Calcium in PDB 8ogi: Structure of Native Human Eosinophil Peroxidase

The structure of Structure of Native Human Eosinophil Peroxidase, PDB code: 8ogi was solved by V.Pfanzagl, C.Obinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.57 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.123, 85.562, 139.395, 90, 90, 90
R / Rfree (%)	17.4 / 18.5

The structure of Structure of Native Human Eosinophil Peroxidase also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Structure of Native Human Eosinophil Peroxidase (pdb code 8ogi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of Native Human Eosinophil Peroxidase, PDB code: 8ogi:

Calcium binding site 1 out of 1 in the Structure of Native Human Eosinophil Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Native Human Eosinophil Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca805 b:17.1 occ:1.00 O A:ASP234 2.3 18.9 1.0 O B:PHE308 2.3 18.0 1.0 OD1 A:ASP234 2.4 19.3 1.0 OD1 B:ASP310 2.4 17.1 1.0 O B:THR306 2.4 16.9 1.0 OG B:SER312 2.4 18.9 1.0 OG1 B:THR306 2.4 18.9 1.0 H B:ASP310 3.2 17.3 0.0 H B:SER312 3.3 16.4 0.0 HB3 B:SER312 3.3 18.9 0.0 C A:ASP234 3.4 17.5 1.0 C B:THR306 3.4 16.9 1.0 CG B:ASP310 3.4 18.5 1.0 CB B:SER312 3.4 19.7 1.0 C B:PHE308 3.5 17.5 1.0 CG A:ASP234 3.6 19.1 1.0 CB B:THR306 3.7 17.7 1.0 H B:THR306 3.7 16.2 0.0 HA A:ASP234 3.8 16.6 0.0 OD2 B:ASP310 3.9 19.4 1.0 CA B:THR306 3.9 16.5 1.0 HA A:LEU235 4.0 16.0 0.0 HA B:VAL309 4.0 16.1 0.0 CA A:ASP234 4.0 17.2 1.0 H B:PHE308 4.0 16.0 0.0 N B:PHE308 4.1 16.8 1.0 N B:ASP310 4.1 18.1 1.0 N B:THR306 4.1 17.1 1.0 N B:SER312 4.1 17.2 1.0 HB2 B:SER312 4.2 18.9 0.0 CB A:ASP234 4.2 17.8 1.0 HB B:THR306 4.3 16.9 0.0 HB2 B:PHE308 4.3 15.4 0.0 CA B:PHE308 4.4 16.6 1.0 HB3 B:LEU305 4.4 15.7 0.0 CA B:SER312 4.4 17.9 1.0 C B:SER307 4.4 17.5 1.0 N A:LEU235 4.4 16.9 1.0 HG23 B:THR306 4.5 18.1 0.0 N B:SER307 4.5 16.8 1.0 HB3 A:ASP234 4.5 17.1 0.0 HD23 A:LEU235 4.5 20.0 0.0 O B:HOH942 4.5 17.2 1.0 OD2 A:ASP234 4.5 19.2 1.0 N B:VAL309 4.5 16.9 1.0 CB B:ASP310 4.6 18.4 1.0 CG2 B:THR306 4.7 18.9 1.0 CA B:VAL309 4.7 17.0 1.0 CA A:LEU235 4.7 16.8 1.0 HA B:SER307 4.8 15.5 0.0 CA B:ASP310 4.8 17.8 1.0 CA B:SER307 4.8 16.6 1.0 H B:ALA311 4.9 16.9 0.0 C B:VAL309 4.9 18.6 1.0 CB B:PHE308 4.9 16.0 1.0 O B:SER307 5.0 18.6 1.0 HB3 B:ASP310 5.0 17.9 0.0 HA B:THR306 5.0 15.7 0.0

V.Pfanzagl, C.Gruber-Grunwald, U.Leitgeb, P.G.Furtmuller, C.Obinger. Posttranslational Modification and Heme Cavity Architecture of Human Eosinophil Peroxidase-Insights From First Crystal Structure and Biochemical Characterization. J.Biol.Chem. V. 299 05402 2023.
ISSN: ESSN 1083-351X
PubMed: 38229400
DOI: 10.1016/J.JBC.2023.105402