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Calcium in PDB 5abo: Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R.

Enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R.

All present enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R.:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R., PDB code: 5abo was solved by F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.410 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.820, 64.220, 95.410, 90.00, 90.00, 90.00
R / Rfree (%) 13.35 / 14.41

Other elements in 5abo:

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R. also contains other interesting chemical elements:

Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R. (pdb code 5abo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R., PDB code: 5abo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5abo

Go back to Calcium Binding Sites List in 5abo
Calcium binding site 1 out of 2 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R.


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. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:10.6
occ:1.00
 OD1 A:ASP48 2.4 11.0 1.0
O A:HOH2124 2.4 12.1 1.0
O A:HOH2107 2.4 11.7 1.0
O A:GLY60 2.4 11.2 1.0
OD1 A:ASP62 2.4 11.7 1.0
OG A:SER64 2.4 11.5 1.0
O A:ASP48 2.5 10.9 1.0
H A:SER64 3.3 12.8 1.0
HA A:ASP48 3.3 12.2 1.0
H A:ASP62 3.4 13.1 1.0
C A:ASP48 3.4 10.6 1.0
CG A:ASP48 3.4 9.9 1.0
CG A:ASP62 3.5 11.8 1.0
CB A:SER64 3.6 11.5 1.0
C A:GLY60 3.6 11.0 1.0
HB3 A:SER64 3.6 13.8 1.0
CA A:ASP48 3.8 10.2 1.0
H A:ILE65 3.9 13.1 1.0
N A:SER64 4.0 10.6 1.0
HB2 A:SER133 4.0 16.9 1.0
OD2 A:ASP62 4.0 12.9 1.0
N A:ASP62 4.2 10.9 1.0
O A:HOH2140 4.2 13.4 1.0
OD2 A:ASP48 4.2 11.1 1.0
H A:GLY60 4.2 15.1 1.0
CB A:ASP48 4.2 10.6 1.0
N A:GLY60 4.3 12.6 1.0
HA3 A:GLY51 4.3 15.5 1.0
CA A:SER64 4.3 11.4 1.0
HA A:ALA61 4.3 12.4 1.0
HB2 A:SER64 4.3 13.8 1.0
H A:GLY63 4.3 12.9 1.0
CA A:GLY60 4.3 11.5 1.0
HA2 A:GLY60 4.4 13.8 1.0
HA A:ALA49 4.4 12.5 1.0
N A:ILE65 4.5 10.9 1.0
H A:GLY51 4.5 14.9 1.0
N A:ALA49 4.5 9.9 1.0
HB A:ILE65 4.5 13.5 1.0
OE2 A:GLU72 4.6 12.6 1.0
O A:GLY51 4.6 12.9 1.0
N A:ALA61 4.6 10.6 1.0
N A:GLY63 4.7 10.7 1.0
CB A:ASP62 4.7 11.7 1.0
OE1 A:GLU72 4.7 12.2 1.0
HB3 A:ASP48 4.8 12.8 1.0
H A:GLY59 4.8 15.9 1.0
CA A:ASP62 4.8 11.0 1.0
C A:SER64 4.8 10.9 1.0
CA A:ALA61 4.8 10.3 1.0
HB2 A:ASP48 4.9 12.8 1.0
C A:GLY59 4.9 12.5 1.0
CA A:ALA49 4.9 10.4 1.0
CB A:SER133 4.9 14.1 1.0
HB3 A:ASP62 4.9 14.1 1.0
O A:HIS47 5.0 11.5 1.0
CA A:GLY51 5.0 12.9 1.0
C A:ASP62 5.0 11.1 1.0

Calcium binding site 2 out of 2 in 5abo

Go back to Calcium Binding Sites List in 5abo
Calcium binding site 2 out of 2 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R.


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. Mutant Vpi-Br. Mutated Residues T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K and A314R. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:10.3
occ:1.00
 O A:SER170 2.4 10.3 1.0
O A:THR189 2.4 11.3 1.0
O A:VAL192 2.4 10.4 1.0
OD2 A:ASP187 2.4 11.3 1.0
OD1 A:ASP194 2.4 11.3 1.0
OG1 A:THR189 2.5 11.9 1.0
OG A:SER170 2.5 10.1 1.0
OD1 A:ASP187 2.7 11.2 1.0
CG A:ASP187 2.9 10.9 1.0
C A:THR189 3.2 11.1 1.0
C A:SER170 3.3 9.6 1.0
CG A:ASP194 3.4 11.5 1.0
HA A:SER170 3.4 11.7 1.0
CB A:THR189 3.5 12.6 1.0
H A:ASP194 3.5 13.2 1.0
CB A:SER170 3.6 9.8 1.0
C A:VAL192 3.6 10.4 1.0
HB A:THR189 3.7 15.2 1.0
CA A:SER170 3.7 9.7 1.0
H A:THR189 3.7 14.3 1.0
H A:VAL192 3.7 13.6 1.0
OD2 A:ASP194 3.7 12.5 1.0
HB2 A:GLN196 3.8 14.9 1.0
CA A:THR189 3.8 11.6 1.0
HB A:VAL192 3.8 16.0 1.0
HA A:PRO190 3.9 13.4 1.0
HB3 A:SER170 4.1 11.8 1.0
HG21 A:ILE171 4.1 12.8 1.0
N A:ASP194 4.2 11.0 1.0
HA A:PHE193 4.2 12.2 1.0
N A:THR189 4.2 11.9 1.0
N A:PRO190 4.2 11.4 1.0
HB2 A:SER170 4.3 11.8 1.0
H A:PHE197 4.4 13.5 1.0
N A:VAL192 4.4 11.3 1.0
CA A:VAL192 4.4 10.9 1.0
CB A:ASP187 4.5 11.2 1.0
CA A:PRO190 4.5 11.2 1.0
O A:ASP194 4.5 10.9 1.0
N A:ILE171 4.5 10.1 1.0
HG23 A:ILE171 4.6 12.8 1.0
H A:GLN196 4.6 14.3 1.0
HA A:ILE171 4.6 12.2 1.0
O A:HOH2294 4.6 11.6 1.0
CB A:VAL192 4.6 13.4 1.0
CB A:ASP194 4.6 12.2 1.0
N A:PHE193 4.6 10.2 1.0
HA A:THR189 4.7 13.9 1.0
HB2 A:ASP187 4.7 13.5 1.0
CB A:GLN196 4.7 12.4 1.0
CA A:PHE193 4.8 10.2 1.0
CA A:ASP194 4.8 11.6 1.0
HB3 A:ASP187 4.8 13.5 1.0
CG2 A:ILE171 4.8 10.6 1.0
CG2 A:THR189 4.8 13.4 1.0
C A:ASP194 4.9 11.0 1.0
HB2 A:PHE197 4.9 13.0 1.0
C A:PHE193 4.9 10.5 1.0
HB3 A:ASP194 5.0 14.6 1.0
C A:PRO190 5.0 10.5 1.0

Reference:

V.Saez-Jimenez, E.Fernendez-Fueyo, F.J.Medrano, A.Romero, A.T.Martinez, F.J.Ruiz-Duenas. Improving the pH-Stability of Versatile Peroxidase By Comparative Structural Analysis with A Naturally-Stable Manganese Peroxidase. Plos One V. 10 40984 2015.
ISSN: ISSN 1932-6203
PubMed: 26496708
DOI: 10.1371/JOURNAL.PONE.0140984
Page generated: Sun Jul 14 16:29:16 2024

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