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Calcium in PDB 4bm1: Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I

Enzymatic activity of Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I

All present enzymatic activity of Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I:
1.11.1.13;

Protein crystallography data

The structure of Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I, PDB code: 4bm1 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) 38.148 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.990, 75.370, 75.610, 69.75, 75.69, 75.82
R / Rfree (%) 13.12 / 14.73

Other elements in 4bm1:

The structure of Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I (pdb code 4bm1). 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 Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I, PDB code: 4bm1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4bm1

Go back to Calcium Binding Sites List in 4bm1
Calcium binding site 1 out of 4 in the Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I


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 Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:7.2
occ:1.00
OD1 A:ASP49 2.3 8.2 1.0
O A:HOH2133 2.4 7.9 1.0
O A:GLY67 2.4 7.6 1.0
OD1 A:ASP69 2.4 7.6 1.0
O A:HOH2119 2.4 8.5 1.0
OG A:SER71 2.4 8.0 1.0
O A:ASP49 2.5 7.5 1.0
H A:SER71 3.3 8.9 1.0
HA A:ASP49 3.3 8.4 1.0
C A:ASP49 3.4 7.0 1.0
CG A:ASP49 3.4 7.8 1.0
H A:ASP69 3.4 8.9 1.0
CG A:ASP69 3.5 7.8 1.0
CB A:SER71 3.6 7.6 1.0
C A:GLY67 3.6 7.5 1.0
HB3 A:SER71 3.6 9.1 1.0
CA A:ASP49 3.8 7.0 1.0
H A:ILE72 3.8 9.5 1.0
N A:SER71 4.0 7.4 1.0
OD2 A:ASP69 4.0 8.1 1.0
HB2 A:SER140 4.1 11.6 1.0
O A:HOH2171 4.2 8.7 1.0
N A:ASP69 4.2 7.5 1.0
OD2 A:ASP49 4.2 8.2 1.0
CB A:ASP49 4.2 7.3 1.0
H A:GLY67 4.2 9.3 1.0
HA3 A:GLY52 4.3 9.2 1.0
CA A:SER71 4.3 7.4 1.0
N A:GLY67 4.3 7.7 1.0
HA A:ALA68 4.3 8.6 1.0
HB2 A:SER71 4.3 9.1 1.0
H A:GLY52 4.3 8.8 1.0
H A:GLY70 4.4 8.8 1.0
CA A:GLY67 4.4 7.4 1.0
HA A:ALA50 4.4 8.7 1.0
N A:ILE72 4.4 7.9 1.0
HA2 A:GLY67 4.4 8.9 1.0
N A:ALA50 4.5 7.2 1.0
HB A:ILE72 4.5 9.9 1.0
O A:GLY52 4.6 7.7 1.0
OE2 A:GLU79 4.6 9.0 1.0
N A:ALA68 4.6 7.5 1.0
CB A:ASP69 4.7 8.2 1.0
N A:GLY70 4.7 7.3 1.0
OE1 A:GLU79 4.7 8.6 1.0
H A:GLY66 4.8 10.0 1.0
HB3 A:ASP49 4.8 8.7 1.0
CA A:ASP69 4.8 7.9 1.0
C A:SER71 4.8 7.9 1.0
HB2 A:ASP49 4.9 8.7 1.0
CA A:ALA68 4.9 7.1 1.0
CA A:ALA50 4.9 7.3 1.0
C A:GLY66 4.9 7.9 1.0
O A:HIS48 4.9 8.3 1.0
HB3 A:ASP69 4.9 9.8 1.0
CA A:GLY52 5.0 7.7 1.0
HG23 A:ILE72 5.0 10.3 1.0
C A:ASP69 5.0 7.9 1.0

Calcium binding site 2 out of 4 in 4bm1

Go back to Calcium Binding Sites List in 4bm1
Calcium binding site 2 out of 4 in the Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I


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 Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:6.2
occ:1.00
O A:SER177 2.4 6.2 1.0
OD2 A:ASP194 2.4 6.2 1.0
O A:THR196 2.4 7.0 1.0
OD1 A:ASP201 2.4 6.6 1.0
O A:ASP199 2.4 6.7 1.0
OG A:SER177 2.5 6.4 1.0
OG1 A:THR196 2.5 6.9 1.0
OD1 A:ASP194 2.7 6.3 1.0
CG A:ASP194 2.9 5.9 1.0
C A:THR196 3.2 6.7 1.0
H A:ASP201 3.3 7.9 1.0
C A:SER177 3.3 5.9 1.0
CG A:ASP201 3.4 6.7 1.0
HA A:SER177 3.4 7.1 1.0
CB A:THR196 3.6 6.6 1.0
CB A:SER177 3.6 6.6 1.0
HB2 A:ASP199 3.6 10.6 1.0
C A:ASP199 3.7 7.0 1.0
CA A:SER177 3.7 5.9 1.0
H A:THR196 3.7 7.9 1.0
HB A:THR196 3.7 7.9 1.0
H A:ASP199 3.7 9.0 1.0
HB2 A:GLN203 3.8 7.7 1.0
CA A:THR196 3.8 7.1 1.0
OD2 A:ASP201 3.9 7.5 1.0
HA A:PRO197 3.9 8.8 1.0
HB3 A:SER177 4.1 8.0 1.0
N A:ASP201 4.1 6.6 1.0
N A:THR196 4.2 6.6 1.0
HG11 A:VAL178 4.2 8.2 1.0
N A:PRO197 4.2 7.0 1.0
HB2 A:SER177 4.3 8.0 1.0
HA A:PHE200 4.3 7.9 1.0
H A:PHE204 4.4 7.3 1.0
N A:ASP199 4.4 7.5 1.0
CB A:ASP199 4.4 8.9 1.0
CA A:ASP199 4.4 7.4 1.0
CB A:ASP194 4.4 6.2 1.0
HG13 A:VAL178 4.4 8.2 1.0
CA A:PRO197 4.5 7.3 1.0
O A:ASP201 4.5 6.8 1.0
H A:GLN203 4.5 7.8 1.0
N A:VAL178 4.6 5.9 1.0
HA A:VAL178 4.6 7.2 1.0
CB A:ASP201 4.6 6.8 1.0
O A:HOH2376 4.6 7.8 1.0
N A:PHE200 4.7 6.5 1.0
HB2 A:ASP194 4.7 7.4 1.0
CA A:ASP201 4.7 6.6 1.0
HB3 A:ASP199 4.7 10.6 1.0
HA A:THR196 4.7 8.5 1.0
CB A:GLN203 4.8 6.4 1.0
HB3 A:ASP194 4.8 7.4 1.0
C A:ASP201 4.8 6.1 1.0
CG1 A:VAL178 4.8 6.8 1.0
HB2 A:PHE204 4.8 7.5 1.0
CG2 A:THR196 4.8 7.1 1.0
CA A:PHE200 4.9 6.6 1.0
HB3 A:ASP201 4.9 8.1 1.0
C A:PRO197 5.0 7.4 1.0
HG21 A:THR196 5.0 8.5 1.0

Calcium binding site 3 out of 4 in 4bm1

Go back to Calcium Binding Sites List in 4bm1
Calcium binding site 3 out of 4 in the Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I


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 Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:7.0
occ:1.00
OD1 B:ASP49 2.3 7.8 1.0
O B:HOH2120 2.4 8.0 1.0
O B:GLY67 2.4 7.1 1.0
OG B:SER71 2.4 7.5 1.0
O B:HOH2108 2.4 7.9 1.0
OD1 B:ASP69 2.4 7.8 1.0
O B:ASP49 2.5 7.1 1.0
H B:SER71 3.3 8.8 1.0
HA B:ASP49 3.3 8.3 1.0
C B:ASP49 3.4 6.9 1.0
CG B:ASP49 3.4 7.7 1.0
H B:ASP69 3.4 8.6 1.0
CG B:ASP69 3.5 7.6 1.0
CB B:SER71 3.6 7.6 1.0
C B:GLY67 3.6 6.9 1.0
HB3 B:SER71 3.6 9.1 1.0
CA B:ASP49 3.8 6.9 1.0
H B:ILE72 3.8 9.2 1.0
N B:SER71 4.0 7.3 1.0
OD2 B:ASP69 4.0 8.0 1.0
HB2 B:SER140 4.1 10.7 1.0
O B:HOH2158 4.2 8.6 1.0
N B:ASP69 4.2 7.2 1.0
OD2 B:ASP49 4.2 8.1 1.0
CB B:ASP49 4.2 7.2 1.0
H B:GLY67 4.3 9.2 1.0
HA3 B:GLY52 4.3 9.4 1.0
CA B:SER71 4.3 7.8 1.0
HB2 B:SER71 4.3 9.1 1.0
HA B:ALA68 4.3 8.3 1.0
N B:GLY67 4.3 7.7 1.0
CA B:GLY67 4.3 7.1 1.0
H B:GLY70 4.4 9.3 1.0
H B:GLY52 4.4 8.8 1.0
HA2 B:GLY67 4.4 8.6 1.0
HA B:ALA50 4.4 8.3 1.0
N B:ILE72 4.4 7.7 1.0
N B:ALA50 4.5 6.7 1.0
HB B:ILE72 4.5 9.9 1.0
O B:GLY52 4.6 7.6 1.0
OE2 B:GLU79 4.6 8.8 1.0
N B:ALA68 4.6 7.1 1.0
CB B:ASP69 4.7 8.0 1.0
N B:GLY70 4.7 7.8 1.0
OE1 B:GLU79 4.7 8.4 1.0
H B:GLY66 4.8 10.1 1.0
HB3 B:ASP49 4.8 8.7 1.0
C B:SER71 4.8 7.7 1.0
CA B:ASP69 4.8 7.4 1.0
HB2 B:ASP49 4.8 8.7 1.0
CA B:ALA68 4.9 6.9 1.0
CA B:ALA50 4.9 6.9 1.0
C B:GLY66 4.9 8.1 1.0
HB3 B:ASP69 4.9 9.5 1.0
O B:HIS48 4.9 8.2 1.0
CA B:GLY52 4.9 7.8 1.0
HG23 B:ILE72 5.0 10.2 1.0
C B:ASP69 5.0 7.9 1.0

Calcium binding site 4 out of 4 in 4bm1

Go back to Calcium Binding Sites List in 4bm1
Calcium binding site 4 out of 4 in the Crystal Structure of Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I


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 Manganese Peroxidase 4 From Pleurotus Ostreatus - Crystal Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:6.0
occ:1.00
O B:SER177 2.4 5.8 1.0
O B:THR196 2.4 6.6 1.0
OD2 B:ASP194 2.4 6.2 1.0
OD1 B:ASP201 2.4 6.6 1.0
O B:ASP199 2.5 6.4 1.0
OG B:SER177 2.5 6.3 1.0
OG1 B:THR196 2.5 7.0 1.0
OD1 B:ASP194 2.7 6.3 1.0
CG B:ASP194 2.9 6.1 1.0
C B:THR196 3.3 6.4 1.0
H B:ASP201 3.3 7.8 1.0
C B:SER177 3.3 5.6 1.0
CG B:ASP201 3.4 6.5 1.0
HA B:SER177 3.4 6.8 1.0
CB B:THR196 3.6 7.0 1.0
CB B:SER177 3.6 6.2 1.0
HB2 B:ASP199 3.6 9.8 1.0
C B:ASP199 3.7 7.1 1.0
CA B:SER177 3.7 5.6 1.0
H B:THR196 3.7 7.6 1.0
HB B:THR196 3.7 8.4 1.0
H B:ASP199 3.8 8.4 1.0
HB2 B:GLN203 3.8 7.7 1.0
CA B:THR196 3.8 6.8 1.0
OD2 B:ASP201 3.8 7.3 1.0
HA B:PRO197 3.8 8.6 1.0
HB3 B:SER177 4.1 7.5 1.0
N B:ASP201 4.1 6.5 1.0
N B:THR196 4.2 6.3 1.0
HG11 B:VAL178 4.2 8.8 1.0
N B:PRO197 4.2 6.9 1.0
HB2 B:SER177 4.3 7.5 1.0
HA B:PHE200 4.3 7.7 1.0
H B:PHE204 4.4 7.3 1.0
CB B:ASP199 4.4 8.2 1.0
N B:ASP199 4.4 7.0 1.0
CA B:ASP199 4.4 7.1 1.0
HG13 B:VAL178 4.4 8.8 1.0
CA B:PRO197 4.4 7.2 1.0
CB B:ASP194 4.5 6.0 1.0
H B:GLN203 4.5 8.2 1.0
O B:ASP201 4.5 6.4 1.0
N B:VAL178 4.6 6.0 1.0
CB B:ASP201 4.6 6.3 1.0
HA B:VAL178 4.6 7.2 1.0
O B:HOH2342 4.6 7.7 1.0
N B:PHE200 4.7 6.6 1.0
CA B:ASP201 4.7 6.4 1.0
HA B:THR196 4.7 8.2 1.0
HB2 B:ASP194 4.8 7.2 1.0
HB3 B:ASP199 4.8 9.8 1.0
C B:ASP201 4.8 6.3 1.0
CB B:GLN203 4.8 6.4 1.0
CG1 B:VAL178 4.8 7.3 1.0
HB3 B:ASP194 4.8 7.2 1.0
HB2 B:PHE204 4.8 7.0 1.0
CG2 B:THR196 4.9 7.2 1.0
HB3 B:ASP201 4.9 7.6 1.0
CA B:PHE200 4.9 6.4 1.0
C B:PRO197 5.0 6.8 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 Dec 12 04:41:15 2020

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