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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:

Iron (Fe) 3 atoms

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: Mon Jul 7 14:50:26 2025

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