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Calcium in PDB 1h3j: Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A

Enzymatic activity of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A

All present enzymatic activity of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A:
1.11.1.7;

Protein crystallography data

The structure of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A, PDB code: 1h3j was solved by J.F.W.Petersen, K.Houborg, P.Harris, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.180, 75.530, 76.600, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 25.6

Other elements in 1h3j:

The structure of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A (pdb code 1h3j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A, PDB code: 1h3j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1h3j

Go back to Calcium Binding Sites List in 1h3j
Calcium binding site 1 out of 4 in the Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.5
occ:1.00
 O A:HOH593 2.2 10.5 1.0
OD1 A:ASP56 2.3 15.1 1.0
OG A:SER78 2.4 12.3 1.0
O A:ASP56 2.4 12.2 1.0
O A:HOH563 2.5 10.5 1.0
O A:GLY74 2.5 15.7 1.0
OD2 A:ASP76 2.6 13.2 1.0
C A:ASP56 3.3 10.0 1.0
CG A:ASP56 3.3 14.3 1.0
CG A:ASP76 3.6 14.7 1.0
CB A:SER78 3.6 11.6 1.0
C A:GLY74 3.7 14.8 1.0
CA A:ASP56 3.7 10.0 1.0
N A:SER78 4.0 11.8 1.0
OD1 A:ASP76 4.1 15.6 1.0
CB A:ASP56 4.1 11.8 1.0
OD2 A:ASP56 4.1 12.3 1.0
O A:HOH521 4.2 18.1 1.0
N A:ASP76 4.2 15.3 1.0
CA A:SER78 4.4 10.0 1.0
N A:GLY74 4.4 16.7 1.0
N A:ALA57 4.4 9.3 1.0
CA A:GLY74 4.4 15.8 1.0
N A:ILE79 4.5 13.8 1.0
OE2 A:GLU86 4.6 13.4 1.0
O A:GLY59 4.6 14.0 1.0
N A:GLY77 4.6 11.7 1.0
OE1 A:GLU86 4.7 18.1 1.0
N A:ALA75 4.7 15.4 1.0
CB A:ASP76 4.9 14.9 1.0
O A:HIS55 4.9 14.8 1.0
C A:SER78 4.9 13.0 1.0
CB A:SER147 4.9 16.8 1.0
CA A:ALA57 4.9 8.7 1.0
CA A:ASP76 4.9 14.1 1.0
CA A:ALA75 4.9 15.0 1.0

Calcium binding site 2 out of 4 in 1h3j

Go back to Calcium Binding Sites List in 1h3j
Calcium binding site 2 out of 4 in the Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:14.1
occ:1.00
 O A:THR203 2.0 10.3 1.0
O A:VAL206 2.4 16.9 1.0
O A:SER184 2.4 12.7 1.0
OG1 A:THR203 2.5 12.2 1.0
OD1 A:ASP208 2.5 20.8 1.0
OD2 A:ASP201 2.6 6.3 1.0
OG A:SER184 2.6 17.1 1.0
OD1 A:ASP201 2.8 8.8 1.0
CG A:ASP201 3.0 7.7 1.0
C A:THR203 3.1 14.1 1.0
C A:SER184 3.4 10.2 1.0
CG A:ASP208 3.5 18.7 1.0
CB A:THR203 3.5 11.8 1.0
C A:VAL206 3.6 16.1 1.0
CB A:SER184 3.7 12.2 1.0
CA A:SER184 3.8 11.0 1.0
CA A:THR203 3.8 13.0 1.0
OD2 A:ASP208 3.8 17.7 1.0
N A:ASP208 4.1 18.2 1.0
N A:PRO204 4.1 16.5 1.0
N A:THR203 4.2 14.2 1.0
N A:VAL206 4.2 14.2 1.0
CA A:VAL206 4.3 14.9 1.0
O A:ASP208 4.4 14.7 1.0
CA A:PRO204 4.5 16.8 1.0
O A:HOH609 4.5 15.7 1.0
CB A:VAL206 4.5 15.2 1.0
CB A:ASP201 4.6 10.2 1.0
N A:PHE207 4.6 14.4 1.0
N A:LEU185 4.6 10.6 1.0
CB A:ASP208 4.7 17.7 1.0
CB A:GLN210 4.7 11.8 1.0
CA A:PHE207 4.7 14.5 1.0
CA A:ASP208 4.7 18.3 1.0
CG2 A:THR203 4.8 15.4 1.0
C A:PRO204 4.9 17.8 1.0
C A:ASP208 4.9 16.6 1.0
C A:PHE207 4.9 17.1 1.0

Calcium binding site 3 out of 4 in 1h3j

Go back to Calcium Binding Sites List in 1h3j
Calcium binding site 3 out of 4 in the Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:15.0
occ:1.00
 O B:HOH554 2.3 10.8 1.0
O B:HOH587 2.3 13.7 1.0
O B:ASP56 2.3 10.4 1.0
OD2 B:ASP56 2.4 15.7 1.0
OG B:SER78 2.5 12.2 1.0
O B:GLY74 2.5 12.3 1.0
OD2 B:ASP76 2.7 18.9 1.0
C B:ASP56 3.2 10.8 1.0
CG B:ASP56 3.3 14.3 1.0
CG B:ASP76 3.6 19.2 1.0
CA B:ASP56 3.7 10.8 1.0
CB B:SER78 3.7 12.3 1.0
C B:GLY74 3.8 13.6 1.0
OD1 B:ASP56 4.0 14.7 1.0
CB B:ASP56 4.1 12.7 1.0
OD1 B:ASP76 4.1 18.8 1.0
N B:SER78 4.1 11.9 1.0
O B:HOH537 4.1 12.2 1.0
N B:ASP76 4.2 15.6 1.0
N B:ALA57 4.4 10.6 1.0
N B:GLY74 4.4 14.7 1.0
CA B:SER78 4.4 12.1 1.0
O B:GLY59 4.5 13.2 1.0
CA B:GLY74 4.5 13.1 1.0
OE2 B:GLU86 4.6 17.1 1.0
N B:ILE79 4.6 13.9 1.0
N B:GLY77 4.6 11.6 1.0
OE1 B:GLU86 4.7 18.7 1.0
CB B:SER147 4.8 15.3 1.0
N B:ALA75 4.8 13.7 1.0
O B:HIS55 4.8 12.3 1.0
CB B:ASP76 4.8 15.8 1.0
CA B:ALA57 4.8 11.3 1.0
CA B:ASP76 4.9 13.7 1.0
CA B:GLY59 4.9 13.6 1.0
C B:SER78 4.9 13.0 1.0
N B:GLY59 5.0 13.3 1.0
N B:ASP56 5.0 11.5 1.0

Calcium binding site 4 out of 4 in 1h3j

Go back to Calcium Binding Sites List in 1h3j
Calcium binding site 4 out of 4 in the Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Recombinant Coprinus Cinereus Peroxidase Determined to 2.0 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:11.0
occ:1.00
 O B:THR203 2.2 9.8 1.0
O B:SER184 2.3 10.1 1.0
OG B:SER184 2.4 11.8 1.0
OD2 B:ASP201 2.5 6.0 1.0
O B:VAL206 2.5 9.9 1.0
OG1 B:THR203 2.6 12.5 1.0
OD1 B:ASP208 2.6 12.5 1.0
OD1 B:ASP201 2.7 5.5 1.0
CG B:ASP201 3.0 5.0 1.0
C B:THR203 3.2 9.8 1.0
C B:SER184 3.3 9.0 1.0
CB B:THR203 3.5 9.8 1.0
CG B:ASP208 3.5 10.4 1.0
CB B:SER184 3.5 9.9 1.0
CA B:SER184 3.7 8.6 1.0
C B:VAL206 3.7 11.4 1.0
CA B:THR203 3.8 9.6 1.0
OD2 B:ASP208 3.9 13.2 1.0
N B:THR203 4.1 9.6 1.0
N B:ASP208 4.2 12.3 1.0
N B:PRO204 4.2 10.4 1.0
N B:VAL206 4.4 12.2 1.0
O B:HOH643 4.4 7.8 1.0
CA B:VAL206 4.5 11.0 1.0
O B:ASP208 4.5 11.2 1.0
CB B:ASP201 4.5 6.1 1.0
N B:LEU185 4.5 8.0 1.0
CA B:PRO204 4.5 11.9 1.0
CB B:VAL206 4.6 10.1 1.0
N B:PHE207 4.7 9.5 1.0
CB B:GLN210 4.7 9.1 1.0
CB B:ASP208 4.7 10.4 1.0
CA B:PHE207 4.8 9.7 1.0
CA B:ASP208 4.8 12.7 1.0
CG2 B:THR203 4.9 11.8 1.0
C B:PRO204 4.9 13.5 1.0
C B:ASP208 4.9 11.2 1.0
C B:PHE207 4.9 12.2 1.0

Reference:

K.Houborg, P.Harris, J.F.W.Petersen, P.Rowland, J.Poulsen, P.Schneider, J.Vind, S.Larsen. Impact of the Physical and Chemical Environment on the Molecular Structure of Coprinus Cinereus Peroxidase Acta Crystallogr.,Sect.D V. 59 989 2003.
ISSN: ISSN 0907-4449
PubMed: 12777760
DOI: 10.1107/S0907444903006772
Page generated: Thu Jul 11 09:50:28 2024

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