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Calcium in PDB 1lyk: The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase

Enzymatic activity of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase

All present enzymatic activity of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase:
1.11.1.7;

Protein crystallography data

The structure of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase, PDB code: 1lyk was solved by K.Houborg, P.Harris, J.F.W.Petersen, P.Rowland, J.-C.N.Poulsen, P.Schneider, J.Vind, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.700, 128.410, 75.480, 90.00, 93.22, 90.00
R / Rfree (%) 17.9 / 23.5

Other elements in 1lyk:

The structure of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase (pdb code 1lyk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase, PDB code: 1lyk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1lyk

Go back to Calcium Binding Sites List in 1lyk
Calcium binding site 1 out of 4 in the The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8345

b:19.4
occ:1.00
 O A:HOH1009 2.3 14.4 1.0
O A:GLY74 2.3 15.6 1.0
OG A:SER78 2.3 18.9 1.0
O A:ASP56 2.4 19.2 1.0
O A:HOH1027 2.4 23.3 1.0
OD1 A:ASP56 2.5 20.2 1.0
OD2 A:ASP76 2.5 22.9 1.0
C A:ASP56 3.4 18.2 1.0
CG A:ASP56 3.5 18.3 1.0
C A:GLY74 3.6 16.3 1.0
CB A:SER78 3.6 18.0 1.0
CG A:ASP76 3.6 20.7 1.0
CA A:ASP56 3.9 18.4 1.0
N A:SER78 4.0 18.3 1.0
OD1 A:ASP76 4.1 20.7 1.0
N A:ASP76 4.1 22.1 1.0
OD2 A:ASP56 4.2 17.3 1.0
O A:HOH1023 4.2 15.6 1.0
CA A:SER78 4.3 18.7 1.0
CB A:ASP56 4.3 19.3 1.0
CA A:GLY74 4.4 17.1 1.0
N A:GLY74 4.4 19.4 1.0
N A:ALA57 4.5 15.5 1.0
N A:ALA75 4.6 18.2 1.0
O A:GLY59 4.6 18.0 1.0
OE2 A:GLU86 4.6 22.6 1.0
N A:ILE79 4.6 19.7 1.0
N A:GLY77 4.6 19.5 1.0
CA A:ALA75 4.8 20.6 1.0
OE1 A:GLU86 4.8 21.3 1.0
CB A:SER147 4.8 21.8 1.0
CB A:ASP76 4.8 22.9 1.0
CA A:ASP76 4.8 20.5 1.0
C A:SER78 4.8 19.4 1.0
CA A:ALA57 4.9 15.0 1.0
C A:ALA75 4.9 21.6 1.0
C A:GLY73 4.9 19.8 1.0
CA A:GLY59 5.0 15.3 1.0
C A:ASP76 5.0 21.5 1.0

Calcium binding site 2 out of 4 in 1lyk

Go back to Calcium Binding Sites List in 1lyk
Calcium binding site 2 out of 4 in the The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca8346

b:13.1
occ:1.00
 O A:SER184 2.2 19.4 1.0
O A:THR203 2.3 14.8 1.0
O A:VAL206 2.3 16.4 1.0
OG A:SER184 2.4 13.1 1.0
OD2 A:ASP201 2.4 10.8 1.0
OD1 A:ASP208 2.5 15.7 1.0
OG1 A:THR203 2.5 13.8 1.0
OD1 A:ASP201 2.9 11.9 1.0
CG A:ASP201 3.0 11.0 1.0
C A:SER184 3.2 15.3 1.0
C A:THR203 3.3 15.2 1.0
CG A:ASP208 3.5 14.9 1.0
CB A:SER184 3.5 13.2 1.0
C A:VAL206 3.6 14.2 1.0
CB A:THR203 3.6 13.8 1.0
CA A:SER184 3.6 14.0 1.0
OD2 A:ASP208 3.9 16.0 1.0
CA A:THR203 3.9 14.8 1.0
N A:ASP208 4.1 15.6 1.0
N A:THR203 4.2 14.8 1.0
N A:PRO204 4.3 16.6 1.0
N A:VAL206 4.3 16.0 1.0
CA A:VAL206 4.4 15.0 1.0
O A:ASP208 4.4 16.4 1.0
N A:LEU185 4.4 15.9 1.0
CB A:ASP201 4.5 12.2 1.0
N A:PHE207 4.5 14.8 1.0
CB A:VAL206 4.6 14.0 1.0
O A:HOH1013 4.6 13.9 1.0
CA A:PHE207 4.7 14.5 1.0
CA A:PRO204 4.7 15.9 1.0
CB A:GLN210 4.7 15.5 1.0
CB A:ASP208 4.7 13.9 1.0
CA A:ASP208 4.8 13.1 1.0
C A:PHE207 4.9 16.9 1.0
CG2 A:THR203 4.9 15.0 1.0
C A:ASP208 4.9 16.9 1.0
CA A:LEU185 5.0 17.0 1.0

Calcium binding site 3 out of 4 in 1lyk

Go back to Calcium Binding Sites List in 1lyk
Calcium binding site 3 out of 4 in the The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca9345

b:17.7
occ:1.00
 O B:HOH2027 2.2 21.3 1.0
O B:HOH2009 2.3 14.8 1.0
O B:ASP56 2.3 14.4 1.0
O B:GLY74 2.4 18.7 1.0
OD1 B:ASP56 2.5 18.4 1.0
OG B:SER78 2.6 16.1 1.0
OD2 B:ASP76 2.7 25.5 1.0
C B:ASP56 3.3 18.2 1.0
CG B:ASP56 3.4 19.3 1.0
C B:GLY74 3.6 19.8 1.0
CG B:ASP76 3.7 25.2 1.0
CA B:ASP56 3.7 18.0 1.0
CB B:SER78 3.9 16.8 1.0
N B:SER78 4.0 19.4 1.0
O B:HOH2023 4.1 25.0 1.0
OD1 B:ASP76 4.2 27.0 1.0
OD2 B:ASP56 4.2 16.2 1.0
CB B:ASP56 4.2 17.3 1.0
N B:ASP76 4.2 22.1 1.0
CA B:GLY74 4.3 20.6 1.0
N B:GLY74 4.4 23.7 1.0
N B:ALA57 4.4 17.7 1.0
CA B:SER78 4.4 19.3 1.0
O B:GLY59 4.5 15.0 1.0
N B:GLY77 4.5 19.1 1.0
OE2 B:GLU86 4.6 19.3 1.0
N B:ILE79 4.6 21.0 1.0
N B:ALA75 4.6 20.4 1.0
OE1 B:GLU86 4.7 20.1 1.0
CB B:SER147 4.7 20.2 1.0
O B:HIS55 4.9 18.3 1.0
CA B:ALA57 4.9 16.5 1.0
CA B:ALA75 4.9 21.5 1.0
CB B:ASP76 4.9 22.4 1.0
CA B:ASP76 4.9 20.2 1.0
C B:SER78 4.9 20.2 1.0
C B:GLY73 5.0 25.7 1.0

Calcium binding site 4 out of 4 in 1lyk

Go back to Calcium Binding Sites List in 1lyk
Calcium binding site 4 out of 4 in the The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Impact of the Physical and Chemical Enviroment on the Molecular Structure of Coprinus Cinereus Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca9346

b:13.0
occ:1.00
 O B:SER184 2.3 18.1 1.0
O B:THR203 2.3 18.6 1.0
O B:VAL206 2.4 20.6 1.0
OG B:SER184 2.4 14.4 1.0
OD2 B:ASP201 2.4 15.3 1.0
OG1 B:THR203 2.4 20.2 1.0
OD1 B:ASP208 2.4 17.2 1.0
OD1 B:ASP201 2.8 14.8 1.0
CG B:ASP201 3.0 15.7 1.0
C B:SER184 3.2 13.9 1.0
C B:THR203 3.3 15.6 1.0
CG B:ASP208 3.4 17.7 1.0
CB B:THR203 3.5 17.8 1.0
CB B:SER184 3.5 14.1 1.0
C B:VAL206 3.6 19.1 1.0
CA B:SER184 3.6 14.9 1.0
CA B:THR203 3.8 18.3 1.0
OD2 B:ASP208 3.8 17.4 1.0
N B:ASP208 4.0 16.6 1.0
N B:THR203 4.2 18.4 1.0
O B:ASP208 4.3 12.5 1.0
N B:PRO204 4.3 16.3 1.0
N B:VAL206 4.4 18.7 1.0
CA B:VAL206 4.4 17.5 1.0
O B:HOH2013 4.5 24.2 1.0
N B:LEU185 4.5 14.5 1.0
CB B:ASP201 4.5 15.3 1.0
N B:PHE207 4.6 18.7 1.0
CB B:ASP208 4.7 17.6 1.0
CB B:VAL206 4.7 13.8 1.0
CA B:PRO204 4.7 17.2 1.0
CB B:GLN210 4.7 14.2 1.0
CA B:PHE207 4.7 18.3 1.0
CA B:ASP208 4.7 15.0 1.0
CG2 B:THR203 4.8 18.6 1.0
C B:PHE207 4.8 16.6 1.0
C B:ASP208 4.8 14.6 1.0

Reference:

K.Houborg, P.Harris, J.Petersen, P.Rowland, J.C.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 12:12:02 2024

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