Atomistry » Calcium » PDB 5fk0-5g38 » 5fnb
Atomistry »
  Calcium »
    PDB 5fk0-5g38 »
      5fnb »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy