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Calcium in PDB 2boq: Crystal Structure of Versatile Peroxidase

Protein crystallography data

The structure of Crystal Structure of Versatile Peroxidase, PDB code: 2boq was solved by T.Choinowski, K.Piontek, A.T.Martinez, M.Perez-Boada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.25 / 1.33
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 62.799, 62.799, 98.222, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.2

Other elements in 2boq:

The structure of Crystal Structure of Versatile Peroxidase also contains other interesting chemical elements:

Arsenic (As) 1 atom
Manganese (Mn) 1 atom
Iron (Fe) 1 atom
Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Versatile Peroxidase (pdb code 2boq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Versatile Peroxidase, PDB code: 2boq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2boq

Go back to Calcium Binding Sites List in 2boq
Calcium binding site 1 out of 2 in the Crystal Structure of Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Versatile Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1351

b:10.8
occ:1.00
OD1 A:ASP48 2.3 11.7 1.0
O A:HOH2081 2.3 11.8 1.0
OG A:SER64 2.4 11.8 1.0
OD1 A:ASP62 2.4 11.7 1.0
O A:ASP48 2.4 11.6 1.0
O A:GLY60 2.5 11.5 1.0
O A:HOH2110 2.5 11.2 1.0
C A:ASP48 3.3 10.3 1.0
CG A:ASP48 3.4 10.8 1.0
CG A:ASP62 3.5 13.1 1.0
CB A:SER64 3.5 12.1 1.0
C A:GLY60 3.7 11.0 1.0
CA A:ASP48 3.7 10.1 1.0
N A:SER64 4.0 11.6 1.0
OD2 A:ASP62 4.0 14.2 1.0
O A:HOH2097 4.1 13.2 1.0
CB A:ASP48 4.2 10.6 1.0
N A:ASP62 4.2 10.6 1.0
OD2 A:ASP48 4.2 12.7 1.0
CA A:SER64 4.3 11.8 1.0
N A:GLY60 4.3 13.3 1.0
CA A:GLY60 4.4 12.5 1.0
O A:GLY51 4.4 13.2 1.0
N A:ALA49 4.5 10.2 1.0
N A:ILE65 4.5 12.9 1.0
OE2 A:GLU72 4.5 13.8 1.0
N A:ALA61 4.7 11.2 1.0
N A:GLY63 4.7 11.8 1.0
CB A:ASP62 4.7 11.5 1.0
OE1 A:GLU72 4.8 13.4 1.0
C A:SER64 4.8 12.6 1.0
CA A:GLY51 4.8 12.6 1.0
CA A:ASP62 4.8 11.0 1.0
O A:HIS47 4.9 12.2 1.0
CA A:ALA49 4.9 10.5 1.0
CA A:ALA61 4.9 11.2 1.0
C A:GLY59 4.9 14.4 1.0
N A:GLY51 5.0 11.6 1.0
CB A:SER133 5.0 12.9 1.0

Calcium binding site 2 out of 2 in 2boq

Go back to Calcium Binding Sites List in 2boq
Calcium binding site 2 out of 2 in the Crystal Structure of Versatile Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Versatile Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1352

b:10.8
occ:1.00
O A:SER170 2.4 10.3 1.0
OD2 A:ASP187 2.4 11.2 1.0
O A:VAL192 2.4 12.1 1.0
O A:THR189 2.4 11.5 1.0
OD1 A:ASP194 2.5 12.0 1.0
OG1 A:THR189 2.5 12.8 1.0
OG A:SER170 2.5 11.5 1.0
OD1 A:ASP187 2.7 11.6 1.0
CG A:ASP187 2.9 10.2 1.0
C A:THR189 3.3 11.8 1.0
C A:SER170 3.3 9.7 1.0
CG A:ASP194 3.5 12.9 1.0
CB A:THR189 3.5 12.6 1.0
CB A:SER170 3.6 10.1 1.0
C A:VAL192 3.6 11.7 1.0
CA A:SER170 3.7 10.2 1.0
OD2 A:ASP194 3.8 13.4 1.0
CA A:THR189 3.8 12.1 1.0
N A:ASP194 4.1 12.3 1.0
N A:PRO190 4.2 12.3 1.0
N A:THR189 4.2 13.0 1.0
CA A:VAL192 4.4 12.8 1.0
N A:VAL192 4.4 11.5 1.0
CB A:ASP187 4.5 11.2 1.0
CA A:PRO190 4.5 12.4 1.0
CB A:VAL192 4.5 12.8 1.0
CB A:GLN196 4.5 14.9 1.0
O A:ASP194 4.5 13.3 1.0
N A:ILE171 4.6 9.7 1.0
O A:HOH2228 4.6 12.1 1.0
N A:PHE193 4.6 11.5 1.0
CB A:ASP194 4.7 13.5 1.0
CA A:PHE193 4.8 11.1 1.0
CA A:ASP194 4.8 12.4 1.0
CG2 A:ILE171 4.8 12.3 1.0
CG2 A:THR189 4.9 14.8 1.0
C A:ASP194 4.9 13.9 1.0
C A:PRO190 5.0 12.6 1.0
C A:PHE193 5.0 12.2 1.0

Reference:

M.Perez-Boada, F.J.Ruiz-Duenas, R.Pogni, R.Basosi, T.Choinowski, M.J.Martinez, K.Piontek, A.T.Martinez. Versatile Peroxidase Oxidation of High Redox Potential Aromatic Compounds: Site-Directed Mutagenesis, Spectroscopic and Crystallographic Investigation of Three Long-Range Electron Transfer Pathways. J.Mol.Biol. V. 354 385 2005.
ISSN: ISSN 0022-2836
PubMed: 16246366
DOI: 10.1016/J.JMB.2005.09.047
Page generated: Fri Jul 12 09:06:48 2024

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