Calcium in PDB 5abn: Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K.

Enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K.

All present enzymatic activity of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K.:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K., PDB code: 5abn 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) 38.499 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.547, 68.498, 84.916, 90.00, 90.00, 90.00
R / Rfree (%) 20.64 / 27.48

Other elements in 5abn:

The structure of Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
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. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K. (pdb code 5abn). 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. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K., PDB code: 5abn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5abn

Go back to Calcium Binding Sites List in 5abn
Calcium binding site 1 out of 2 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K.


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. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:39.1
occ:1.00
 O A:HOH2009 2.4 33.0 1.0
OD1 A:ASP48 2.4 30.3 1.0
O A:ASP48 2.4 28.8 1.0
O A:GLY60 2.4 39.3 1.0
O A:HOH2006 2.4 30.0 1.0
OD1 A:ASP62 2.5 38.9 1.0
OG A:SER64 2.6 33.7 1.0
C A:ASP48 3.2 34.2 1.0
CG A:ASP48 3.3 33.7 1.0
CG A:ASP62 3.5 37.9 1.0
CB A:SER64 3.6 38.1 1.0
CA A:ASP48 3.6 40.8 1.0
C A:GLY60 3.6 43.6 1.0
N A:SER64 4.0 42.9 1.0
OD2 A:ASP62 4.1 48.8 1.0
CB A:ASP48 4.1 31.9 1.0
OD2 A:ASP48 4.1 33.7 1.0
N A:ASP62 4.1 35.8 1.0
CA A:SER64 4.3 38.3 1.0
O A:HOH2011 4.3 39.1 1.0
N A:ALA49 4.4 34.5 1.0
N A:GLY60 4.4 46.0 1.0
CA A:GLY60 4.4 39.3 1.0
N A:ILE65 4.5 37.4 1.0
O A:GLY51 4.5 58.0 1.0
OE2 A:GLU72 4.5 35.4 1.0
N A:ALA61 4.7 40.3 1.0
CB A:ASP62 4.7 36.0 1.0
CA A:GLY51 4.7 37.4 1.0
N A:GLY63 4.7 40.3 1.0
OE1 A:GLU72 4.8 39.8 1.0
C A:SER64 4.8 34.6 1.0
CA A:ASP62 4.8 46.0 1.0
CA A:ALA49 4.8 36.4 1.0
CB A:SER133 4.9 42.9 1.0
CA A:ALA61 4.9 39.7 1.0
O A:HIS47 4.9 34.3 1.0
N A:GLY51 5.0 40.4 1.0
N A:ASP48 5.0 29.9 1.0
C A:ASP62 5.0 44.9 1.0

Calcium binding site 2 out of 2 in 5abn

Go back to Calcium Binding Sites List in 5abn
Calcium binding site 2 out of 2 in the Crystal Structure Analysis of Fungal Versatile Peroxidase From Pleurotus Eryngii. Mutant Vpi. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K.


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. Mutated Residues D69S, T70D, S86E, D146T, Q202L, H232E, Q239R and S301K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:57.0
occ:1.00
 OD2 A:ASP187 2.3 62.0 1.0
O A:SER170 2.4 59.4 1.0
OG A:SER170 2.4 65.8 1.0
O A:THR189 2.6 57.6 1.0
OD1 A:ASP194 2.6 84.3 1.0
O A:VAL192 2.6 76.9 1.0
OG1 A:THR189 2.7 73.5 1.0
OD1 A:ASP187 2.7 62.4 1.0
CG A:ASP187 2.9 65.7 1.0
C A:SER170 3.2 50.7 1.0
C A:THR189 3.3 58.3 1.0
CB A:SER170 3.5 55.8 1.0
CA A:SER170 3.5 53.1 1.0
CG A:ASP194 3.6 75.5 1.0
CB A:THR189 3.8 65.1 1.0
C A:VAL192 3.8 78.4 1.0
CA A:THR189 3.9 61.3 1.0
N A:ASP194 4.0 74.5 1.0
O A:ASP194 4.1 74.6 1.0
OD2 A:ASP194 4.1 90.5 1.0
N A:PRO190 4.2 54.2 1.0
N A:THR189 4.2 63.8 1.0
CA A:PRO190 4.4 55.4 1.0
N A:ILE171 4.4 51.2 1.0
CB A:ASP187 4.4 60.8 1.0
CB A:GLN196 4.5 80.2 1.0
N A:VAL192 4.6 74.7 1.0
CA A:VAL192 4.6 78.7 1.0
CA A:ASP194 4.7 67.6 1.0
C A:ASP194 4.7 79.9 1.0
CB A:ASP194 4.7 64.2 1.0
N A:PHE193 4.8 79.9 1.0
CB A:VAL192 4.8 75.5 1.0
C A:PRO190 4.9 61.6 1.0
CA A:PHE193 4.9 73.0 1.0
CA A:ILE171 4.9 54.2 1.0
C A:PHE193 5.0 77.7 1.0
N A:PHE197 5.0 69.4 1.0
N A:SER170 5.0 43.1 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: Sat Dec 12 05:17:15 2020

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