:GLY69 5.0 19.8 1.0 CA A:SER49 5.0 17.0 1.0 C A:ALA67 5.0 19.6 1.0

Calcium binding site 2 out of 4 in the Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lignin Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1352 b:11.3 occ:1.00 OD1 A:ASP201 2.5 10.3 1.0 OD2 A:ASP194 2.5 10.5 1.0 O A:SER177 2.5 8.6 1.0 O A:THR196 2.5 11.7 1.0 OG1 A:THR196 2.5 11.0 1.0 O A:ILE199 2.6 10.6 1.0 OG A:SER177 2.6 10.9 1.0 OD1 A:ASP194 2.8 11.9 1.0 CG A:ASP194 3.0 11.2 1.0 C A:THR196 3.4 11.4 1.0 CG A:ASP201 3.5 12.4 1.0 C A:SER177 3.5 11.1 1.0 CB A:THR196 3.6 12.1 1.0 CB A:SER177 3.7 12.2 1.0 CA A:SER177 3.8 9.4 1.0 C A:ILE199 3.8 12.8 1.0 OD2 A:ASP201 3.8 12.3 1.0 CA A:THR196 3.9 10.6 1.0 N A:ASP201 4.1 10.8 1.0 N A:THR196 4.3 10.6 1.0 N A:PRO197 4.3 10.4 1.0 N A:ILE199 4.4 13.4 1.0 O A:ASP201 4.5 12.8 1.0 CA A:ILE199 4.5 13.7 1.0 CB A:ASP194 4.5 8.3 1.0 CA A:PRO197 4.5 12.9 1.0 CB A:ILE199 4.6 15.8 1.0 O A:HOH373 4.6 13.7 1.0 CB A:GLN203 4.6 11.8 1.0 CB A:ASP201 4.7 10.7 1.0 N A:VAL178 4.7 11.3 1.0 N A:PHE200 4.7 10.7 1.0 CA A:ASP201 4.7 12.0 1.0 C A:ASP201 4.8 11.4 1.0 CA A:PHE200 4.8 10.1 1.0 CG2 A:THR196 4.9 11.2 1.0 CG1 A:VAL178 4.9 11.1 1.0 C A:PHE200 4.9 11.8 1.0 N A:GLN203 4.9 9.6 1.0

Calcium binding site 3 out of 4 in the Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lignin Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2351 b:13.2 occ:1.00 O B:HOH576 2.4 12.8 1.0 OD1 B:ASP48 2.5 13.8 1.0 OD1 B:ASP68 2.5 12.6 1.0 OG B:SER70 2.5 10.9 1.0 O B:HOH577 2.5 12.8 1.0 O B:ASP48 2.5 12.0 1.0 O B:GLY66 2.6 11.7 1.0 C B:ASP48 3.5 11.3 1.0 CG B:ASP48 3.5 14.8 1.0 CG B:ASP68 3.5 15.2 1.0 CB B:SER70 3.7 12.3 1.0 C B:GLY66 3.8 13.3 1.0 CA B:ASP48 3.8 10.9 1.0 N B:SER70 3.9 14.0 1.0 OD2 B:ASP68 4.0 13.9 1.0 N B:ASP68 4.1 12.2 1.0 CB B:ASP48 4.2 12.0 1.0 O B:HOH433 4.3 17.0 1.0 CA B:SER70 4.3 14.3 1.0 OD2 B:ASP48 4.3 14.0 1.0 N B:GLY66 4.3 14.4 1.0 N B:ILE71 4.4 12.5 1.0 CA B:GLY66 4.5 11.5 1.0 CB B:ALA51 4.6 12.4 1.0 O B:ALA51 4.6 15.8 1.0 N B:SER49 4.6 10.7 1.0 OE2 B:GLU78 4.6 15.1 1.0 N B:GLY69 4.6 11.7 1.0 CB B:ASP68 4.7 13.4 1.0 N B:ALA67 4.7 12.1 1.0 OE1 B:GLU78 4.7 14.4 1.0 C B:SER70 4.8 14.5 1.0 CA B:ALA67 4.8 12.9 1.0 CA B:ASP68 4.9 13.6 1.0 O B:HIS47 4.9 13.5 1.0 C B:ASP68 5.0 13.5 1.0 C B:GLY69 5.0 13.9 1.0

Calcium binding site 4 out of 4 in the Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lignin Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2352 b:12.1 occ:1.00 O B:SER177 2.5 9.2 1.0 O B:THR196 2.5 11.2 1.0 O B:ILE199 2.5 11.6 1.0 OD1 B:ASP201 2.5 12.1 1.0 OD2 B:ASP194 2.5 12.2 1.0 OG1 B:THR196 2.6 12.4 1.0 OG B:SER177 2.6 8.9 1.0 OD1 B:ASP194 2.7 9.9 1.0 CG B:ASP194 3.0 10.6 1.0 C B:THR196 3.4 12.1 1.0 CG B:ASP201 3.5 12.9 1.0 C B:SER177 3.5 11.5 1.0 CB B:THR196 3.6 12.5 1.0 CB B:SER177 3.7 9.9 1.0 C B:ILE199 3.7 11.0 1.0 CA B:SER177 3.7 9.8 1.0 OD2 B:ASP201 3.8 13.3 1.0 CA B:THR196 3.9 11.9 1.0 N B:ASP201 4.1 11.9 1.0 N B:PRO197 4.3 13.5 1.0 N B:THR196 4.3 12.5 1.0 N B:ILE199 4.4 12.8 1.0 CA B:ILE199 4.5 12.2 1.0 O B:ASP201 4.5 13.7 1.0 CA B:PRO197 4.5 14.9 1.0 CB B:ASP194 4.5 10.4 1.0 CB B:ILE199 4.5 14.3 1.0 CB B:ASP201 4.6 12.0 1.0 N B:VAL178 4.6 10.4 1.0 O B:HOH466 4.6 15.5 1.0 N B:PHE200 4.7 10.8 1.0 CB B:GLN203 4.7 12.2 1.0 CA B:ASP201 4.7 11.2 1.0 CA B:PHE200 4.8 11.3 1.0 C B:ASP201 4.8 12.9 1.0 CG1 B:VAL178 4.9 10.6 1.0 CG2 B:THR196 4.9 10.8 1.0 C B:PHE200 4.9 12.1 1.0 C B:PRO197 5.0 14.8 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