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Calcium in PDB 4atj: Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid

Enzymatic activity of Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid

All present enzymatic activity of Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid:
1.11.1.7;

Protein crystallography data

The structure of Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid, PDB code: 4atj was solved by K.Meno, S.Jennings, A.T.Smith, A.Henriksen, M.Gajhede, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.930, 62.270, 78.230, 90.00, 104.27, 90.00
R / Rfree (%) 16.2 / 19.4

Other elements in 4atj:

The structure of Distal Heme Pocket Mutant (H42E) 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 Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid (pdb code 4atj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid, PDB code: 4atj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4atj

Go back to Calcium Binding Sites List in 4atj
Calcium binding site 1 out of 4 in the Distal Heme Pocket Mutant (H42E) 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 Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca351

b:15.8
occ:1.00
 O A:THR171 2.4 10.3 1.0
OD2 A:ASP222 2.5 18.1 1.0
O A:ILE228 2.5 10.0 1.0
O A:THR225 2.5 12.3 1.0
OG1 A:THR225 2.6 7.9 1.0
OD1 A:ASP230 2.6 11.8 1.0
OG1 A:THR171 2.7 6.2 1.0
CG A:ASP222 3.5 18.4 1.0
C A:THR171 3.5 10.0 1.0
CG A:ASP230 3.5 15.4 1.0
C A:THR225 3.5 12.9 1.0
CB A:THR225 3.7 11.3 1.0
C A:ILE228 3.7 14.8 1.0
CB A:THR171 3.8 8.2 1.0
OD2 A:ASP230 3.8 15.8 1.0
CB A:ASP222 3.9 15.1 1.0
CA A:THR171 3.9 8.0 1.0
N A:ASP230 4.1 13.5 1.0
CA A:THR225 4.1 10.5 1.0
CB A:LYS232 4.2 21.8 1.0
CG2 A:THR171 4.4 5.8 1.0
N A:THR225 4.4 14.7 1.0
N A:ILE228 4.4 10.7 1.0
CA A:ILE228 4.5 10.9 1.0
OD1 A:ASP222 4.5 20.3 1.0
O A:ASP230 4.5 12.3 1.0
N A:PHE172 4.6 8.4 1.0
CB A:ILE228 4.6 9.8 1.0
N A:PRO226 4.7 11.3 1.0
N A:PHE229 4.7 13.4 1.0
CB A:ASP230 4.7 11.8 1.0
CG A:LYS232 4.7 23.8 1.0
CA A:PHE229 4.7 11.1 1.0
CA A:ASP230 4.8 10.1 1.0
C A:ASP230 4.8 13.1 1.0
C A:PHE229 4.9 13.9 1.0
N A:LYS232 4.9 12.6 1.0
CG2 A:THR225 4.9 10.2 1.0

Calcium binding site 2 out of 4 in 4atj

Go back to Calcium Binding Sites List in 4atj
Calcium binding site 2 out of 4 in the Distal Heme Pocket Mutant (H42E) 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 Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca352

b:19.4
occ:1.00
 O A:VAL46 2.5 11.1 1.0
O A:ASP43 2.5 13.4 1.0
OD1 A:ASP50 2.6 10.1 1.0
OD1 A:ASP43 2.6 12.4 1.0
OG A:SER52 2.6 8.9 1.0
O A:GLY48 2.6 14.2 1.0
C A:ASP43 3.4 9.5 1.0
CG A:ASP50 3.6 10.6 1.0
C A:VAL46 3.6 11.0 1.0
CB A:SER52 3.6 10.1 1.0
CG A:ASP43 3.6 11.6 1.0
C A:GLY48 3.9 13.5 1.0
CA A:ASP43 3.9 8.4 1.0
N A:ASP50 4.0 12.4 1.0
N A:SER52 4.0 10.1 1.0
OD2 A:ASP50 4.0 15.1 1.0
CA A:VAL46 4.3 10.4 1.0
CB A:VAL46 4.3 10.6 1.0
CA A:SER52 4.4 13.5 1.0
CB A:ASP43 4.4 10.2 1.0
N A:GLY48 4.4 14.0 1.0
C A:ASN47 4.4 15.4 1.0
N A:VAL46 4.4 10.4 1.0
N A:CYS44 4.4 8.4 1.0
OD2 A:ASP43 4.5 16.1 1.0
OE1 A:GLU64 4.5 16.1 1.0
CB A:ASN47 4.5 20.9 1.0
N A:ASN47 4.5 13.4 1.0
N A:ALA51 4.6 11.5 1.0
O A:ASN47 4.7 14.6 1.0
CA A:CYS49 4.7 12.0 1.0
CB A:ASP50 4.7 11.8 1.0
CA A:ASP50 4.7 10.8 1.0
N A:ILE53 4.7 11.8 1.0
CA A:ASN47 4.7 15.2 1.0
N A:CYS49 4.7 11.5 1.0
CA A:GLY48 4.8 13.4 1.0
C A:ASP50 4.8 9.0 1.0
CA A:CYS44 4.8 8.5 1.0
C A:CYS49 4.9 12.1 1.0
CG1 A:VAL46 4.9 9.2 1.0
OE2 A:GLU64 5.0 16.6 1.0

Calcium binding site 3 out of 4 in 4atj

Go back to Calcium Binding Sites List in 4atj
Calcium binding site 3 out of 4 in the Distal Heme Pocket Mutant (H42E) 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 Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca351

b:15.8
occ:1.00
 O B:THR171 2.4 10.3 1.0
OD2 B:ASP222 2.5 18.1 1.0
O B:ILE228 2.5 10.0 1.0
O B:THR225 2.5 12.3 1.0
OG1 B:THR225 2.6 7.9 1.0
OD1 B:ASP230 2.6 11.8 1.0
OG1 B:THR171 2.7 6.2 1.0
CG B:ASP222 3.5 18.4 1.0
C B:THR171 3.5 10.0 1.0
CG B:ASP230 3.5 15.4 1.0
C B:THR225 3.5 12.9 1.0
CB B:THR225 3.7 11.3 1.0
C B:ILE228 3.7 14.8 1.0
CB B:THR171 3.8 8.2 1.0
OD2 B:ASP230 3.8 15.8 1.0
CB B:ASP222 3.9 15.1 1.0
CA B:THR171 3.9 8.0 1.0
N B:ASP230 4.1 13.5 1.0
CA B:THR225 4.1 10.5 1.0
CB B:LYS232 4.2 21.8 1.0
CG2 B:THR171 4.4 5.8 1.0
N B:THR225 4.4 14.7 1.0
N B:ILE228 4.4 10.7 1.0
CA B:ILE228 4.5 10.9 1.0
OD1 B:ASP222 4.5 20.3 1.0
O B:ASP230 4.5 12.3 1.0
N B:PHE172 4.6 8.4 1.0
CB B:ILE228 4.6 9.8 1.0
N B:PRO226 4.7 11.3 1.0
N B:PHE229 4.7 13.4 1.0
CB B:ASP230 4.7 11.8 1.0
CG B:LYS232 4.7 23.8 1.0
CA B:PHE229 4.7 11.1 1.0
CA B:ASP230 4.8 10.1 1.0
C B:ASP230 4.8 13.1 1.0
C B:PHE229 4.9 13.9 1.0
N B:LYS232 4.9 12.6 1.0
CG2 B:THR225 4.9 10.2 1.0

Calcium binding site 4 out of 4 in 4atj

Go back to Calcium Binding Sites List in 4atj
Calcium binding site 4 out of 4 in the Distal Heme Pocket Mutant (H42E) 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 Distal Heme Pocket Mutant (H42E) of Recombinant Horseradish Peroxidase in Complex with Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca352

b:19.4
occ:1.00
 O B:VAL46 2.5 11.1 1.0
O B:ASP43 2.5 13.4 1.0
OD1 B:ASP50 2.6 10.1 1.0
OD1 B:ASP43 2.6 12.4 1.0
OG B:SER52 2.6 8.9 1.0
O B:GLY48 2.6 14.2 1.0
C B:ASP43 3.4 9.5 1.0
CG B:ASP50 3.6 10.6 1.0
C B:VAL46 3.6 11.0 1.0
CB B:SER52 3.6 10.1 1.0
CG B:ASP43 3.6 11.6 1.0
C B:GLY48 3.9 13.5 1.0
CA B:ASP43 3.9 8.4 1.0
N B:ASP50 4.0 12.4 1.0
N B:SER52 4.0 10.1 1.0
OD2 B:ASP50 4.0 15.1 1.0
CA B:VAL46 4.3 10.4 1.0
CB B:VAL46 4.3 10.6 1.0
CA B:SER52 4.4 13.5 1.0
CB B:ASP43 4.4 10.2 1.0
N B:GLY48 4.4 14.0 1.0
C B:ASN47 4.4 15.4 1.0
N B:VAL46 4.4 10.4 1.0
N B:CYS44 4.4 8.4 1.0
OD2 B:ASP43 4.5 16.1 1.0
OE1 B:GLU64 4.5 16.1 1.0
CB B:ASN47 4.5 20.9 1.0
N B:ASN47 4.5 13.4 1.0
N B:ALA51 4.6 11.5 1.0
O B:ASN47 4.7 14.6 1.0
CA B:CYS49 4.7 12.0 1.0
CB B:ASP50 4.7 11.8 1.0
CA B:ASP50 4.7 10.8 1.0
N B:ILE53 4.7 11.8 1.0
CA B:ASN47 4.7 15.2 1.0
N B:CYS49 4.7 11.5 1.0
CA B:GLY48 4.8 13.4 1.0
C B:ASP50 4.8 9.0 1.0
CA B:CYS44 4.8 8.5 1.0
C B:CYS49 4.9 12.1 1.0
CG1 B:VAL46 4.9 9.2 1.0
OE2 B:GLU64 5.0 16.6 1.0

Reference:

K.Meno, S.Jennings, A.T.Smith, A.Henriksen, M.Gajhede. Structural Analysis of the Two Horseradish Peroxidase Catalytic Residue Variants H42E and R38S/H42E: Implications For the Catalytic Cycle. Acta Crystallogr.,Sect.D V. 58 1803 2002.
ISSN: ISSN 0907-4449
PubMed: 12351824
DOI: 10.1107/S090744490201329X
Page generated: Sat Jul 13 22:18:43 2024

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