Calcium in PDB 1fhf: The Structure of Soybean Peroxidase
Enzymatic activity of The Structure of Soybean Peroxidase
All present enzymatic activity of The Structure of Soybean Peroxidase:
1.11.1.7;
Protein crystallography data
The structure of The Structure of Soybean Peroxidase, PDB code: 1fhf
was solved by
A.Henriksen,
O.Mirza,
C.Indiana,
K.Welinder,
K.Teilum,
M.Gajhede,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
11.00 /
2.80
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.454,
106.454,
104.996,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
27.1 /
28.9
|
Other elements in 1fhf:
The structure of The Structure of Soybean Peroxidase also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the The Structure of Soybean Peroxidase
(pdb code 1fhf). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
The Structure of Soybean Peroxidase, PDB code: 1fhf:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1fhf
Go back to
Calcium Binding Sites List in 1fhf
Calcium binding site 1 out
of 6 in the The Structure of Soybean Peroxidase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Structure of Soybean Peroxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:13.2
occ:1.00
|
OG
|
A:SER52
|
2.3
|
20.6
|
1.0
|
OD1
|
A:ASP43
|
2.4
|
12.4
|
1.0
|
O
|
A:VAL46
|
2.5
|
13.7
|
1.0
|
O
|
A:ASP43
|
2.5
|
13.9
|
1.0
|
O
|
A:GLY48
|
2.6
|
14.6
|
1.0
|
OD1
|
A:ASP50
|
2.7
|
19.3
|
1.0
|
C
|
A:ASP43
|
3.3
|
13.2
|
1.0
|
CG
|
A:ASP43
|
3.4
|
13.0
|
1.0
|
CB
|
A:SER52
|
3.5
|
19.0
|
1.0
|
CA
|
A:ASP43
|
3.6
|
13.0
|
1.0
|
CG2
|
A:VAL53
|
3.7
|
18.5
|
1.0
|
C
|
A:VAL46
|
3.7
|
14.7
|
1.0
|
C
|
A:GLY48
|
3.8
|
13.9
|
1.0
|
CG
|
A:ASP50
|
3.9
|
16.5
|
1.0
|
N
|
A:SER52
|
3.9
|
18.7
|
1.0
|
N
|
A:GLY48
|
4.1
|
14.7
|
1.0
|
CB
|
A:ASP43
|
4.1
|
12.7
|
1.0
|
N
|
A:ASP50
|
4.1
|
16.3
|
1.0
|
CA
|
A:SER52
|
4.2
|
18.9
|
1.0
|
N
|
A:VAL53
|
4.2
|
18.4
|
1.0
|
OD2
|
A:ASP43
|
4.3
|
13.7
|
1.0
|
OD2
|
A:ASP50
|
4.4
|
15.1
|
1.0
|
N
|
A:CYS44
|
4.5
|
12.0
|
1.0
|
OE1
|
A:GLU64
|
4.5
|
18.2
|
1.0
|
CB
|
A:GLN47
|
4.5
|
15.4
|
1.0
|
CA
|
A:VAL46
|
4.5
|
13.6
|
1.0
|
N
|
A:GLY51
|
4.5
|
18.4
|
1.0
|
C
|
A:SER52
|
4.6
|
18.8
|
1.0
|
OE2
|
A:GLU64
|
4.6
|
15.2
|
1.0
|
CB
|
A:VAL46
|
4.6
|
13.9
|
1.0
|
CA
|
A:GLY48
|
4.6
|
13.1
|
1.0
|
N
|
A:VAL46
|
4.6
|
13.7
|
1.0
|
C
|
A:GLN47
|
4.7
|
14.9
|
1.0
|
O
|
A:HIS42
|
4.7
|
12.1
|
1.0
|
N
|
A:GLN47
|
4.7
|
15.0
|
1.0
|
C
|
A:GLY51
|
4.7
|
19.3
|
1.0
|
C
|
A:ASP50
|
4.8
|
16.9
|
1.0
|
N
|
A:CYS49
|
4.8
|
14.7
|
1.0
|
CA
|
A:ASP50
|
4.9
|
16.4
|
1.0
|
CA
|
A:GLN47
|
4.9
|
15.1
|
1.0
|
CB
|
A:VAL53
|
4.9
|
17.9
|
1.0
|
CA
|
A:CYS49
|
4.9
|
16.1
|
1.0
|
N
|
A:ASP43
|
5.0
|
12.8
|
1.0
|
CB
|
A:ASP50
|
5.0
|
15.7
|
1.0
|
CD
|
A:GLU64
|
5.0
|
16.1
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1fhf
Go back to
Calcium Binding Sites List in 1fhf
Calcium binding site 2 out
of 6 in the The Structure of Soybean Peroxidase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Structure of Soybean Peroxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:16.0
occ:1.00
|
OG1
|
A:THR170
|
2.3
|
11.9
|
1.0
|
O
|
A:GLN227
|
2.3
|
19.6
|
1.0
|
OG1
|
A:THR224
|
2.3
|
15.4
|
1.0
|
OD2
|
A:ASP221
|
2.5
|
17.8
|
1.0
|
OD1
|
A:ASP229
|
2.5
|
17.9
|
1.0
|
O
|
A:THR170
|
2.5
|
10.8
|
1.0
|
O
|
A:THR224
|
2.8
|
17.4
|
1.0
|
CG
|
A:ASP229
|
3.4
|
18.7
|
1.0
|
C
|
A:GLN227
|
3.5
|
18.7
|
1.0
|
C
|
A:THR170
|
3.5
|
9.9
|
1.0
|
CB
|
A:THR224
|
3.5
|
14.4
|
1.0
|
CB
|
A:THR170
|
3.6
|
9.5
|
1.0
|
CG
|
A:ASP221
|
3.7
|
19.8
|
1.0
|
C
|
A:THR224
|
3.7
|
16.8
|
1.0
|
OD2
|
A:ASP229
|
3.8
|
19.4
|
1.0
|
N
|
A:ASP229
|
3.8
|
17.8
|
1.0
|
CA
|
A:THR170
|
4.0
|
9.6
|
1.0
|
O
|
A:ASP229
|
4.0
|
17.7
|
1.0
|
CA
|
A:THR224
|
4.1
|
15.9
|
1.0
|
CG2
|
A:THR170
|
4.2
|
8.6
|
1.0
|
CB
|
A:ASP221
|
4.3
|
19.6
|
1.0
|
CA
|
A:GLN227
|
4.4
|
19.8
|
1.0
|
CB
|
A:ARG231
|
4.4
|
19.5
|
1.0
|
N
|
A:GLN227
|
4.4
|
20.7
|
1.0
|
N
|
A:PHE228
|
4.4
|
18.0
|
1.0
|
N
|
A:THR224
|
4.5
|
16.8
|
1.0
|
CA
|
A:PHE228
|
4.5
|
17.5
|
1.0
|
CA
|
A:ASP229
|
4.5
|
17.8
|
1.0
|
CB
|
A:ASP229
|
4.6
|
17.6
|
1.0
|
C
|
A:PHE228
|
4.6
|
17.6
|
1.0
|
OD1
|
A:ASP221
|
4.6
|
21.1
|
1.0
|
C
|
A:ASP229
|
4.6
|
17.6
|
1.0
|
CB
|
A:GLN227
|
4.7
|
19.3
|
1.0
|
N
|
A:PHE171
|
4.7
|
8.9
|
1.0
|
CG2
|
A:THR224
|
4.7
|
12.9
|
1.0
|
CG
|
A:ARG231
|
4.7
|
22.3
|
1.0
|
N
|
A:PRO225
|
4.9
|
17.3
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1fhf
Go back to
Calcium Binding Sites List in 1fhf
Calcium binding site 3 out
of 6 in the The Structure of Soybean Peroxidase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Structure of Soybean Peroxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:13.2
occ:1.00
|
OG
|
B:SER52
|
2.3
|
20.6
|
1.0
|
OD1
|
B:ASP43
|
2.4
|
12.4
|
1.0
|
O
|
B:VAL46
|
2.5
|
13.7
|
1.0
|
O
|
B:ASP43
|
2.5
|
13.9
|
1.0
|
O
|
B:GLY48
|
2.6
|
14.6
|
1.0
|
OD1
|
B:ASP50
|
2.7
|
19.3
|
1.0
|
C
|
B:ASP43
|
3.3
|
13.2
|
1.0
|
CG
|
B:ASP43
|
3.4
|
13.0
|
1.0
|
CB
|
B:SER52
|
3.5
|
19.0
|
1.0
|
CA
|
B:ASP43
|
3.6
|
13.0
|
1.0
|
CG2
|
B:VAL53
|
3.7
|
18.5
|
1.0
|
C
|
B:VAL46
|
3.7
|
14.7
|
1.0
|
C
|
B:GLY48
|
3.8
|
13.9
|
1.0
|
CG
|
B:ASP50
|
3.9
|
16.5
|
1.0
|
N
|
B:SER52
|
3.9
|
18.7
|
1.0
|
N
|
B:GLY48
|
4.1
|
14.7
|
1.0
|
CB
|
B:ASP43
|
4.1
|
12.7
|
1.0
|
N
|
B:ASP50
|
4.1
|
16.3
|
1.0
|
CA
|
B:SER52
|
4.2
|
18.9
|
1.0
|
N
|
B:VAL53
|
4.2
|
18.4
|
1.0
|
OD2
|
B:ASP43
|
4.3
|
13.7
|
1.0
|
OD2
|
B:ASP50
|
4.4
|
15.1
|
1.0
|
N
|
B:CYS44
|
4.5
|
12.0
|
1.0
|
OE1
|
B:GLU64
|
4.5
|
18.2
|
1.0
|
CB
|
B:GLN47
|
4.5
|
15.4
|
1.0
|
CA
|
B:VAL46
|
4.5
|
13.6
|
1.0
|
N
|
B:GLY51
|
4.5
|
18.4
|
1.0
|
C
|
B:SER52
|
4.6
|
18.8
|
1.0
|
OE2
|
B:GLU64
|
4.6
|
15.2
|
1.0
|
CB
|
B:VAL46
|
4.6
|
13.9
|
1.0
|
CA
|
B:GLY48
|
4.6
|
13.1
|
1.0
|
N
|
B:VAL46
|
4.6
|
13.7
|
1.0
|
C
|
B:GLN47
|
4.7
|
14.9
|
1.0
|
O
|
B:HIS42
|
4.7
|
12.1
|
1.0
|
N
|
B:GLN47
|
4.7
|
15.0
|
1.0
|
C
|
B:GLY51
|
4.7
|
19.3
|
1.0
|
C
|
B:ASP50
|
4.8
|
16.9
|
1.0
|
N
|
B:CYS49
|
4.8
|
14.7
|
1.0
|
CA
|
B:ASP50
|
4.9
|
16.4
|
1.0
|
CA
|
B:GLN47
|
4.9
|
15.1
|
1.0
|
CB
|
B:VAL53
|
4.9
|
17.9
|
1.0
|
CA
|
B:CYS49
|
4.9
|
16.1
|
1.0
|
N
|
B:ASP43
|
5.0
|
12.8
|
1.0
|
CB
|
B:ASP50
|
5.0
|
15.7
|
1.0
|
CD
|
B:GLU64
|
5.0
|
16.1
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1fhf
Go back to
Calcium Binding Sites List in 1fhf
Calcium binding site 4 out
of 6 in the The Structure of Soybean Peroxidase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Structure of Soybean Peroxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:16.0
occ:1.00
|
OG1
|
B:THR170
|
2.3
|
11.9
|
1.0
|
O
|
B:GLN227
|
2.3
|
19.6
|
1.0
|
OG1
|
B:THR224
|
2.3
|
15.4
|
1.0
|
OD2
|
B:ASP221
|
2.5
|
17.8
|
1.0
|
OD1
|
B:ASP229
|
2.5
|
17.9
|
1.0
|
O
|
B:THR170
|
2.5
|
10.8
|
1.0
|
O
|
B:THR224
|
2.8
|
17.4
|
1.0
|
CG
|
B:ASP229
|
3.4
|
18.7
|
1.0
|
C
|
B:GLN227
|
3.5
|
18.7
|
1.0
|
C
|
B:THR170
|
3.5
|
9.9
|
1.0
|
CB
|
B:THR224
|
3.5
|
14.4
|
1.0
|
CB
|
B:THR170
|
3.6
|
9.5
|
1.0
|
CG
|
B:ASP221
|
3.7
|
19.8
|
1.0
|
C
|
B:THR224
|
3.7
|
16.8
|
1.0
|
OD2
|
B:ASP229
|
3.8
|
19.4
|
1.0
|
N
|
B:ASP229
|
3.8
|
17.8
|
1.0
|
CA
|
B:THR170
|
4.0
|
9.6
|
1.0
|
O
|
B:ASP229
|
4.0
|
17.7
|
1.0
|
CA
|
B:THR224
|
4.1
|
15.9
|
1.0
|
CG2
|
B:THR170
|
4.2
|
8.6
|
1.0
|
CB
|
B:ASP221
|
4.3
|
19.6
|
1.0
|
CA
|
B:GLN227
|
4.4
|
19.8
|
1.0
|
CB
|
B:ARG231
|
4.4
|
19.5
|
1.0
|
N
|
B:GLN227
|
4.4
|
20.7
|
1.0
|
N
|
B:PHE228
|
4.4
|
18.0
|
1.0
|
N
|
B:THR224
|
4.5
|
16.8
|
1.0
|
CA
|
B:PHE228
|
4.5
|
17.5
|
1.0
|
CA
|
B:ASP229
|
4.5
|
17.8
|
1.0
|
CB
|
B:ASP229
|
4.6
|
17.6
|
1.0
|
C
|
B:PHE228
|
4.6
|
17.6
|
1.0
|
OD1
|
B:ASP221
|
4.6
|
21.1
|
1.0
|
C
|
B:ASP229
|
4.6
|
17.6
|
1.0
|
CB
|
B:GLN227
|
4.7
|
19.3
|
1.0
|
N
|
B:PHE171
|
4.7
|
8.9
|
1.0
|
CG2
|
B:THR224
|
4.7
|
12.9
|
1.0
|
CG
|
B:ARG231
|
4.7
|
22.3
|
1.0
|
N
|
B:PRO225
|
4.9
|
17.3
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1fhf
Go back to
Calcium Binding Sites List in 1fhf
Calcium binding site 5 out
of 6 in the The Structure of Soybean Peroxidase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The Structure of Soybean Peroxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca501
b:13.2
occ:1.00
|
OG
|
C:SER52
|
2.3
|
20.6
|
1.0
|
OD1
|
C:ASP43
|
2.4
|
12.4
|
1.0
|
O
|
C:VAL46
|
2.5
|
13.7
|
1.0
|
O
|
C:ASP43
|
2.5
|
13.9
|
1.0
|
O
|
C:GLY48
|
2.7
|
14.6
|
1.0
|
OD1
|
C:ASP50
|
2.7
|
19.3
|
1.0
|
C
|
C:ASP43
|
3.3
|
13.2
|
1.0
|
CG
|
C:ASP43
|
3.4
|
13.0
|
1.0
|
CB
|
C:SER52
|
3.5
|
19.0
|
1.0
|
CA
|
C:ASP43
|
3.6
|
13.0
|
1.0
|
CG2
|
C:VAL53
|
3.7
|
18.5
|
1.0
|
C
|
C:VAL46
|
3.7
|
14.7
|
1.0
|
C
|
C:GLY48
|
3.8
|
13.9
|
1.0
|
CG
|
C:ASP50
|
3.9
|
16.5
|
1.0
|
N
|
C:SER52
|
3.9
|
18.7
|
1.0
|
N
|
C:GLY48
|
4.1
|
14.7
|
1.0
|
CB
|
C:ASP43
|
4.1
|
12.7
|
1.0
|
N
|
C:ASP50
|
4.1
|
16.3
|
1.0
|
CA
|
C:SER52
|
4.2
|
18.9
|
1.0
|
N
|
C:VAL53
|
4.2
|
18.4
|
1.0
|
OD2
|
C:ASP43
|
4.3
|
13.7
|
1.0
|
OD2
|
C:ASP50
|
4.4
|
15.1
|
1.0
|
N
|
C:CYS44
|
4.5
|
12.0
|
1.0
|
OE1
|
C:GLU64
|
4.5
|
18.2
|
1.0
|
CB
|
C:GLN47
|
4.5
|
15.4
|
1.0
|
CA
|
C:VAL46
|
4.5
|
13.6
|
1.0
|
N
|
C:GLY51
|
4.5
|
18.4
|
1.0
|
C
|
C:SER52
|
4.6
|
18.8
|
1.0
|
OE2
|
C:GLU64
|
4.6
|
15.2
|
1.0
|
CB
|
C:VAL46
|
4.6
|
13.9
|
1.0
|
CA
|
C:GLY48
|
4.6
|
13.1
|
1.0
|
N
|
C:VAL46
|
4.6
|
13.7
|
1.0
|
C
|
C:GLN47
|
4.7
|
14.9
|
1.0
|
O
|
C:HIS42
|
4.7
|
12.1
|
1.0
|
N
|
C:GLN47
|
4.7
|
15.0
|
1.0
|
C
|
C:GLY51
|
4.7
|
19.3
|
1.0
|
C
|
C:ASP50
|
4.8
|
16.9
|
1.0
|
N
|
C:CYS49
|
4.8
|
14.7
|
1.0
|
CA
|
C:ASP50
|
4.9
|
16.4
|
1.0
|
CA
|
C:GLN47
|
4.9
|
15.1
|
1.0
|
CB
|
C:VAL53
|
4.9
|
17.9
|
1.0
|
CA
|
C:CYS49
|
4.9
|
16.1
|
1.0
|
N
|
C:ASP43
|
5.0
|
12.8
|
1.0
|
CB
|
C:ASP50
|
5.0
|
15.7
|
1.0
|
CD
|
C:GLU64
|
5.0
|
16.1
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1fhf
Go back to
Calcium Binding Sites List in 1fhf
Calcium binding site 6 out
of 6 in the The Structure of Soybean Peroxidase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The Structure of Soybean Peroxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca502
b:16.0
occ:1.00
|
OG1
|
C:THR170
|
2.3
|
11.9
|
1.0
|
O
|
C:GLN227
|
2.3
|
19.6
|
1.0
|
OG1
|
C:THR224
|
2.3
|
15.4
|
1.0
|
OD2
|
C:ASP221
|
2.5
|
17.8
|
1.0
|
OD1
|
C:ASP229
|
2.5
|
17.9
|
1.0
|
O
|
C:THR170
|
2.5
|
10.8
|
1.0
|
O
|
C:THR224
|
2.8
|
17.4
|
1.0
|
CG
|
C:ASP229
|
3.4
|
18.7
|
1.0
|
C
|
C:GLN227
|
3.5
|
18.7
|
1.0
|
C
|
C:THR170
|
3.5
|
9.9
|
1.0
|
CB
|
C:THR224
|
3.5
|
14.4
|
1.0
|
CB
|
C:THR170
|
3.6
|
9.5
|
1.0
|
CG
|
C:ASP221
|
3.7
|
19.8
|
1.0
|
C
|
C:THR224
|
3.7
|
16.8
|
1.0
|
OD2
|
C:ASP229
|
3.8
|
19.4
|
1.0
|
N
|
C:ASP229
|
3.8
|
17.8
|
1.0
|
CA
|
C:THR170
|
4.0
|
9.6
|
1.0
|
O
|
C:ASP229
|
4.0
|
17.7
|
1.0
|
CA
|
C:THR224
|
4.1
|
15.9
|
1.0
|
CG2
|
C:THR170
|
4.2
|
8.6
|
1.0
|
CB
|
C:ASP221
|
4.3
|
19.6
|
1.0
|
CA
|
C:GLN227
|
4.4
|
19.8
|
1.0
|
CB
|
C:ARG231
|
4.4
|
19.5
|
1.0
|
N
|
C:GLN227
|
4.4
|
20.7
|
1.0
|
N
|
C:PHE228
|
4.4
|
18.0
|
1.0
|
N
|
C:THR224
|
4.5
|
16.8
|
1.0
|
CA
|
C:PHE228
|
4.5
|
17.5
|
1.0
|
CA
|
C:ASP229
|
4.5
|
17.8
|
1.0
|
CB
|
C:ASP229
|
4.6
|
17.6
|
1.0
|
C
|
C:PHE228
|
4.6
|
17.6
|
1.0
|
OD1
|
C:ASP221
|
4.6
|
21.1
|
1.0
|
C
|
C:ASP229
|
4.6
|
17.6
|
1.0
|
CB
|
C:GLN227
|
4.7
|
19.3
|
1.0
|
N
|
C:PHE171
|
4.7
|
8.9
|
1.0
|
CG2
|
C:THR224
|
4.7
|
12.9
|
1.0
|
CG
|
C:ARG231
|
4.7
|
22.3
|
1.0
|
N
|
C:PRO225
|
4.9
|
17.3
|
1.0
|
|
Reference:
A.Henriksen,
O.Mirza,
C.Indiani,
K.Teilum,
G.Smulevich,
K.G.Welinder,
M.Gajhede.
Structure of Soybean Seed Coat Peroxidase: A Plant Peroxidase with Unusual Stability and Haem-Apoprotein Interactions. Protein Sci. V. 10 108 2001.
ISSN: ISSN 0961-8368
PubMed: 11266599
DOI: 10.1110/PS.37301
Page generated: Thu Jul 11 08:07:16 2024
|