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Calcium in PDB 2vka: Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase

Enzymatic activity of Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase

All present enzymatic activity of Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase:
1.11.1.16;

Protein crystallography data

The structure of Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase, PDB code: 2vka was solved by F.J.Ruiz-Duenas, M.Morales, M.J.Mate, A.Romero, M.J.Martinez, A.Smith, A.T.Martinez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.12 / 2.00
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 96.290, 96.290, 98.530, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.5

Other elements in 2vka:

The structure of Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase also contains other interesting chemical elements:

Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase (pdb code 2vka). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase, PDB code: 2vka:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2vka

Go back to Calcium Binding Sites List in 2vka
Calcium binding site 1 out of 2 in the Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1319

b:2.0
occ:1.00
 O A:SER170 2.4 8.2 1.0
O A:THR189 2.4 9.0 1.0
O A:VAL192 2.4 7.3 1.0
OD2 A:ASP187 2.4 5.4 1.0
OD1 A:ASP194 2.5 6.6 1.0
OG A:SER170 2.6 9.0 1.0
OG1 A:THR189 2.6 6.3 1.0
OD1 A:ASP187 2.6 8.6 1.0
CG A:ASP187 2.9 7.3 1.0
C A:THR189 3.3 7.4 1.0
C A:SER170 3.3 7.4 1.0
CG A:ASP194 3.5 8.7 1.0
CB A:THR189 3.6 6.7 1.0
C A:VAL192 3.6 7.5 1.0
CB A:SER170 3.7 6.9 1.0
CA A:SER170 3.7 7.3 1.0
OD2 A:ASP194 3.8 6.2 1.0
CA A:THR189 3.9 6.6 1.0
N A:ASP194 4.2 7.7 1.0
N A:THR189 4.2 7.0 1.0
N A:PRO190 4.3 7.3 1.0
N A:VAL192 4.4 8.0 1.0
CA A:VAL192 4.4 7.4 1.0
CB A:ASP187 4.4 7.0 1.0
O A:ASP194 4.5 8.1 1.0
CB A:VAL192 4.5 7.3 1.0
N A:ILE171 4.5 7.2 1.0
O A:HOH2260 4.5 2.0 1.0
CA A:PRO190 4.5 7.2 1.0
CB A:GLN196 4.6 7.4 1.0
N A:PHE193 4.6 7.3 1.0
CB A:ASP194 4.7 7.1 1.0
CA A:PHE193 4.8 7.3 1.0
CA A:ASP194 4.8 8.2 1.0
CG2 A:ILE171 4.8 6.0 1.0
C A:ASP194 4.8 8.6 1.0
CG2 A:THR189 4.9 5.9 1.0
C A:PHE193 5.0 6.8 1.0
C A:PRO190 5.0 7.5 1.0

Calcium binding site 2 out of 2 in 2vka

Go back to Calcium Binding Sites List in 2vka
Calcium binding site 2 out of 2 in the Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1321

b:2.4
occ:1.00
 O A:HOH2074 2.4 2.0 1.0
O A:GLY60 2.4 4.7 1.0
OD1 A:ASP62 2.4 5.4 1.0
OD1 A:ASP48 2.5 6.2 1.0
O A:ASP48 2.5 7.7 1.0
OG A:SER64 2.6 6.5 1.0
O A:HOH2103 2.7 2.0 1.0
C A:ASP48 3.4 7.9 1.0
CG A:ASP48 3.4 6.1 1.0
CG A:ASP62 3.5 6.3 1.0
CB A:SER64 3.6 3.9 1.0
C A:GLY60 3.6 6.0 1.0
CA A:ASP48 3.8 7.3 1.0
OD2 A:ASP62 3.9 4.9 1.0
N A:SER64 4.0 5.4 1.0
O A:HOH2083 4.1 2.0 1.0
N A:ASP62 4.2 5.1 1.0
OD2 A:ASP48 4.2 8.5 1.0
CB A:ASP48 4.2 6.5 1.0
CA A:GLY60 4.3 5.8 1.0
CA A:SER64 4.3 5.6 1.0
N A:GLY60 4.3 5.9 1.0
N A:ILE65 4.4 5.8 1.0
O A:GLY51 4.5 7.3 1.0
N A:ALA49 4.5 7.1 1.0
OE2 A:GLU72 4.6 7.9 1.0
N A:GLY63 4.6 5.4 1.0
N A:ALA61 4.7 6.5 1.0
OE1 A:GLU72 4.7 6.9 1.0
CB A:ASP62 4.7 4.9 1.0
C A:SER64 4.8 5.2 1.0
CA A:GLY51 4.8 7.9 1.0
CA A:ASP62 4.8 6.0 1.0
CA A:ALA61 4.9 5.8 1.0
CA A:ALA49 4.9 7.1 1.0
C A:GLY59 4.9 4.8 1.0
N A:GLY51 4.9 7.9 1.0

Reference:

F.J.Ruiz-Duenas, M.Morales, M.J.Mate, A.Romero, M.J.Martinez, A.Smith, A.T.Martinez. Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase Biochemistry V. 47 1685 2008.
ISSN: ISSN 0006-2960
PubMed: 18201105
DOI: 10.1021/BI7020298
Page generated: Tue Jul 8 08:38:57 2025

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