Atomistry » Calcium » PDB 1fak-1fn6 » 1fhf
Atomistry »
  Calcium »
    PDB 1fak-1fn6 »
      1fhf »

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: Thu Jul 11 08:07:16 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy