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Calcium in PDB 1ly8: The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures

Enzymatic activity of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures

All present enzymatic activity of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures:
1.11.1.7;

Protein crystallography data

The structure of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures, PDB code: 1ly8 was solved by K.Houborg, P.Harris, J.-C.N.Poulsen, A.Svendsen, P.Schneider, S.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.490, 114.860, 73.610, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.9

Other elements in 1ly8:

The structure of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures (pdb code 1ly8). 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 Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures, PDB code: 1ly8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ly8

Go back to Calcium Binding Sites List in 1ly8
Calcium binding site 1 out of 4 in the The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca9001

b:10.3
occ:1.00
 OG A:SER78 2.4 10.5 1.0
OD1 A:ASP56 2.4 9.5 1.0
O A:ASP56 2.4 9.7 1.0
O A:HOH9029 2.4 17.9 1.0
O A:GLY74 2.5 12.1 1.0
O A:HOH9218 2.5 8.9 1.0
OD2 A:ASP76 2.6 11.3 1.0
C A:ASP56 3.3 9.6 1.0
CG A:ASP56 3.3 10.3 1.0
CB A:SER78 3.6 10.1 1.0
C A:GLY74 3.6 11.8 1.0
CG A:ASP76 3.7 11.4 1.0
CA A:ASP56 3.7 9.8 1.0
N A:SER78 3.9 9.9 1.0
OD1 A:ASP76 4.1 11.2 1.0
OD2 A:ASP56 4.1 10.8 1.0
N A:ASP76 4.1 11.2 1.0
CB A:ASP56 4.1 10.1 1.0
O A:HOH9010 4.2 6.5 1.0
CA A:SER78 4.3 10.1 1.0
CA A:GLY74 4.4 11.8 1.0
N A:GLY74 4.4 12.2 1.0
N A:ALA57 4.4 9.3 1.0
OE2 A:GLU86 4.5 12.9 1.0
N A:ILE79 4.5 10.0 1.0
N A:GLY77 4.5 11.0 1.0
OE1 A:GLU86 4.6 12.3 1.0
N A:ALA75 4.6 11.8 1.0
O A:GLY59 4.6 11.4 1.0
CB A:SER147 4.7 12.7 1.0
C A:SER78 4.8 10.1 1.0
CB A:ASP76 4.8 11.2 1.0
CA A:ASP76 4.8 11.1 1.0
CA A:ALA75 4.8 11.5 1.0
CA A:ALA57 4.9 9.4 1.0
C A:ASP76 4.9 11.0 1.0
C A:GLY77 5.0 10.2 1.0
CA A:GLY59 5.0 11.0 1.0
CD A:GLU86 5.0 12.9 1.0
O A:HIS55 5.0 10.3 1.0
C A:ALA75 5.0 11.8 1.0

Calcium binding site 2 out of 4 in 1ly8

Go back to Calcium Binding Sites List in 1ly8
Calcium binding site 2 out of 4 in the The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca9004

b:9.6
occ:1.00
 OD2 A:ASP201 2.3 10.2 1.0
O A:SER184 2.3 8.4 1.0
O A:VAL206 2.4 10.7 1.0
O A:THR203 2.4 10.9 1.0
OD1 A:ASP208 2.4 10.7 1.0
OG A:SER184 2.5 9.5 1.0
OG1 A:THR203 2.5 10.2 1.0
CG A:ASP201 3.0 10.6 1.0
OD1 A:ASP201 3.0 11.2 1.0
C A:THR203 3.3 10.7 1.0
C A:SER184 3.3 9.0 1.0
CG A:ASP208 3.4 10.2 1.0
CB A:THR203 3.5 10.4 1.0
CB A:SER184 3.6 9.0 1.0
C A:VAL206 3.6 11.2 1.0
CA A:SER184 3.7 8.8 1.0
OD2 A:ASP208 3.8 10.6 1.0
CA A:THR203 3.8 10.4 1.0
N A:ASP208 4.0 11.3 1.0
N A:THR203 4.2 10.0 1.0
N A:PRO204 4.3 10.9 1.0
N A:VAL206 4.3 11.0 1.0
O A:HOH9070 4.4 16.2 1.0
CA A:VAL206 4.4 11.2 1.0
CB A:ASP201 4.5 9.9 1.0
O A:ASP208 4.5 10.6 1.0
CB A:VAL206 4.5 11.0 1.0
N A:LEU185 4.5 9.3 1.0
CB A:GLN210 4.6 10.4 1.0
N A:PHE207 4.6 11.4 1.0
CB A:ASP208 4.6 11.0 1.0
CA A:PHE207 4.7 11.4 1.0
CA A:ASP208 4.7 10.9 1.0
CA A:PRO204 4.7 10.9 1.0
C A:PHE207 4.8 11.4 1.0
CG2 A:THR203 4.8 10.6 1.0
C A:ASP208 4.9 10.8 1.0
CD2 A:LEU185 4.9 10.2 1.0

Calcium binding site 3 out of 4 in 1ly8

Go back to Calcium Binding Sites List in 1ly8
Calcium binding site 3 out of 4 in the The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca9002

b:11.1
occ:1.00
 OD1 B:ASP56 2.3 9.8 1.0
OG B:SER78 2.3 10.1 1.0
O B:HOH9017 2.3 13.3 1.0
O B:ASP56 2.4 9.0 1.0
O B:GLY74 2.4 10.8 1.0
O B:HOH9196 2.6 9.4 1.0
OD2 B:ASP76 2.6 11.4 1.0
C B:ASP56 3.3 9.3 1.0
CG B:ASP56 3.4 9.4 1.0
CB B:SER78 3.6 10.4 1.0
CG B:ASP76 3.6 11.6 1.0
C B:GLY74 3.6 10.9 1.0
CA B:ASP56 3.7 9.6 1.0
N B:SER78 3.9 10.5 1.0
N B:ASP76 4.1 10.9 1.0
OD1 B:ASP76 4.1 11.3 1.0
O B:HOH9121 4.1 14.8 1.0
CB B:ASP56 4.1 9.6 1.0
OD2 B:ASP56 4.2 9.0 1.0
CA B:SER78 4.3 10.6 1.0
N B:GLY74 4.4 11.4 1.0
CA B:GLY74 4.4 11.0 1.0
N B:ILE79 4.4 10.4 1.0
N B:ALA57 4.5 8.6 1.0
N B:GLY77 4.5 11.0 1.0
OE2 B:GLU86 4.6 13.6 1.0
OE1 B:GLU86 4.6 13.0 1.0
N B:ALA75 4.6 10.3 1.0
O B:GLY59 4.6 10.3 1.0
CA B:ALA75 4.7 10.7 1.0
CB B:SER147 4.8 14.2 1.0
CB B:ASP76 4.8 11.5 1.0
CA B:ASP76 4.8 11.3 1.0
C B:SER78 4.8 10.7 1.0
C B:ASP76 4.9 11.3 1.0
C B:ALA75 4.9 11.1 1.0
C B:GLY77 4.9 10.7 1.0
CA B:ALA57 4.9 8.9 1.0
CA B:GLY59 4.9 10.2 1.0
O B:HIS55 5.0 11.7 1.0

Calcium binding site 4 out of 4 in 1ly8

Go back to Calcium Binding Sites List in 1ly8
Calcium binding site 4 out of 4 in the The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability and Insight Into Modelling of Protein Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca9003

b:8.3
occ:1.00
 OD2 B:ASP201 2.2 11.9 1.0
O B:SER184 2.3 8.9 1.0
O B:THR203 2.3 9.4 1.0
O B:VAL206 2.4 9.7 1.0
OG B:SER184 2.4 6.7 1.0
OD1 B:ASP208 2.5 9.9 1.0
OG1 B:THR203 2.5 10.3 1.0
CG B:ASP201 3.1 11.8 1.0
OD1 B:ASP201 3.2 11.5 1.0
C B:SER184 3.3 8.5 1.0
C B:THR203 3.3 10.1 1.0
CG B:ASP208 3.4 9.8 1.0
CB B:THR203 3.5 10.2 1.0
CB B:SER184 3.5 7.9 1.0
C B:VAL206 3.6 9.8 1.0
CA B:SER184 3.6 8.3 1.0
OD2 B:ASP208 3.8 9.8 1.0
CA B:THR203 3.8 9.9 1.0
N B:ASP208 4.0 9.6 1.0
N B:THR203 4.2 9.9 1.0
N B:VAL206 4.3 10.2 1.0
N B:PRO204 4.3 10.3 1.0
CA B:VAL206 4.3 10.2 1.0
O B:HOH9212 4.5 21.5 1.0
O B:ASP208 4.5 9.1 1.0
CB B:ASP201 4.5 11.8 1.0
N B:LEU185 4.5 8.7 1.0
CB B:VAL206 4.5 10.2 1.0
N B:PHE207 4.6 9.7 1.0
CB B:ASP208 4.6 10.1 1.0
CA B:PHE207 4.7 9.8 1.0
CA B:ASP208 4.7 9.4 1.0
CB B:GLN210 4.7 10.0 1.0
CA B:PRO204 4.7 10.2 1.0
CG2 B:THR203 4.8 10.0 1.0
C B:PHE207 4.8 9.7 1.0
C B:ASP208 4.9 9.5 1.0
CD2 B:LEU185 5.0 9.1 1.0

Reference:

K.Houborg, P.Harris, J.C.Poulsen, P.Schneider, A.Svendsen, S.Larsen. The Structure of A Mutant Enzyme of Coprinus Cinereus Peroxidase Provides An Understanding of Its Increased Thermostability. Acta Crystallogr.,Sect.D V. 59 997 2003.
ISSN: ISSN 0907-4449
PubMed: 12777761
DOI: 10.1107/S0907444903006784
Page generated: Sat Dec 12 03:06:09 2020

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