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:
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 Jul 13 22:44:44 2024
|
