Calcium in PDB 1qpa: Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65)

The structure of Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65), PDB code: 1qpa was solved by T.H.Choinowski, K.Piontek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.790, 94.020, 81.260, 90.00, 106.47, 90.00
R / Rfree (%)	16.2 / n/a

The structure of Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65) also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65) (pdb code 1qpa). 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 Isozyme LIP4.65 (Pi 4.65), PDB code: 1qpa:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca351 b:13.2 occ:1.00 O A:SER177 2.4 12.1 1.0 OD1 A:ASP201 2.4 14.7 1.0 O A:THR196 2.4 10.5 1.0 OD2 A:ASP194 2.5 8.8 1.0 O A:GLN199 2.5 12.4 1.0 OG1 A:THR196 2.6 12.2 1.0 OG A:SER177 2.7 11.4 1.0 OD1 A:ASP194 2.7 11.0 1.0 CG A:ASP194 3.0 9.0 1.0 C A:THR196 3.3 10.8 1.0 C A:SER177 3.4 11.3 1.0 CG A:ASP201 3.5 13.9 1.0 CB A:THR196 3.6 12.1 1.0 CB A:SER177 3.7 11.2 1.0 C A:GLN199 3.7 12.6 1.0 CA A:SER177 3.7 11.9 1.0 OD2 A:ASP201 3.7 15.5 1.0 CA A:THR196 3.9 11.6 1.0 N A:ASP201 4.1 11.2 1.0 N A:PRO197 4.2 10.5 1.0 N A:THR196 4.3 13.0 1.0 O A:ASP201 4.4 14.3 1.0 N A:GLN199 4.5 11.8 1.0 CA A:GLN199 4.5 12.6 1.0 CB A:ASP194 4.5 10.1 1.0 CA A:PRO197 4.5 11.2 1.0 N A:ILE178 4.5 9.9 1.0 O A:HOH754 4.6 10.9 1.0 CB A:GLN199 4.6 15.7 1.0 CB A:ASP201 4.7 12.8 1.0 CB A:GLN203 4.7 12.6 1.0 N A:PHE200 4.8 11.9 1.0 CA A:ASP201 4.8 12.9 1.0 C A:ASP201 4.8 13.1 1.0 CG2 A:THR196 4.9 12.5 1.0 CG2 A:ILE178 4.9 9.1 1.0 CA A:PHE200 4.9 12.4 1.0 C A:PRO197 5.0 12.1 1.0

Calcium binding site 2 out of 4 in the Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca352 b:14.6 occ:1.00 O A:GLY66 2.5 13.5 1.0 OD1 A:ASP68 2.5 17.7 1.0 O A:HOH709 2.5 13.6 1.0 OD1 A:ASP48 2.5 10.9 1.0 OG A:SER70 2.5 15.9 1.0 O A:ASP48 2.6 12.8 1.0 O A:HOH710 2.7 14.2 1.0 CG A:ASP48 3.5 11.0 1.0 C A:ASP48 3.6 11.6 1.0 CG A:ASP68 3.6 18.8 1.0 C A:GLY66 3.7 11.0 1.0 CB A:SER70 3.7 12.4 1.0 N A:SER70 3.8 11.1 1.0 CA A:ASP48 3.9 11.7 1.0 OD2 A:ASP68 4.0 18.2 1.0 N A:ASP68 4.2 12.6 1.0 OD2 A:ASP48 4.2 11.3 1.0 O A:HOH708 4.2 15.0 1.0 CA A:SER70 4.3 11.8 1.0 CB A:ASP48 4.3 11.2 1.0 N A:GLY66 4.3 12.3 1.0 CA A:GLY66 4.4 11.0 1.0 N A:ILE71 4.5 12.6 1.0 N A:SER49 4.6 9.8 1.0 O A:ALA51 4.6 14.0 1.0 N A:GLY69 4.6 14.8 1.0 CB A:ALA51 4.7 12.0 1.0 OE2 A:GLU78 4.7 17.1 1.0 OE1 A:GLU78 4.7 16.9 1.0 N A:ALA67 4.7 12.1 1.0 CB A:ASP68 4.7 15.8 1.0 C A:SER70 4.8 11.8 1.0 CA A:ASP68 4.9 15.0 1.0 C A:GLY69 4.9 12.9 1.0 CA A:ALA67 4.9 12.8 1.0 C A:GLY65 5.0 12.9 1.0 C A:ASP68 5.0 15.1 1.0 O A:HIS47 5.0 13.2 1.0

Calcium binding site 3 out of 4 in the Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca351 b:13.2 occ:1.00 O B:SER177 2.4 13.2 1.0 OD1 B:ASP201 2.5 15.2 1.0 O B:THR196 2.5 13.4 1.0 OD2 B:ASP194 2.5 15.1 1.0 O B:GLN199 2.5 12.9 1.0 OG1 B:THR196 2.6 13.6 1.0 OG B:SER177 2.6 12.2 1.0 OD1 B:ASP194 2.8 14.5 1.0 CG B:ASP194 3.0 13.6 1.0 C B:THR196 3.3 13.1 1.0 C B:SER177 3.4 13.3 1.0 CG B:ASP201 3.5 15.8 1.0 CB B:THR196 3.6 13.5 1.0 CB B:SER177 3.7 13.7 1.0 CA B:SER177 3.7 13.2 1.0 C B:GLN199 3.7 13.5 1.0 OD2 B:ASP201 3.8 16.3 1.0 CA B:THR196 3.9 12.5 1.0 N B:ASP201 4.2 13.9 1.0 N B:PRO197 4.2 13.6 1.0 N B:THR196 4.4 13.4 1.0 N B:GLN199 4.4 11.7 1.0 O B:ASP201 4.4 14.6 1.0 CB B:ASP194 4.5 12.6 1.0 CA B:GLN199 4.5 12.9 1.0 O B:HOH613 4.5 13.8 1.0 CA B:PRO197 4.5 13.9 1.0 CB B:GLN199 4.6 16.1 1.0 N B:ILE178 4.6 11.4 1.0 CB B:ASP201 4.7 14.4 1.0 CB B:GLN203 4.7 13.7 1.0 CA B:ASP201 4.7 14.4 1.0 N B:PHE200 4.8 14.3 1.0 C B:ASP201 4.8 14.2 1.0 CG2 B:ILE178 4.8 12.8 1.0 CG2 B:THR196 4.9 12.7 1.0 C B:PRO197 4.9 14.2 1.0 CA B:PHE200 5.0 14.4 1.0

Calcium binding site 4 out of 4 in the Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lignin Peroxidase Isozyme LIP4.65 (Pi 4.65) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca352 b:18.2 occ:1.00 OD1 B:ASP68 2.4 20.8 1.0 O B:GLY66 2.5 17.2 1.0 O B:HOH405 2.5 20.5 1.0 OD1 B:ASP48 2.5 16.8 1.0 O B:HOH404 2.6 18.9 1.0 O B:ASP48 2.6 18.8 1.0 OG B:SER70 2.6 18.8 1.0 CG B:ASP68 3.5 21.6 1.0 CG B:ASP48 3.5 14.5 1.0 CB B:SER70 3.5 18.5 1.0 C B:ASP48 3.5 16.9 1.0 C B:GLY66 3.7 16.9 1.0 CA B:ASP48 3.8 15.6 1.0 OD2 B:ASP68 3.9 23.2 1.0 N B:SER70 3.9 18.8 1.0 N B:ASP68 4.2 17.3 1.0 CB B:ASP48 4.2 14.4 1.0 OD2 B:ASP48 4.2 14.0 1.0 CA B:SER70 4.2 19.4 1.0 N B:GLY66 4.3 18.1 1.0 O B:HOH403 4.4 17.4 1.0 CA B:GLY66 4.4 17.3 1.0 O B:ALA51 4.5 18.5 1.0 N B:GLY69 4.5 19.5 1.0 N B:ILE71 4.5 20.7 1.0 OE2 B:GLU78 4.5 24.8 1.0 CB B:ALA51 4.5 18.5 1.0 N B:SER49 4.6 15.0 1.0 CB B:ASP68 4.7 20.3 1.0 C B:SER70 4.8 20.1 1.0 N B:ALA67 4.8 15.9 1.0 OE1 B:GLU78 4.8 22.8 1.0 CA B:ALA67 4.9 16.1 1.0 CA B:ASP68 4.9 19.4 1.0 C B:GLY65 4.9 17.8 1.0 C B:GLY69 5.0 19.1 1.0 C B:ASP68 5.0 20.0 1.0

T.Choinowski, W.Blodig, K.H.Winterhalter, K.Piontek. The Crystal Structure of Lignin Peroxidase at 1.70 A Resolution Reveals A Hydroxy Group on the Cbeta of Tryptophan 171: A Novel Radical Site Formed During the Redox Cycle. J.Mol.Biol. V. 286 809 1999.
ISSN: ISSN 0022-2836
PubMed: 10024453
DOI: 10.1006/JMBI.1998.2507