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Calcium in PDB 5fnb: Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R

Enzymatic activity of Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R

All present enzymatic activity of Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R:
1.11.1.16; 1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R, PDB code: 5fnb 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) 49.015 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.060, 106.010, 107.600, 90.00, 90.00, 90.00
R / Rfree (%) 18.51 / 21.94

Other elements in 5fnb:

The structure of Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R 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 From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R (pdb code 5fnb). 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 From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R, PDB code: 5fnb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5fnb

Go back to Calcium Binding Sites List in 5fnb
Calcium binding site 1 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R


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 From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:14.8
occ:1.00
 OD1 A:ASP48 2.4 15.8 1.0
O A:ASP48 2.4 14.7 1.0
OG A:SER64 2.4 14.9 1.0
O A:HOH2069 2.4 16.2 1.0
O A:GLY60 2.4 16.0 1.0
O A:HOH2076 2.5 15.3 1.0
OD1 A:ASP62 2.5 17.5 1.0
C A:ASP48 3.3 16.8 1.0
CG A:ASP48 3.4 16.6 1.0
CG A:ASP62 3.6 17.4 1.0
C A:GLY60 3.6 15.5 1.0
CB A:SER64 3.6 15.6 1.0
CA A:ASP48 3.8 14.3 1.0
N A:SER64 4.0 14.4 1.0
OD2 A:ASP62 4.1 17.8 1.0
N A:ASP62 4.2 14.9 1.0
CB A:ASP48 4.2 15.7 1.0
OD2 A:ASP48 4.2 17.4 1.0
O A:HOH2089 4.3 13.3 1.0
CA A:SER64 4.3 13.4 1.0
CA A:GLY60 4.4 16.7 1.0
N A:GLY60 4.4 17.2 1.0
N A:ILE65 4.5 12.4 1.0
N A:ALA49 4.5 14.6 1.0
N A:GLY63 4.5 15.4 1.0
OE2 A:GLU72 4.6 15.4 1.0
OE1 A:GLU72 4.6 17.8 1.0
O A:GLY51 4.6 17.7 1.0
N A:ALA61 4.7 14.3 1.0
CB A:ASP62 4.7 14.0 1.0
C A:SER64 4.8 14.4 1.0
CA A:ASP62 4.8 15.3 1.0
CA A:ALA61 4.9 11.8 1.0
CA A:ALA49 4.9 13.3 1.0
CB A:SER133 4.9 16.1 1.0
O A:HIS47 4.9 14.8 1.0
CA A:GLY51 4.9 14.0 1.0
C A:ASP62 5.0 15.8 1.0
C A:GLY63 5.0 14.3 1.0

Calcium binding site 2 out of 4 in 5fnb

Go back to Calcium Binding Sites List in 5fnb
Calcium binding site 2 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R


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 From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:15.3
occ:1.00
 OD2 A:ASP187 2.3 14.9 1.0
O A:SER170 2.4 12.7 1.0
O A:VAL192 2.4 14.5 1.0
O A:THR189 2.4 15.3 1.0
OG A:SER170 2.4 16.1 1.0
OD1 A:ASP194 2.5 15.1 1.0
OG1 A:THR189 2.5 16.6 1.0
OD1 A:ASP187 2.7 17.1 1.0
CG A:ASP187 2.9 13.4 1.0
C A:THR189 3.2 14.3 1.0
C A:SER170 3.3 13.6 1.0
CG A:ASP194 3.4 15.6 1.0
CB A:THR189 3.5 15.1 1.0
CB A:SER170 3.6 13.3 1.0
C A:VAL192 3.6 14.3 1.0
CA A:SER170 3.6 11.8 1.0
CA A:THR189 3.8 14.6 1.0
OD2 A:ASP194 3.8 16.1 1.0
N A:ASP194 4.1 16.4 1.0
N A:THR189 4.1 15.0 1.0
N A:PRO190 4.2 14.7 1.0
CB A:ASP187 4.4 14.7 1.0
N A:VAL192 4.4 14.1 1.0
CA A:VAL192 4.4 15.2 1.0
N A:ILE171 4.5 14.2 1.0
CA A:PRO190 4.5 15.0 1.0
O A:ASP194 4.5 15.2 1.0
O A:HOH2209 4.5 10.8 1.0
N A:PHE193 4.6 16.2 1.0
CB A:GLN196 4.6 13.7 1.0
CB A:ASP194 4.6 15.5 1.0
CB A:VAL192 4.7 16.4 1.0
CA A:PHE193 4.7 14.2 1.0
CA A:ASP194 4.7 15.6 1.0
C A:ASP194 4.8 17.6 1.0
CG2 A:ILE171 4.9 14.6 1.0
CG2 A:THR189 4.9 15.5 1.0
C A:PHE193 4.9 14.5 1.0
C A:PRO190 5.0 14.1 1.0
N A:PHE197 5.0 15.4 1.0

Calcium binding site 3 out of 4 in 5fnb

Go back to Calcium Binding Sites List in 5fnb
Calcium binding site 3 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R


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 From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:16.3
occ:1.00
 O B:HOH2049 2.4 16.4 1.0
O B:GLY60 2.4 15.4 1.0
O B:ASP48 2.4 13.1 1.0
O B:HOH2053 2.4 14.7 1.0
OD1 B:ASP48 2.5 16.1 1.0
OD1 B:ASP62 2.5 18.5 1.0
OG B:SER64 2.5 15.2 1.0
C B:ASP48 3.3 17.7 1.0
CG B:ASP48 3.4 16.7 1.0
CG B:ASP62 3.5 16.0 1.0
C B:GLY60 3.5 16.4 1.0
CB B:SER64 3.6 17.8 1.0
CA B:ASP48 3.8 15.8 1.0
N B:SER64 3.9 13.8 1.0
OD2 B:ASP62 4.0 14.5 1.0
N B:ASP62 4.1 15.8 1.0
OD2 B:ASP48 4.2 15.7 1.0
CB B:ASP48 4.2 15.8 1.0
N B:GLY60 4.2 17.4 1.0
CA B:GLY60 4.2 17.7 1.0
O B:HOH2062 4.2 12.1 1.0
CA B:SER64 4.3 17.1 1.0
N B:ILE65 4.4 16.3 1.0
O B:GLY51 4.4 15.3 1.0
N B:ALA49 4.5 15.2 1.0
OE2 B:GLU72 4.5 19.7 1.0
N B:GLY63 4.5 16.4 1.0
N B:ALA61 4.6 15.5 1.0
OE1 B:GLU72 4.7 19.5 1.0
CB B:ASP62 4.7 17.1 1.0
CA B:GLY51 4.8 17.2 1.0
CA B:ASP62 4.8 15.2 1.0
CA B:ALA61 4.8 15.2 1.0
C B:SER64 4.8 18.4 1.0
C B:GLY59 4.9 17.2 1.0
CA B:ALA49 4.9 13.8 1.0
CB B:SER133 4.9 17.2 1.0
N B:GLY51 4.9 15.4 1.0
O B:HIS47 4.9 17.6 1.0
C B:ASP62 4.9 17.1 1.0
C B:GLY63 5.0 16.9 1.0
C B:GLY51 5.0 18.2 1.0
C B:ALA61 5.0 17.1 1.0

Calcium binding site 4 out of 4 in 5fnb

Go back to Calcium Binding Sites List in 5fnb
Calcium binding site 4 out of 4 in the Crystal Structure of Fungal Versatile Peroxidase From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R


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 From Pleurotus Eryngii Septuple Mutant E37K, H39R, V160A, T184M, Q202L, D213A & G330R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:15.8
occ:1.00
 O B:SER170 2.3 17.3 1.0
O B:THR189 2.3 19.2 1.0
O B:VAL192 2.4 19.7 1.0
OD1 B:ASP194 2.4 17.8 1.0
OD2 B:ASP187 2.4 18.5 1.0
OG B:SER170 2.4 16.3 1.0
OG1 B:THR189 2.6 19.8 1.0
OD1 B:ASP187 2.8 18.9 1.0
CG B:ASP187 3.0 19.1 1.0
C B:THR189 3.3 18.8 1.0
C B:SER170 3.3 16.8 1.0
CG B:ASP194 3.3 17.9 1.0
CB B:SER170 3.5 15.1 1.0
C B:VAL192 3.6 15.5 1.0
CA B:SER170 3.6 14.9 1.0
CB B:THR189 3.6 20.0 1.0
OD2 B:ASP194 3.7 18.2 1.0
CA B:THR189 3.9 19.8 1.0
N B:ASP194 4.1 15.4 1.0
N B:THR189 4.3 18.2 1.0
N B:PRO190 4.3 20.3 1.0
N B:VAL192 4.4 18.8 1.0
CA B:VAL192 4.4 16.7 1.0
O B:ASP194 4.4 14.5 1.0
CB B:ASP187 4.5 17.8 1.0
N B:ILE171 4.5 17.1 1.0
O B:HOH2166 4.6 21.6 1.0
CB B:ASP194 4.6 16.4 1.0
CA B:PRO190 4.6 18.6 1.0
N B:PHE193 4.6 16.0 1.0
CB B:VAL192 4.6 19.4 1.0
CA B:ASP194 4.7 16.3 1.0
CA B:PHE193 4.7 16.7 1.0
CB B:GLN196 4.8 18.4 1.0
C B:ASP194 4.8 16.8 1.0
C B:PHE193 4.9 16.9 1.0
CG2 B:ILE171 4.9 19.9 1.0
CG2 B:THR189 5.0 21.9 1.0

Reference:

V.Saez-Jimenez, S.Acebes, E.Garcia-Ruiz, A.Romero, V.Guallar, M.Alcalde, F.J.Medrano, A.T.Martinez, F.J.Ruiz-Duenas. Unveiling the Basis of Alkaline Stability of An Evolved Versatile Peroxidase. Biochem.J. V. 473 1917 2016.
ISSN: ISSN 0264-6021
PubMed: 27118867
DOI: 10.1042/BCJ20160248
Page generated: Sun Jul 14 19:16:55 2024

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