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Calcium in PDB 3atj: Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid

Enzymatic activity of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid

All present enzymatic activity of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid:
1.11.1.7;

Protein crystallography data

The structure of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid, PDB code: 3atj was solved by K.Meno, C.G.White, A.T.Smith, M.Gajhede, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.105, 62.283, 78.160, 90.00, 104.31, 90.00
R / Rfree (%) 17.4 / 20.3

Other elements in 3atj:

The structure of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid (pdb code 3atj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid, PDB code: 3atj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3atj

Go back to Calcium Binding Sites List in 3atj
Calcium binding site 1 out of 4 in the Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca351

b:12.3
occ:1.00
 OD2 A:ASP222 2.4 10.4 1.0
O A:ILE228 2.4 7.3 1.0
O A:THR171 2.4 11.3 1.0
OG1 A:THR225 2.5 8.8 1.0
O A:THR225 2.6 12.5 1.0
OD1 A:ASP230 2.6 15.1 1.0
OG1 A:THR171 2.7 5.0 1.0
CG A:ASP230 3.4 14.4 1.0
C A:THR171 3.4 9.4 1.0
CG A:ASP222 3.5 13.8 1.0
C A:THR225 3.6 12.1 1.0
CB A:THR225 3.6 11.3 1.0
C A:ILE228 3.6 11.2 1.0
OD2 A:ASP230 3.7 17.7 1.0
CB A:THR171 3.8 5.7 1.0
CA A:THR171 3.9 6.2 1.0
CB A:ASP222 4.0 11.2 1.0
CA A:THR225 4.1 12.2 1.0
N A:ASP230 4.1 12.4 1.0
N A:ILE228 4.3 11.2 1.0
CG2 A:THR171 4.3 6.3 1.0
N A:THR225 4.4 14.9 1.0
CA A:ILE228 4.4 9.2 1.0
CB A:LYS232 4.4 15.3 1.0
OD1 A:ASP222 4.5 9.6 1.0
O A:ASP230 4.6 10.8 1.0
N A:PHE172 4.6 6.9 1.0
CB A:ILE228 4.6 10.3 1.0
N A:PHE229 4.6 11.2 1.0
CB A:ASP230 4.7 11.1 1.0
N A:PRO226 4.7 12.5 1.0
CA A:PHE229 4.7 9.8 1.0
CG A:LYS232 4.8 17.9 1.0
CA A:ASP230 4.8 10.5 1.0
CG2 A:THR225 4.9 9.4 1.0
C A:PHE229 4.9 11.7 1.0
C A:ASP230 4.9 11.3 1.0

Calcium binding site 2 out of 4 in 3atj

Go back to Calcium Binding Sites List in 3atj
Calcium binding site 2 out of 4 in the Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca352

b:8.4
occ:1.00
 OD1 A:ASP50 2.4 7.9 1.0
O A:ASP43 2.4 6.9 1.0
O A:VAL46 2.4 7.5 1.0
OD1 A:ASP43 2.5 6.1 1.0
O A:HOH721 2.6 9.6 1.0
O A:GLY48 2.6 8.4 1.0
OG A:SER52 2.6 12.6 1.0
C A:ASP43 3.3 5.7 1.0
CG A:ASP50 3.4 11.0 1.0
C A:VAL46 3.6 6.5 1.0
CG A:ASP43 3.6 5.5 1.0
CB A:SER52 3.7 9.7 1.0
CA A:ASP43 3.8 2.8 1.0
C A:GLY48 3.8 8.1 1.0
OD2 A:ASP50 3.9 11.3 1.0
N A:ASP50 4.0 9.6 1.0
N A:SER52 4.0 9.2 1.0
CB A:VAL46 4.3 5.6 1.0
CB A:ASP43 4.3 2.0 1.0
CA A:VAL46 4.3 5.7 1.0
N A:GLY48 4.3 7.9 1.0
CA A:SER52 4.4 9.6 1.0
N A:CYS44 4.4 4.0 1.0
N A:VAL46 4.4 4.2 1.0
C A:ASN47 4.4 10.4 1.0
OD2 A:ASP43 4.5 10.7 1.0
N A:ALA51 4.6 9.4 1.0
N A:ASN47 4.6 7.9 1.0
N A:ILE53 4.6 8.7 1.0
CB A:ASP50 4.6 9.4 1.0
OE1 A:GLU64 4.6 9.5 1.0
CB A:ASN47 4.6 12.1 1.0
CA A:ASP50 4.7 8.6 1.0
CA A:GLY48 4.7 8.4 1.0
CA A:CYS49 4.7 7.9 1.0
N A:CYS49 4.7 7.2 1.0
OE2 A:GLU64 4.7 9.6 1.0
CA A:ASN47 4.8 9.4 1.0
O A:ASN47 4.8 12.6 1.0
C A:ASP50 4.8 8.5 1.0
O A:HIS42 4.8 5.9 1.0
C A:CYS49 4.9 8.5 1.0
CA A:CYS44 4.9 7.2 1.0
CG1 A:VAL46 4.9 3.4 1.0
C A:SER52 4.9 8.9 1.0

Calcium binding site 3 out of 4 in 3atj

Go back to Calcium Binding Sites List in 3atj
Calcium binding site 3 out of 4 in the Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca351

b:12.3
occ:1.00
 OD2 B:ASP222 2.4 10.4 1.0
O B:ILE228 2.4 7.3 1.0
O B:THR171 2.4 11.3 1.0
OG1 B:THR225 2.5 8.8 1.0
O B:THR225 2.6 12.5 1.0
OD1 B:ASP230 2.6 15.1 1.0
OG1 B:THR171 2.7 5.0 1.0
CG B:ASP230 3.4 14.4 1.0
C B:THR171 3.4 9.4 1.0
CG B:ASP222 3.5 13.8 1.0
C B:THR225 3.6 12.1 1.0
CB B:THR225 3.6 11.3 1.0
C B:ILE228 3.6 11.2 1.0
OD2 B:ASP230 3.7 17.7 1.0
CB B:THR171 3.8 5.7 1.0
CA B:THR171 3.9 6.2 1.0
CB B:ASP222 4.0 11.2 1.0
CA B:THR225 4.1 12.2 1.0
N B:ASP230 4.1 12.4 1.0
N B:ILE228 4.3 11.2 1.0
CG2 B:THR171 4.3 6.3 1.0
N B:THR225 4.4 14.9 1.0
CA B:ILE228 4.4 9.2 1.0
CB B:LYS232 4.4 15.3 1.0
OD1 B:ASP222 4.5 9.6 1.0
O B:ASP230 4.6 10.8 1.0
N B:PHE172 4.6 6.9 1.0
CB B:ILE228 4.6 10.3 1.0
N B:PHE229 4.6 11.2 1.0
CB B:ASP230 4.7 11.1 1.0
N B:PRO226 4.7 12.5 1.0
CA B:PHE229 4.7 9.8 1.0
CG B:LYS232 4.8 17.9 1.0
CA B:ASP230 4.8 10.5 1.0
CG2 B:THR225 4.9 9.4 1.0
C B:PHE229 4.9 11.7 1.0
C B:ASP230 4.9 11.3 1.0

Calcium binding site 4 out of 4 in 3atj

Go back to Calcium Binding Sites List in 3atj
Calcium binding site 4 out of 4 in the Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Heme Ligand Mutant of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca352

b:8.4
occ:1.00
 OD1 B:ASP50 2.4 7.9 1.0
O B:ASP43 2.4 6.9 1.0
O B:VAL46 2.4 7.5 1.0
OD1 B:ASP43 2.5 6.1 1.0
O B:HOH1721 2.6 9.6 1.0
O B:GLY48 2.6 8.4 1.0
OG B:SER52 2.6 12.6 1.0
C B:ASP43 3.3 5.7 1.0
CG B:ASP50 3.4 11.0 1.0
C B:VAL46 3.6 6.5 1.0
CG B:ASP43 3.6 5.5 1.0
CB B:SER52 3.7 9.7 1.0
CA B:ASP43 3.8 2.8 1.0
C B:GLY48 3.8 8.1 1.0
OD2 B:ASP50 3.9 11.3 1.0
N B:ASP50 4.0 9.6 1.0
N B:SER52 4.0 9.2 1.0
CB B:VAL46 4.3 5.6 1.0
CB B:ASP43 4.3 2.0 1.0
CA B:VAL46 4.3 5.7 1.0
N B:GLY48 4.3 7.9 1.0
CA B:SER52 4.4 9.6 1.0
N B:CYS44 4.4 4.0 1.0
N B:VAL46 4.4 4.2 1.0
C B:ASN47 4.4 10.4 1.0
OD2 B:ASP43 4.5 10.7 1.0
N B:ALA51 4.6 9.4 1.0
N B:ASN47 4.6 7.9 1.0
N B:ILE53 4.6 8.7 1.0
CB B:ASP50 4.6 9.4 1.0
OE1 B:GLU64 4.6 9.5 1.0
CB B:ASN47 4.6 12.1 1.0
CA B:ASP50 4.7 8.6 1.0
CA B:GLY48 4.7 8.4 1.0
CA B:CYS49 4.7 7.9 1.0
N B:CYS49 4.7 7.2 1.0
OE2 B:GLU64 4.7 9.6 1.0
CA B:ASN47 4.8 9.4 1.0
O B:ASN47 4.8 12.6 1.0
C B:ASP50 4.8 8.5 1.0
O B:HIS42 4.8 5.9 1.0
C B:CYS49 4.9 8.5 1.0
CA B:CYS44 4.9 7.2 1.0
CG1 B:VAL46 4.9 3.4 1.0
C B:SER52 4.9 8.9 1.0

Reference:

K.Meno, C.G.White, A.T.Smith, M.Gajhede. Structural and Catalytical Implications of A F221M Mutation in the Proximal Pocket of Horseradish Peroxidase C (Hrp C) To Be Published.
Page generated: Tue Jul 8 10:55:21 2025

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