Calcium in PDB 1b80: Rec. Lignin Peroxidase H8 Oxidatively Processed

All present enzymatic activity of Rec. Lignin Peroxidase H8 Oxidatively Processed:
1.11.1.14;

The structure of Rec. Lignin Peroxidase H8 Oxidatively Processed, PDB code: 1b80 was solved by W.Blodig, A.T.Smith, W.A.Doyle, K.Piontek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.73
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.480, 94.930, 230.130, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.8

The structure of Rec. Lignin Peroxidase H8 Oxidatively Processed also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Rec. Lignin Peroxidase H8 Oxidatively Processed (pdb code 1b80). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Rec. Lignin Peroxidase H8 Oxidatively Processed, PDB code: 1b80:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Rec. Lignin Peroxidase H8 Oxidatively Processed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rec. Lignin Peroxidase H8 Oxidatively Processed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca351 b:21.9 occ:1.00 OD1 A:ASP48 2.5 20.4 1.0 O A:ASP48 2.5 17.6 1.0 O A:HOH459 2.5 19.2 1.0 O A:HOH565 2.6 23.4 1.0 OD1 A:ASP68 2.6 21.1 1.0 O A:GLY66 2.6 19.5 1.0 OG A:SER70 2.6 22.4 1.0 C A:ASP48 3.5 20.2 1.0 CG A:ASP68 3.5 22.9 1.0 CG A:ASP48 3.5 20.0 1.0 CB A:SER70 3.7 22.8 1.0 C A:GLY66 3.8 18.9 1.0 CA A:ASP48 3.8 18.3 1.0 OD2 A:ASP68 3.9 22.1 1.0 N A:SER70 4.0 21.1 1.0 N A:ASP68 4.1 18.7 1.0 O A:HOH562 4.3 25.9 1.0 OD2 A:ASP48 4.3 19.8 1.0 CB A:ASP48 4.3 17.7 1.0 CA A:SER70 4.3 21.9 1.0 N A:GLY66 4.4 23.6 1.0 N A:ILE71 4.4 21.6 1.0 CB A:ALA51 4.4 20.3 1.0 CA A:GLY66 4.5 21.6 1.0 O A:ALA51 4.6 24.2 1.0 N A:SER49 4.6 15.8 1.0 N A:GLY69 4.6 21.2 1.0 CB A:ASP68 4.7 20.7 1.0 OE2 A:GLU78 4.7 25.9 1.0 N A:ALA67 4.7 18.8 1.0 OE1 A:GLU78 4.7 24.8 1.0 CA A:ALA67 4.8 18.3 1.0 CA A:ASP68 4.9 20.9 1.0 C A:SER70 4.9 23.8 1.0 O A:HIS47 4.9 18.1 1.0 C A:GLY69 5.0 18.2 1.0 C A:GLY65 5.0 24.6 1.0 C A:ASP68 5.0 22.0 1.0 CA A:SER49 5.0 17.5 1.0

Calcium binding site 2 out of 4 in the Rec. Lignin Peroxidase H8 Oxidatively Processed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rec. Lignin Peroxidase H8 Oxidatively Processed within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca352 b:9.6 occ:1.00 O A:THR196 2.4 10.2 1.0 O A:SER177 2.5 10.3 1.0 OD2 A:ASP194 2.5 8.8 1.0 O A:ILE199 2.5 10.6 1.0 OD1 A:ASP201 2.5 10.8 1.0 OG A:SER177 2.6 9.6 1.0 OG1 A:THR196 2.6 12.7 1.0 OD1 A:ASP194 2.7 10.5 1.0 CG A:ASP194 3.0 10.9 1.0 C A:THR196 3.4 11.1 1.0 C A:SER177 3.4 8.3 1.0 CG A:ASP201 3.5 12.6 1.0 CB A:THR196 3.6 13.8 1.0 CB A:SER177 3.7 8.7 1.0 CA A:SER177 3.7 8.0 1.0 C A:ILE199 3.7 12.9 1.0 OD2 A:ASP201 3.8 11.2 1.0 CA A:THR196 3.9 10.5 1.0 N A:ASP201 4.1 10.5 1.0 N A:PRO197 4.3 11.4 1.0 N A:THR196 4.3 11.6 1.0 N A:ILE199 4.4 11.9 1.0 CB A:ASP194 4.5 8.2 1.0 CA A:ILE199 4.5 12.6 1.0 CA A:PRO197 4.5 11.0 1.0 O A:ASP201 4.6 10.7 1.0 O A:HOH373 4.6 12.7 1.0 CB A:ILE199 4.6 14.3 1.0 N A:VAL178 4.6 10.0 1.0 CB A:GLN203 4.6 9.8 1.0 CB A:ASP201 4.7 9.4 1.0 N A:PHE200 4.7 10.4 1.0 CA A:ASP201 4.7 10.4 1.0 CA A:PHE200 4.8 11.2 1.0 C A:ASP201 4.8 9.0 1.0 CG1 A:VAL178 4.9 10.9 1.0 CG2 A:THR196 4.9 12.7 1.0 C A:PHE200 4.9 11.0 1.0 N A:GLN203 5.0 9.4 1.0 C A:PRO197 5.0 12.6 1.0

Calcium binding site 3 out of 4 in the Rec. Lignin Peroxidase H8 Oxidatively Processed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rec. Lignin Peroxidase H8 Oxidatively Processed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca351 b:13.0 occ:1.00 O B:HOH576 2.4 12.6 1.0 OD1 B:ASP48 2.5 11.2 1.0 OD1 B:ASP68 2.5 13.7 1.0 O B:ASP48 2.5 12.2 1.0 O B:GLY66 2.6 12.2 1.0 OG B:SER70 2.6 13.5 1.0 O B:HOH577 2.6 14.1 1.0 C B:ASP48 3.5 13.3 1.0 CG B:ASP48 3.5 14.4 1.0 CG B:ASP68 3.6 16.0 1.0 CB B:SER70 3.6 13.9 1.0 C B:GLY66 3.7 13.3 1.0 CA B:ASP48 3.8 12.2 1.0 OD2 B:ASP68 3.9 15.2 1.0 N B:SER70 4.0 13.2 1.0 N B:ASP68 4.1 13.4 1.0 O B:HOH433 4.2 16.6 1.0 CB B:ASP48 4.2 12.2 1.0 OD2 B:ASP48 4.2 12.6 1.0 CA B:SER70 4.3 14.2 1.0 N B:GLY66 4.3 13.5 1.0 CA B:GLY66 4.4 12.2 1.0 N B:ILE71 4.5 13.4 1.0 N B:GLY69 4.6 12.1 1.0 OE2 B:GLU78 4.6 14.9 1.0 N B:SER49 4.6 11.4 1.0 O B:ALA51 4.6 14.4 1.0 CB B:ALA51 4.7 13.7 1.0 CB B:ASP68 4.7 13.6 1.0 N B:ALA67 4.7 13.1 1.0 OE1 B:GLU78 4.7 14.6 1.0 C B:SER70 4.8 15.3 1.0 CA B:ASP68 4.8 14.6 1.0 CA B:ALA67 4.9 11.7 1.0 C B:ASP68 4.9 14.3 1.0 O B:HIS47 5.0 12.9 1.0 C B:GLY69 5.0 12.0 1.0

Calcium binding site 4 out of 4 in the Rec. Lignin Peroxidase H8 Oxidatively Processed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rec. Lignin Peroxidase H8 Oxidatively Processed within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca352 b:11.3 occ:1.00 O B:THR196 2.4 10.6 1.0 O B:SER177 2.5 10.9 1.0 OD1 B:ASP201 2.5 11.8 1.0 OD2 B:ASP194 2.5 10.4 1.0 OG B:SER177 2.6 8.7 1.0 O B:ILE199 2.6 11.7 1.0 OG1 B:THR196 2.6 12.7 1.0 OD1 B:ASP194 2.8 11.9 1.0 CG B:ASP194 3.0 10.9 1.0 C B:THR196 3.3 10.3 1.0 CG B:ASP201 3.4 14.2 1.0 C B:SER177 3.5 10.9 1.0 CB B:THR196 3.6 13.3 1.0 CB B:SER177 3.7 10.1 1.0 C B:ILE199 3.8 10.5 1.0 CA B:SER177 3.8 9.9 1.0 OD2 B:ASP201 3.8 15.3 1.0 CA B:THR196 3.9 10.3 1.0 N B:ASP201 4.1 11.9 1.0 N B:PRO197 4.2 12.9 1.0 N B:THR196 4.3 10.4 1.0 N B:ILE199 4.4 10.8 1.0 CA B:ILE199 4.5 10.8 1.0 CA B:PRO197 4.5 12.0 1.0 CB B:ASP194 4.5 11.7 1.0 O B:HOH466 4.5 12.0 1.0 CB B:ILE199 4.6 13.3 1.0 O B:ASP201 4.6 12.1 1.0 CB B:ASP201 4.6 12.7 1.0 N B:VAL178 4.6 9.2 1.0 CB B:GLN203 4.7 10.3 1.0 N B:PHE200 4.7 10.4 1.0 CA B:ASP201 4.8 11.2 1.0 CA B:PHE200 4.8 11.0 1.0 CG1 B:VAL178 4.8 10.9 1.0 CG2 B:THR196 4.8 13.2 1.0 C B:ASP201 4.9 11.2 1.0 C B:PHE200 4.9 12.2 1.0 C B:PRO197 4.9 11.8 1.0 N B:GLN203 5.0 11.7 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