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Calcium in PDB 4blz: Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI

Enzymatic activity of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI

All present enzymatic activity of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI:
1.11.1.16;

Protein crystallography data

The structure of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI, PDB code: 4blz 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) 49.085 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.540, 38.620, 98.190, 90.00, 91.15, 90.00
R / Rfree (%) 22.31 / 27.18

Other elements in 4blz:

The structure of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI (pdb code 4blz). 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 of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI, PDB code: 4blz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4blz

Go back to Calcium Binding Sites List in 4blz
Calcium binding site 1 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca400

b:19.5
occ:1.00
 O A:SER171 2.7 13.6 1.0
O A:VAL193 2.7 19.6 1.0
OD1 A:ASP195 2.8 19.5 1.0
O A:THR190 2.8 19.8 1.0
OD2 A:ASP188 2.9 16.1 1.0
OG1 A:THR190 2.9 24.4 1.0
OG A:SER171 3.0 15.7 1.0
OD1 A:ASP188 3.0 16.9 1.0
CG A:ASP188 3.3 16.9 1.0
C A:THR190 3.4 19.1 1.0
CG A:ASP195 3.5 19.5 1.0
C A:SER171 3.6 13.4 1.0
OD2 A:ASP195 3.7 20.8 1.0
CB A:THR190 3.8 25.2 1.0
CA A:SER171 3.8 14.3 1.0
C A:VAL193 3.9 19.5 1.0
CB A:SER171 3.9 15.4 1.0
CA A:THR190 3.9 19.8 1.0
N A:ASP195 4.1 17.9 1.0
N A:THR190 4.2 20.2 1.0
N A:PRO191 4.2 17.2 1.0
CA A:PRO191 4.4 17.2 1.0
N A:VAL193 4.5 17.7 1.0
CB A:VAL193 4.5 18.6 1.0
CA A:VAL193 4.5 18.6 1.0
CB A:GLN197 4.6 14.8 1.0
CB A:ASP195 4.6 18.9 1.0
O A:HOH2204 4.7 14.6 1.0
O A:ASP195 4.7 17.5 1.0
CA A:ASP195 4.7 18.3 1.0
N A:ILE172 4.8 13.7 1.0
CB A:ASP188 4.8 16.7 1.0
C A:ASP195 4.8 17.1 1.0
N A:PHE194 4.9 19.3 1.0
C A:PRO191 4.9 17.2 1.0
CA A:PHE194 4.9 18.5 1.0
CG2 A:ILE172 4.9 15.3 1.0
C A:PHE194 5.0 18.7 1.0

Calcium binding site 2 out of 4 in 4blz

Go back to Calcium Binding Sites List in 4blz
Calcium binding site 2 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:28.1
occ:1.00
 O A:GLY61 2.8 19.6 1.0
O A:ASP49 2.9 17.1 1.0
OD1 A:ASP63 2.9 29.4 1.0
O A:HOH2072 3.0 24.9 1.0
O A:HOH2064 3.0 24.9 1.0
OD1 A:ASP49 3.0 24.8 1.0
OG A:SER65 3.0 23.9 1.0
C A:ASP49 3.5 18.4 1.0
CG A:ASP49 3.7 24.0 1.0
C A:GLY61 3.8 20.6 1.0
CB A:SER65 3.8 25.0 1.0
CA A:ASP49 3.8 20.1 1.0
CG A:ASP63 3.9 30.1 1.0
N A:SER65 4.0 24.3 1.0
O A:HOH2087 4.2 19.3 1.0
N A:ASP63 4.2 22.6 1.0
OD2 A:ASP49 4.3 24.4 1.0
OD2 A:ASP63 4.3 32.8 1.0
CB A:ASP49 4.4 21.8 1.0
CA A:SER65 4.4 24.9 1.0
O A:GLY52 4.4 19.2 1.0
OE2 A:GLU73 4.4 29.9 1.0
N A:ILE66 4.5 24.4 1.0
N A:GLY61 4.5 21.8 1.0
N A:ALA50 4.6 19.5 1.0
CA A:GLY61 4.6 20.9 1.0
N A:GLY64 4.6 24.1 1.0
OE1 A:GLU73 4.7 28.2 1.0
CA A:GLY52 4.7 19.2 1.0
N A:ALA62 4.7 20.7 1.0
CB A:SER134 4.8 25.9 1.0
CA A:ALA62 4.8 21.5 1.0
C A:SER65 4.8 25.3 1.0
N A:GLY52 4.9 19.4 1.0
O A:HIS48 4.9 15.3 1.0
C A:GLY60 5.0 22.4 1.0
C A:GLY52 5.0 19.6 1.0

Calcium binding site 3 out of 4 in 4blz

Go back to Calcium Binding Sites List in 4blz
Calcium binding site 3 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca400

b:19.7
occ:1.00
 O B:SER171 2.8 18.0 1.0
O B:VAL193 2.8 23.4 1.0
OD1 B:ASP195 2.8 19.1 1.0
O B:THR190 2.8 19.1 1.0
OD2 B:ASP188 2.9 18.9 1.0
OG B:SER171 2.9 18.6 1.0
OG1 B:THR190 3.0 22.9 1.0
OD1 B:ASP188 3.0 19.2 1.0
CG B:ASP188 3.3 18.5 1.0
C B:THR190 3.4 19.2 1.0
CG B:ASP195 3.5 18.5 1.0
C B:SER171 3.6 17.3 1.0
CB B:THR190 3.7 22.7 1.0
OD2 B:ASP195 3.7 18.6 1.0
CA B:SER171 3.8 17.1 1.0
CB B:SER171 3.8 18.1 1.0
C B:VAL193 3.8 22.5 1.0
CA B:THR190 3.9 21.3 1.0
N B:PRO191 4.2 19.0 1.0
N B:THR190 4.2 20.9 1.0
N B:ASP195 4.2 18.3 1.0
CB B:VAL193 4.4 22.2 1.0
N B:VAL193 4.4 20.3 1.0
CA B:PRO191 4.4 18.5 1.0
CA B:VAL193 4.5 21.8 1.0
O B:HOH2210 4.6 14.2 1.0
CB B:GLN197 4.7 20.0 1.0
O B:ASP195 4.7 20.0 1.0
CB B:ASP195 4.7 19.2 1.0
N B:ILE172 4.8 17.1 1.0
CB B:ASP188 4.8 16.5 1.0
N B:PHE194 4.8 21.4 1.0
CA B:ASP195 4.9 19.0 1.0
C B:PRO191 4.9 17.8 1.0
CA B:PHE194 4.9 19.3 1.0
C B:ASP195 4.9 19.6 1.0

Calcium binding site 4 out of 4 in 4blz

Go back to Calcium Binding Sites List in 4blz
Calcium binding site 4 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Fungal Versatile Peroxidase I From Pleurotus Ostreatus - Crystal Form VI within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:26.6
occ:1.00
 O B:GLY61 2.8 25.3 1.0
OD1 B:ASP63 2.8 23.4 1.0
O B:ASP49 2.9 18.8 1.0
OG B:SER65 3.0 21.2 1.0
O B:HOH2061 3.0 22.0 1.0
OD1 B:ASP49 3.0 27.5 1.0
O B:HOH2066 3.1 26.9 1.0
CG B:ASP63 3.5 24.1 1.0
CG B:ASP49 3.6 25.2 1.0
C B:ASP49 3.6 19.3 1.0
OD2 B:ASP63 3.8 25.4 1.0
CB B:SER65 3.9 22.0 1.0
CA B:ASP49 3.9 21.8 1.0
C B:GLY61 3.9 25.0 1.0
N B:SER65 3.9 20.7 1.0
OD2 B:ASP49 4.0 23.7 1.0
N B:ASP63 4.0 20.9 1.0
O B:HOH2080 4.2 20.2 1.0
CB B:ASP49 4.3 23.6 1.0
CA B:SER65 4.4 21.5 1.0
N B:ILE66 4.5 20.6 1.0
N B:GLY64 4.5 19.6 1.0
N B:GLY61 4.5 24.5 1.0
O B:GLY52 4.5 22.9 1.0
OE2 B:GLU73 4.6 21.0 1.0
N B:ALA50 4.6 18.7 1.0
CB B:ASP63 4.7 22.8 1.0
CA B:GLY61 4.7 25.6 1.0
CA B:ASP63 4.8 21.2 1.0
OE1 B:GLU73 4.8 20.9 1.0
CA B:ALA62 4.8 21.9 1.0
N B:ALA62 4.8 23.7 1.0
C B:SER65 4.9 20.0 1.0
C B:ASP63 4.9 20.2 1.0
C B:GLY60 4.9 24.4 1.0
C B:ALA62 5.0 21.2 1.0
CA B:GLY52 5.0 22.6 1.0
C B:GLY64 5.0 21.3 1.0

Reference:

E.Fernandez-Fueyo, F.J.Ruiz-Duenas, M.J.Martinez, A.Romero, K.E.Hammel, F.J.Medrano, A.T.Martinez. Ligninolytic Peroxidase Genes in the Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic and Stability Properties, and Lignin-Degrading Ability. Biotechnol.Biofuels V. 7 2 2014.
ISSN: ISSN 1754-6834
PubMed: 24387130
DOI: 10.1186/1754-6834-7-2
Page generated: Sat Jul 13 22:43:27 2024

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