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Calcium in PDB 3fjw: Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

Enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii

All present enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii, PDB code: 3fjw was solved by K.Piontek, A.T.Martinez, T.Choinowski, D.A.Plattner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.17 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.141, 92.762, 113.278, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 24.6

Other elements in 3fjw:

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii (pdb code 3fjw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii, PDB code: 3fjw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3fjw

Go back to Calcium Binding Sites List in 3fjw
Calcium binding site 1 out of 4 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca351

b:18.0
occ:1.00
 O A:HOH507 2.2 17.7 1.0
O A:GLY60 2.3 17.0 1.0
O A:ASP48 2.3 18.0 1.0
OD1 A:ASP48 2.4 16.6 1.0
O A:HOH415 2.5 20.7 1.0
OD1 A:ASP62 2.5 19.0 1.0
OG A:SER64 2.7 16.3 1.0
C A:ASP48 3.1 17.6 1.0
CG A:ASP48 3.2 16.9 1.0
C A:GLY60 3.5 17.1 1.0
CA A:ASP48 3.6 17.5 1.0
CG A:ASP62 3.6 18.7 1.0
CB A:SER64 3.7 15.5 1.0
N A:ASP62 4.0 16.2 1.0
OD2 A:ASP48 4.0 16.7 1.0
CB A:ASP48 4.0 17.1 1.0
N A:SER64 4.0 15.8 1.0
OD2 A:ASP62 4.1 19.0 1.0
N A:ALA49 4.2 17.0 1.0
CA A:GLY60 4.3 17.3 1.0
N A:GLY60 4.3 17.5 1.0
CA A:SER64 4.4 15.7 1.0
O A:HOH402 4.4 6.9 1.0
N A:GLY63 4.4 16.9 1.0
N A:ILE65 4.4 14.9 1.0
N A:ALA61 4.5 16.4 1.0
CA A:ALA49 4.7 15.7 1.0
O A:GLY51 4.7 17.3 1.0
CB A:ASP62 4.7 17.8 1.0
CA A:ASP62 4.7 17.1 1.0
CA A:ALA61 4.7 16.4 1.0
OE2 A:GLU72 4.7 19.7 1.0
CA A:GLY51 4.8 15.9 1.0
O A:HIS47 4.8 18.9 1.0
C A:ALA61 4.9 16.5 1.0
C A:SER64 4.9 15.1 1.0
N A:ASP48 4.9 17.8 1.0
C A:ASP62 4.9 17.3 1.0
N A:GLY51 4.9 15.4 1.0
C A:GLY63 5.0 16.2 1.0
OE1 A:GLU72 5.0 19.3 1.0

Calcium binding site 2 out of 4 in 3fjw

Go back to Calcium Binding Sites List in 3fjw
Calcium binding site 2 out of 4 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca352

b:13.1
occ:1.00
 OG1 A:THR189 2.3 10.6 1.0
O A:THR189 2.4 11.0 1.0
O A:SER170 2.4 13.6 1.0
OD1 A:ASP194 2.5 18.5 1.0
O A:VAL192 2.6 15.2 1.0
OD2 A:ASP187 2.6 10.4 1.0
OG A:SER170 2.6 12.7 1.0
OD1 A:ASP187 2.7 11.0 1.0
CG A:ASP187 3.0 11.1 1.0
C A:THR189 3.2 11.2 1.0
CB A:THR189 3.3 10.3 1.0
CG A:ASP194 3.4 18.6 1.0
C A:SER170 3.4 12.6 1.0
OD2 A:ASP194 3.7 19.5 1.0
CA A:THR189 3.7 10.4 1.0
CB A:SER170 3.7 12.5 1.0
C A:VAL192 3.8 15.3 1.0
CA A:SER170 3.8 12.9 1.0
N A:THR189 4.1 10.5 1.0
N A:ASP194 4.2 16.7 1.0
N A:PRO190 4.2 11.7 1.0
N A:VAL192 4.4 13.6 1.0
O A:HOH450 4.4 15.0 1.0
CA A:VAL192 4.5 14.2 1.0
CB A:GLN196 4.5 18.1 1.0
CB A:ASP187 4.5 11.2 1.0
N A:ILE171 4.6 11.9 1.0
CB A:VAL192 4.6 14.1 1.0
CB A:ASP194 4.6 17.7 1.0
CA A:PRO190 4.6 11.6 1.0
CG2 A:THR189 4.7 9.6 1.0
O A:ASP194 4.7 17.0 1.0
CG2 A:ILE171 4.8 12.3 1.0
CA A:ASP194 4.8 17.5 1.0
N A:PHE193 4.8 15.4 1.0
C A:ASP194 4.9 17.9 1.0
C A:PRO190 5.0 12.1 1.0

Calcium binding site 3 out of 4 in 3fjw

Go back to Calcium Binding Sites List in 3fjw
Calcium binding site 3 out of 4 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca351

b:18.4
occ:1.00
 O B:HOH425 2.1 17.2 1.0
O B:GLY60 2.3 18.0 1.0
OG B:SER64 2.4 14.9 1.0
OD1 B:ASP62 2.4 17.1 1.0
OD1 B:ASP48 2.4 16.9 1.0
O B:HOH365 2.5 6.7 1.0
O B:ASP48 2.5 16.3 1.0
C B:ASP48 3.4 16.1 1.0
CB B:SER64 3.4 15.2 1.0
C B:GLY60 3.5 16.8 1.0
CG B:ASP62 3.5 16.8 1.0
CG B:ASP48 3.5 16.8 1.0
N B:SER64 3.8 15.7 1.0
CA B:ASP48 3.8 16.7 1.0
OD2 B:ASP62 4.0 16.6 1.0
N B:GLY60 4.1 16.4 1.0
CA B:GLY60 4.1 16.7 1.0
CA B:SER64 4.1 15.7 1.0
N B:ASP62 4.1 16.1 1.0
O B:HOH459 4.3 11.6 1.0
CB B:ASP48 4.3 16.6 1.0
OD2 B:ASP48 4.4 17.7 1.0
N B:ILE65 4.4 16.2 1.0
O B:GLY51 4.5 14.9 1.0
N B:ALA61 4.5 16.3 1.0
OE1 B:GLU72 4.5 15.9 1.0
N B:ALA49 4.6 15.7 1.0
OE2 B:GLU72 4.6 16.0 1.0
N B:GLY63 4.6 16.5 1.0
CA B:GLY51 4.6 15.2 1.0
C B:SER64 4.7 15.8 1.0
CB B:ASP62 4.8 16.3 1.0
CA B:ALA61 4.8 15.9 1.0
CA B:ASP62 4.9 16.2 1.0
C B:GLY63 4.9 15.7 1.0
N B:GLY51 4.9 14.8 1.0
C B:GLY51 5.0 15.6 1.0
C B:ASP62 5.0 16.7 1.0
CA B:ALA49 5.0 15.6 1.0
C B:GLY59 5.0 16.7 1.0
O B:HIS47 5.0 16.7 1.0

Calcium binding site 4 out of 4 in 3fjw

Go back to Calcium Binding Sites List in 3fjw
Calcium binding site 4 out of 4 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca352

b:14.9
occ:1.00
 OD2 B:ASP187 2.3 11.2 1.0
O B:VAL192 2.4 11.6 1.0
O B:SER170 2.4 12.5 1.0
OD1 B:ASP194 2.4 13.6 1.0
O B:THR189 2.4 11.0 1.0
OG B:SER170 2.5 11.1 1.0
OG1 B:THR189 2.6 10.6 1.0
OD1 B:ASP187 2.9 10.3 1.0
CG B:ASP187 3.0 10.5 1.0
C B:THR189 3.3 11.4 1.0
C B:SER170 3.4 11.6 1.0
CG B:ASP194 3.5 13.8 1.0
CB B:THR189 3.6 11.2 1.0
C B:VAL192 3.6 11.6 1.0
CB B:SER170 3.7 11.3 1.0
CA B:SER170 3.7 11.6 1.0
CA B:THR189 3.9 11.4 1.0
N B:ASP194 4.0 13.0 1.0
OD2 B:ASP194 4.0 15.1 1.0
N B:THR189 4.2 11.2 1.0
N B:PRO190 4.3 11.1 1.0
O B:ASP194 4.3 11.0 1.0
CA B:VAL192 4.4 11.0 1.0
N B:VAL192 4.4 11.3 1.0
CB B:ASP187 4.5 10.6 1.0
CB B:GLN196 4.5 13.1 1.0
N B:ILE171 4.5 10.7 1.0
O B:HOH385 4.6 18.7 1.0
CB B:VAL192 4.6 10.9 1.0
N B:PHE193 4.6 12.0 1.0
CA B:PRO190 4.7 11.0 1.0
CB B:ASP194 4.7 13.0 1.0
CA B:ASP194 4.7 12.6 1.0
C B:ASP194 4.7 12.2 1.0
CA B:PHE193 4.7 12.2 1.0
C B:PHE193 4.9 12.5 1.0
CG2 B:THR189 4.9 11.1 1.0
N B:PHE197 4.9 12.8 1.0

Reference:

K.Piontek, T.Choinowski, M.Perez-Boada, F.J.Ruiz-Duenas, M.J.Martinez, D.A.Plattner, A.T.Martinez. Structural and Site-Directed Mutagenesis Study of Versatile Peroxidase Oxidizing Both Mn(II) and Aromatic Substrates To Be Published.
Page generated: Tue Jul 8 12:23:29 2025

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