Calcium in PDB 1gzb: Peroxidase

All present enzymatic activity of Peroxidase:
1.11.1.7;

The structure of Peroxidase, PDB code: 1gzb was solved by K.Fukuyama, N.Kunishima, F.Amada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.80
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 (%)	18.8 / n/a

The structure of Peroxidase also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Peroxidase (pdb code 1gzb). 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: 1gzb:
Jump to Calcium binding site number: 1; 2;

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:17.6 occ:1.00 OD1 A:ASP57 2.4 12.0 1.0 OD1 A:ASP77 2.5 15.1 1.0 O A:HOH424 2.5 12.1 1.0 O A:GLY75 2.5 13.6 1.0 O A:ASP57 2.5 11.1 1.0 OG A:SER79 2.5 10.7 1.0 O A:HOH425 2.6 13.5 1.0 C A:ASP57 3.4 12.3 1.0 CG A:ASP57 3.4 10.5 1.0 CG A:ASP77 3.6 14.2 1.0 C A:GLY75 3.7 14.0 1.0 CB A:SER79 3.7 11.2 1.0 CA A:ASP57 3.7 12.0 1.0 N A:SER79 4.0 12.4 1.0 N A:ASP77 4.1 13.4 1.0 OD2 A:ASP77 4.2 13.7 1.0 CB A:ASP57 4.2 11.0 1.0 OD2 A:ASP57 4.2 10.0 1.0 N A:GLY75 4.3 13.7 1.0 CA A:SER79 4.4 13.3 1.0 CA A:GLY75 4.4 13.3 1.0 O A:HOH363 4.4 14.7 1.0 N A:GLY78 4.5 12.5 1.0 N A:ALA58 4.5 11.6 1.0 N A:ILE80 4.6 13.6 1.0 O A:GLY60 4.6 14.3 1.0 OE2 A:GLU87 4.7 14.5 1.0 N A:ALA76 4.7 14.4 1.0 CB A:ASP77 4.7 13.6 1.0 CA A:ASP77 4.8 13.4 1.0 CB A:SER148 4.9 13.6 1.0 CA A:ALA76 4.9 15.3 1.0 C A:SER79 4.9 14.3 1.0 O A:HIS56 4.9 11.9 1.0 OE1 A:GLU87 4.9 12.6 1.0 C A:ASP77 4.9 12.6 1.0 CA A:ALA58 4.9 11.9 1.0 C A:GLY78 5.0 13.1 1.0 C A:GLY74 5.0 14.7 1.0

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:9.4 occ:1.00 O A:THR204 2.4 12.4 1.0 OG1 A:THR204 2.5 12.7 1.0 O A:VAL207 2.5 12.2 1.0 O A:SER185 2.5 11.4 1.0 OD1 A:ASP209 2.5 13.3 1.0 OD2 A:ASP202 2.5 12.5 1.0 OG A:SER185 2.6 7.6 1.0 OD1 A:ASP202 2.7 11.4 1.0 CG A:ASP202 3.0 11.4 1.0 C A:THR204 3.3 12.9 1.0 CG A:ASP209 3.4 11.7 1.0 C A:SER185 3.5 10.1 1.0 CB A:THR204 3.5 11.5 1.0 CB A:SER185 3.6 9.0 1.0 C A:VAL207 3.7 12.4 1.0 CA A:SER185 3.7 9.4 1.0 CA A:THR204 3.9 12.3 1.0 OD2 A:ASP209 3.9 11.7 1.0 N A:ASP209 4.1 10.9 1.0 N A:THR204 4.2 11.8 1.0 N A:VAL207 4.3 13.1 1.0 N A:PRO205 4.3 13.4 1.0 CA A:VAL207 4.4 11.6 1.0 CB A:VAL207 4.5 10.6 1.0 CB A:ASP202 4.5 11.3 1.0 O A:ASP209 4.6 10.5 1.0 CA A:PRO205 4.6 15.2 1.0 CB A:ASP209 4.6 11.4 1.0 O A:HOH515 4.6 11.3 1.0 N A:PHE208 4.7 11.9 1.0 N A:LEU186 4.7 11.1 1.0 CA A:ASP209 4.7 11.0 1.0 CD1 A:LEU186 4.8 15.7 1.0 CB A:GLN211 4.8 11.9 1.0 CA A:PHE208 4.8 12.6 1.0 CG2 A:THR204 4.8 10.6 1.0 C A:ASP209 4.9 11.2 1.0 C A:PHE208 4.9 11.7 1.0 C A:PRO205 4.9 15.2 1.0

N.Kunishima, F.Amada, K.Fukuyama, M.Kawamoto, T.Matsunaga, H.Matsubara. Pentacoordination of the Heme Iron of Arthromyces Ramosus Peroxidase Shown By A 1.8 A Resolution Crystallographic Study at pH 4.5. Febs Lett. V. 378 291 1996.
ISSN: ISSN 0014-5793
PubMed: 8557120
DOI: 10.1016/0014-5793(95)01458-6