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Calcium in PDB 1gza: Peroxidase

Enzymatic activity of Peroxidase

All present enzymatic activity of Peroxidase:
1.11.1.7;

Protein crystallography data

The structure of Peroxidase, PDB code: 1gza was solved by K.Fukuyama, H.Itakura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.06
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.570, 74.570, 117.470, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / n/a

Other elements in 1gza:

The structure of Peroxidase also contains other interesting chemical elements:

Iodine (I) 1 atom
Iron (Fe) 1 atom

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 1gza

Go back to Calcium Binding Sites List in 1gza
Calcium binding site 1 out of 2 in the Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca346

b:14.8
occ:1.00
OD1 A:ASP57 2.3 15.1 1.0
OD1 A:ASP77 2.4 15.9 1.0
O A:HOH425 2.4 15.3 1.0
O A:ASP57 2.5 13.0 1.0
O A:GLY75 2.5 15.7 1.0
O A:HOH424 2.5 12.0 1.0
OG A:SER79 2.5 12.6 1.0
CG A:ASP57 3.4 14.7 1.0
C A:ASP57 3.4 13.4 1.0
CG A:ASP77 3.5 14.9 1.0
CB A:SER79 3.7 10.4 1.0
C A:GLY75 3.7 15.8 1.0
CA A:ASP57 3.8 13.2 1.0
N A:SER79 3.9 12.5 1.0
OD2 A:ASP77 4.1 16.1 1.0
N A:ASP77 4.1 14.9 1.0
OD2 A:ASP57 4.2 15.1 1.0
CB A:ASP57 4.2 12.7 1.0
O A:HOH363 4.3 17.4 1.0
CA A:SER79 4.3 12.8 1.0
N A:GLY75 4.4 15.4 1.0
N A:GLY78 4.5 12.2 1.0
CA A:GLY75 4.5 15.2 1.0
N A:ILE80 4.5 12.8 1.0
N A:ALA58 4.6 12.9 1.0
O A:GLY60 4.6 14.6 1.0
N A:ALA76 4.7 15.7 1.0
OE2 A:GLU87 4.7 14.9 1.0
CB A:ASP77 4.7 13.1 1.0
CA A:ASP77 4.8 14.6 1.0
C A:SER79 4.8 14.1 1.0
CA A:ALA76 4.9 15.9 1.0
OE1 A:GLU87 4.9 14.7 1.0
C A:ASP77 4.9 13.2 1.0
CB A:SER148 4.9 14.3 1.0
O A:HIS56 5.0 14.4 1.0
C A:GLY78 5.0 13.1 1.0

Calcium binding site 2 out of 2 in 1gza

Go back to Calcium Binding Sites List in 1gza
Calcium binding site 2 out of 2 in the Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca347

b:12.7
occ:1.00
OG A:SER185 2.4 11.3 1.0
O A:SER185 2.4 11.1 1.0
OD1 A:ASP209 2.4 14.2 1.0
OD2 A:ASP202 2.5 11.0 1.0
O A:THR204 2.5 12.8 1.0
O A:VAL207 2.5 13.4 1.0
OG1 A:THR204 2.5 15.0 1.0
OD1 A:ASP202 2.6 12.2 1.0
CG A:ASP202 2.9 12.9 1.0
C A:THR204 3.4 13.2 1.0
C A:SER185 3.4 11.7 1.0
CG A:ASP209 3.5 13.0 1.0
CB A:SER185 3.6 10.6 1.0
CB A:THR204 3.7 13.1 1.0
CA A:SER185 3.7 11.3 1.0
C A:VAL207 3.7 11.9 1.0
OD2 A:ASP209 3.9 14.1 1.0
CA A:THR204 4.0 12.4 1.0
N A:ASP209 4.1 13.4 1.0
N A:THR204 4.2 13.6 1.0
N A:VAL207 4.4 12.8 1.0
N A:PRO205 4.4 13.0 1.0
O A:ASP209 4.4 12.2 1.0
CB A:ASP202 4.4 11.0 1.0
CA A:VAL207 4.5 11.7 1.0
O A:HOH515 4.5 13.4 1.0
CB A:ASP209 4.6 11.4 1.0
CA A:PRO205 4.6 13.9 1.0
N A:LEU186 4.6 12.1 1.0
CB A:VAL207 4.6 10.2 1.0
N A:PHE208 4.7 13.5 1.0
CA A:ASP209 4.7 12.5 1.0
CA A:PHE208 4.8 12.7 1.0
CD1 A:LEU186 4.8 13.2 1.0
CB A:GLN211 4.8 9.0 1.0
C A:ASP209 4.8 13.2 1.0
C A:PHE208 4.9 14.1 1.0
CG2 A:THR204 4.9 11.5 1.0

Reference:

K.Fukuyama, K.Sato, H.Itakura, S.Takahashi, T.Hosoya. Binding of Iodide to Arthromyces Ramosus Peroxidase Investigated with X-Ray Crystallographic Analysis, 1H and 127I uc(Nmr) Spectroscopy, and Steady-State Kinetics. J.Biol.Chem. V. 272 5752 1997.
ISSN: ISSN 0021-9258
PubMed: 9038188
DOI: 10.1074/JBC.272.9.5752
Page generated: Sat Dec 12 02:58:35 2020

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