Calcium in PDB 1lga: Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms

The structure of Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms, PDB code: 1lga was solved by T.L.Poulos, S.L.Edwards, H.Wariishi, M.H.Gold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.700, 77.500, 100.000, 90.00, 101.00, 90.00
R / Rfree (%)	15 / n/a

The structure of Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

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

Calcium binding site 1 out of 4 in the Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca398 b:5.5 occ:1.00 O A:SER177 2.3 9.7 1.0 OD1 A:ASP201 2.4 7.3 1.0 O A:THR196 2.4 9.3 1.0 O A:ILE199 2.5 10.1 1.0 OD2 A:ASP194 2.5 9.9 1.0 OG1 A:THR196 2.6 10.3 1.0 OG A:SER177 2.6 7.1 1.0 OD1 A:ASP194 2.9 2.0 1.0 CG A:ASP194 3.0 6.5 1.0 C A:THR196 3.3 9.2 1.0 C A:SER177 3.4 7.7 1.0 CG A:ASP201 3.4 4.9 1.0 CB A:SER177 3.6 8.2 1.0 C A:ILE199 3.7 8.5 1.0 CA A:SER177 3.7 5.8 1.0 CB A:THR196 3.7 12.8 1.0 OD2 A:ASP201 3.9 2.9 1.0 CA A:THR196 3.9 11.4 1.0 N A:ASP201 4.2 7.7 1.0 N A:PRO197 4.2 8.7 1.0 N A:THR196 4.2 11.6 1.0 O A:ASP201 4.4 8.9 1.0 N A:ILE199 4.5 8.4 1.0 CA A:ILE199 4.5 8.8 1.0 CB A:ILE199 4.5 9.3 1.0 CA A:PRO197 4.5 6.7 1.0 CB A:ASP194 4.5 7.5 1.0 N A:VAL178 4.5 4.8 1.0 CB A:ASP201 4.6 5.7 1.0 N A:PHE200 4.7 8.2 1.0 CA A:PHE200 4.7 8.1 1.0 CB A:GLN203 4.7 2.0 1.0 CG1 A:VAL178 4.7 2.0 1.0 O A:HOH447 4.8 12.0 1.0 CA A:ASP201 4.8 7.2 1.0 C A:ASP201 4.8 6.9 1.0 C A:PHE200 4.9 7.2 1.0 CG2 A:THR196 5.0 3.9 1.0

Calcium binding site 2 out of 4 in the Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca399 b:9.4 occ:1.00 O A:GLY66 2.3 8.3 1.0 O A:ASP48 2.4 5.4 1.0 OG A:SER70 2.4 9.9 1.0 O A:HOH511 2.4 6.1 1.0 O A:HOH473 2.5 2.2 1.0 OD1 A:ASP48 2.6 5.8 1.0 OD1 A:ASP68 2.6 15.3 1.0 C A:ASP48 3.3 5.3 1.0 CG A:ASP48 3.5 9.2 1.0 C A:GLY66 3.5 6.1 1.0 CG A:ASP68 3.7 7.7 1.0 CB A:SER70 3.7 4.8 1.0 CA A:ASP48 3.8 6.1 1.0 N A:SER70 4.1 6.7 1.0 OD2 A:ASP68 4.1 9.1 1.0 N A:ASP68 4.2 8.0 1.0 CB A:ASP48 4.2 7.0 1.0 CA A:GLY66 4.3 7.6 1.0 OD2 A:ASP48 4.3 11.1 1.0 O A:HOH472 4.4 8.3 1.0 N A:GLY66 4.4 8.4 1.0 N A:SER49 4.4 5.4 1.0 O A:ALA51 4.4 4.4 1.0 CA A:SER70 4.4 6.8 1.0 CB A:ALA51 4.5 4.8 1.0 N A:ILE71 4.5 5.4 1.0 N A:ALA67 4.6 8.2 1.0 OE2 A:GLU78 4.7 9.6 1.0 N A:GLY69 4.7 9.6 1.0 OE1 A:GLU78 4.8 8.5 1.0 CB A:ASP68 4.9 5.0 1.0 O A:HIS47 4.9 6.5 1.0 CA A:ALA67 4.9 5.6 1.0 C A:SER70 4.9 7.2 1.0 CA A:ASP68 4.9 9.0 1.0 CA A:SER49 5.0 8.0 1.0

Calcium binding site 3 out of 4 in the Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca398 b:7.7 occ:1.00 OD1 B:ASP201 2.3 8.1 1.0 O B:SER177 2.3 4.8 1.0 O B:ILE199 2.4 8.8 1.0 O B:THR196 2.4 8.9 1.0 OG B:SER177 2.6 6.5 1.0 OD2 B:ASP194 2.6 10.8 1.0 OD1 B:ASP194 2.8 6.0 1.0 OG1 B:THR196 2.8 5.6 1.0 CG B:ASP194 3.1 8.5 1.0 CG B:ASP201 3.3 9.8 1.0 C B:THR196 3.3 8.6 1.0 C B:SER177 3.3 4.6 1.0 CB B:SER177 3.6 8.0 1.0 C B:ILE199 3.6 7.1 1.0 CA B:SER177 3.7 4.8 1.0 CB B:THR196 3.7 5.2 1.0 OD2 B:ASP201 3.8 6.4 1.0 CA B:THR196 4.0 7.7 1.0 N B:ASP201 4.1 6.7 1.0 N B:PRO197 4.2 7.2 1.0 N B:THR196 4.4 10.2 1.0 CA B:ILE199 4.5 5.7 1.0 CB B:ASP201 4.5 6.5 1.0 N B:ILE199 4.5 5.2 1.0 O B:ASP201 4.5 3.6 1.0 CA B:PRO197 4.5 9.2 1.0 N B:VAL178 4.5 6.0 1.0 CB B:ILE199 4.6 7.1 1.0 N B:PHE200 4.6 7.1 1.0 CB B:ASP194 4.6 8.3 1.0 CA B:ASP201 4.7 3.9 1.0 O B:HOH436 4.7 4.2 1.0 CA B:PHE200 4.7 6.2 1.0 CG1 B:VAL178 4.7 2.0 1.0 CB B:GLN203 4.7 2.0 1.0 C B:PHE200 4.8 3.6 1.0 C B:ASP201 4.8 4.2 1.0 CG2 B:ILE199 4.9 2.0 1.0 CA B:VAL178 5.0 5.0 1.0 C B:PRO197 5.0 9.2 1.0

Calcium binding site 4 out of 4 in the Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystallographic Refinement of Lignin Peroxidase at 2 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca399 b:8.6 occ:1.00 O B:HOH499 2.3 2.0 1.0 O B:HOH459 2.4 9.4 1.0 O B:GLY66 2.4 9.8 1.0 OG B:SER70 2.5 7.1 1.0 O B:ASP48 2.5 3.8 1.0 OD1 B:ASP48 2.6 9.5 1.0 OD1 B:ASP68 2.6 12.0 1.0 C B:ASP48 3.4 6.1 1.0 CG B:ASP48 3.5 7.3 1.0 CG B:ASP68 3.6 7.7 1.0 C B:GLY66 3.6 3.6 1.0 CA B:ASP48 3.8 2.6 1.0 CB B:SER70 3.8 5.1 1.0 N B:SER70 3.9 2.9 1.0 OD2 B:ASP68 4.1 6.8 1.0 N B:ASP68 4.2 4.6 1.0 CB B:ASP48 4.2 2.5 1.0 OD2 B:ASP48 4.2 7.5 1.0 O B:HOH430 4.3 4.2 1.0 CA B:SER70 4.3 4.0 1.0 O B:ALA51 4.4 8.2 1.0 N B:GLY66 4.4 6.4 1.0 N B:ILE71 4.5 4.8 1.0 CA B:GLY66 4.5 3.7 1.0 OE2 B:GLU78 4.5 8.8 1.0 CB B:ALA51 4.5 6.4 1.0 N B:SER49 4.6 6.7 1.0 N B:ALA67 4.6 3.5 1.0 N B:GLY69 4.7 5.7 1.0 OE1 B:GLU78 4.7 8.8 1.0 CB B:ASP68 4.8 6.4 1.0 C B:SER70 4.8 5.5 1.0 O B:HIS47 4.9 4.3 1.0 CA B:ALA67 4.9 2.4 1.0 CA B:ASP68 4.9 4.8 1.0 C B:GLY65 5.0 6.7 1.0 C B:GLY69 5.0 4.2 1.0

T.L.Poulos, S.L.Edwards, H.Wariishi, M.H.Gold. Crystallographic Refinement of Lignin Peroxidase at 2 A. J.Biol.Chem. V. 268 4429 1993.
ISSN: ISSN 0021-9258
PubMed: 8440725