Calcium in PDB 3q3u: Trametes Cervina Lignin Peroxidase

The structure of Trametes Cervina Lignin Peroxidase, PDB code: 3q3u was solved by F.R.Calvino, A.Romero, Y.Miki, A.T.Martinez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.90 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.904, 72.931, 95.232, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 19.6

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

Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Trametes Cervina Lignin Peroxidase (pdb code 3q3u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Trametes Cervina Lignin Peroxidase, PDB code: 3q3u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Trametes Cervina Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trametes Cervina Lignin Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca340 b:7.2 occ:1.00 O A:HOH416 2.4 2.4 1.0 OD1 A:ASP48 2.4 3.9 1.0 OG A:SER70 2.4 4.0 1.0 O A:GLY66 2.4 7.3 1.0 OD1 A:ASP68 2.4 4.0 1.0 O A:HOH373 2.4 3.3 1.0 O A:ASP48 2.5 5.2 1.0 C A:ASP48 3.4 3.7 1.0 CG A:ASP68 3.5 4.4 1.0 CG A:ASP48 3.5 7.1 1.0 CB A:SER70 3.6 6.1 1.0 C A:GLY66 3.6 7.4 1.0 CA A:ASP48 3.8 4.8 1.0 OD2 A:ASP68 3.9 7.2 1.0 N A:SER70 4.0 8.2 1.0 N A:ASP68 4.1 7.8 1.0 O A:HOH394 4.2 5.6 1.0 CB A:ASP48 4.2 5.0 1.0 CA A:SER70 4.3 7.3 1.0 CA A:GLY66 4.3 7.3 1.0 N A:GLY66 4.4 8.2 1.0 N A:ILE71 4.4 6.0 1.0 OD2 A:ASP48 4.4 8.1 1.0 N A:ALA49 4.5 5.2 1.0 O A:GLY51 4.5 6.5 1.0 OE2 A:GLU78 4.5 5.8 1.0 N A:ALA67 4.7 6.9 1.0 CB A:ASP68 4.7 7.1 1.0 N A:GLY69 4.7 7.5 1.0 OE1 A:GLU78 4.7 7.2 1.0 C A:SER70 4.8 7.1 1.0 CA A:ASP68 4.8 7.7 1.0 CA A:GLY51 4.9 4.5 1.0 O A:HIS47 4.9 4.4 1.0 CA A:ALA49 4.9 5.3 1.0 N A:GLY51 4.9 5.3 1.0 CA A:ALA67 4.9 8.4 1.0 CB A:SER139 5.0 5.5 1.0

Calcium binding site 2 out of 2 in the Trametes Cervina Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trametes Cervina Lignin Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca341 b:5.4 occ:1.00 OD2 A:ASP193 2.3 5.4 1.0 O A:THR195 2.4 6.0 1.0 O A:SER176 2.4 5.2 1.0 O A:VAL198 2.4 6.9 1.0 OD1 A:ASP200 2.5 4.9 1.0 OG A:SER176 2.5 3.5 1.0 OG1 A:THR195 2.5 6.5 1.0 OD1 A:ASP193 2.6 3.8 1.0 CG A:ASP193 2.8 3.7 1.0 C A:THR195 3.3 4.7 1.0 C A:SER176 3.4 5.1 1.0 CG A:ASP200 3.5 5.5 1.0 CB A:THR195 3.6 5.7 1.0 CB A:SER176 3.6 4.2 1.0 C A:VAL198 3.6 6.9 1.0 CA A:SER176 3.7 5.0 1.0 OD2 A:ASP200 3.9 6.6 1.0 CA A:THR195 3.9 5.8 1.0 N A:ASP200 4.1 6.5 1.0 N A:THR195 4.2 5.9 1.0 N A:PRO196 4.2 5.5 1.0 CB A:ASP193 4.4 6.3 1.0 CA A:PRO196 4.4 4.6 1.0 N A:VAL198 4.4 6.2 1.0 CA A:VAL198 4.4 7.8 1.0 O A:ASP200 4.5 5.5 1.0 O A:HOH355 4.5 4.0 1.0 N A:ILE177 4.6 5.2 1.0 CB A:VAL198 4.6 6.7 1.0 N A:PHE199 4.7 5.7 1.0 CB A:GLN202 4.7 6.0 1.0 CB A:ASP200 4.7 4.3 1.0 CA A:ASP200 4.8 5.6 1.0 CA A:PHE199 4.8 4.8 1.0 C A:ASP200 4.8 5.1 1.0 CG2 A:ILE177 4.9 3.3 1.0 CG2 A:THR195 4.9 4.6 1.0 C A:PRO196 4.9 4.8 1.0 C A:PHE199 5.0 6.2 1.0

Y.Miki, F.R.Calvino, R.Pogni, S.Giansanti, F.J.Ruiz-Duenas, M.J.Martinez, R.Basosi, A.Romero, A.T.Martinez. Crystallographic, Kinetic, and Spectroscopic Study of the First Ligninolytic Peroxidase Presenting A Catalytic Tyrosine. J.Biol.Chem. V. 286 15525 2011.
ISSN: ISSN 0021-9258
PubMed: 21367853
DOI: 10.1074/JBC.M111.220996