Calcium in PDB 4a5g: Raphanus Sativus Anionic Peroxidase.

All present enzymatic activity of Raphanus Sativus Anionic Peroxidase.:
1.11.1.7;

The structure of Raphanus Sativus Anionic Peroxidase., PDB code: 4a5g was solved by N.Jimenez-Arroyo, B.Valderrama, P.Gil-Rodriguez, S.P.Rojas-Trejo, E.Rudino-Pinera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.287 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.148, 41.192, 137.796, 90.00, 96.91, 90.00
R / Rfree (%)	16.29 / 18.52

The structure of Raphanus Sativus Anionic Peroxidase. also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Raphanus Sativus Anionic Peroxidase. (pdb code 4a5g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Raphanus Sativus Anionic Peroxidase., PDB code: 4a5g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Raphanus Sativus Anionic Peroxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Raphanus Sativus Anionic Peroxidase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1308 b:22.4 occ:1.00 O A:VAL48 2.4 19.8 1.0 O A:ASP45 2.5 19.0 1.0 OD1 A:ASP52 2.5 23.6 1.0 OG A:SER54 2.5 19.2 1.0 OD1 A:ASP45 2.6 18.6 1.0 O A:HOH2062 2.6 21.1 1.0 O A:GLY50 2.6 18.8 1.0 C A:ASP45 3.3 22.7 1.0 C A:VAL48 3.5 23.1 1.0 CG A:ASP52 3.5 24.2 1.0 CB A:SER54 3.6 17.9 1.0 CG A:ASP45 3.6 22.1 1.0 CA A:ASP45 3.7 21.3 1.0 C A:GLY50 3.8 22.8 1.0 N A:SER54 3.8 19.7 1.0 N A:ASP52 4.0 21.6 1.0 OD2 A:ASP52 4.0 23.2 1.0 CA A:SER54 4.2 21.3 1.0 C A:LEU49 4.2 23.8 1.0 CB A:ASP45 4.3 16.6 1.0 CA A:VAL48 4.3 20.1 1.0 N A:GLY50 4.3 20.4 1.0 CB A:VAL48 4.3 23.2 1.0 O A:LEU49 4.4 26.2 1.0 N A:VAL48 4.5 18.0 1.0 N A:CYS46 4.5 20.4 1.0 N A:LEU49 4.5 19.1 1.0 N A:ALA53 4.5 16.4 1.0 OD2 A:ASP45 4.5 18.3 1.0 CB A:ASP52 4.6 22.1 1.0 CA A:GLY50 4.6 19.2 1.0 CB A:LEU49 4.6 26.1 1.0 N A:ILE55 4.6 17.0 1.0 CA A:ASP52 4.6 22.6 1.0 CA A:LEU49 4.6 23.6 1.0 N A:CYS51 4.7 19.7 1.0 OE1 A:GLU66 4.7 20.6 1.0 O A:HIS44 4.7 24.3 1.0 CA A:CYS51 4.7 19.5 1.0 C A:ASP52 4.7 22.2 1.0 OE2 A:GLU66 4.7 22.3 1.0 CG1 A:VAL48 4.9 21.8 1.0 C A:CYS51 4.9 23.9 1.0 C A:SER54 4.9 23.1 1.0 C A:ALA53 4.9 21.9 1.0 CA A:CYS46 4.9 20.7 1.0

Calcium binding site 2 out of 4 in the Raphanus Sativus Anionic Peroxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Raphanus Sativus Anionic Peroxidase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1309 b:20.2 occ:1.00 O A:THR172 2.4 18.4 1.0 OD2 A:ASP223 2.4 18.6 1.0 OD1 A:ASP231 2.5 18.2 1.0 O A:ALA229 2.5 21.0 1.0 OG1 A:THR172 2.6 17.9 1.0 O A:THR226 2.6 18.6 1.0 OG1 A:THR226 2.7 19.9 1.0 C A:THR172 3.3 20.1 1.0 CG A:ASP231 3.3 22.6 1.0 CG A:ASP223 3.4 22.3 1.0 C A:THR226 3.6 20.5 1.0 OD2 A:ASP231 3.6 25.9 1.0 CB A:THR172 3.6 19.7 1.0 C A:ALA229 3.6 20.1 1.0 CB A:THR226 3.7 21.1 1.0 CA A:THR172 3.8 19.1 1.0 CB A:ASP223 3.9 17.4 1.0 CA A:THR226 4.0 19.9 1.0 N A:ASP231 4.2 18.6 1.0 CG2 A:THR172 4.3 14.7 1.0 OD1 A:ASP223 4.3 21.4 1.0 N A:ALA229 4.4 17.2 1.0 N A:THR226 4.4 20.5 1.0 CA A:ALA229 4.4 18.9 1.0 N A:PHE173 4.5 20.8 1.0 CB A:ASN233 4.5 21.4 1.0 O A:ASP231 4.6 19.1 1.0 CB A:ASP231 4.6 19.0 1.0 N A:PHE230 4.6 22.2 1.0 CB A:ALA229 4.7 18.1 1.0 N A:PRO227 4.7 20.7 1.0 CA A:PHE230 4.7 20.2 1.0 CA A:ASP231 4.8 19.6 1.0 CG2 A:THR226 4.9 17.0 1.0 C A:PHE230 4.9 23.8 1.0 C A:ASP231 4.9 21.1 1.0 C A:PRO227 5.0 22.0 1.0 CA A:PHE173 5.0 21.4 1.0

Calcium binding site 3 out of 4 in the Raphanus Sativus Anionic Peroxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Raphanus Sativus Anionic Peroxidase. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1307 b:25.1 occ:1.00 O B:VAL48 2.3 26.7 1.0 OD1 B:ASP45 2.4 19.2 1.0 OD1 B:ASP52 2.4 21.3 1.0 O B:ASP45 2.5 19.0 1.0 OG B:SER54 2.6 21.2 1.0 O B:GLY50 2.6 18.3 1.0 O B:HOH2074 2.6 21.1 1.0 C B:ASP45 3.3 21.4 1.0 CG B:ASP52 3.4 23.4 1.0 C B:VAL48 3.5 24.4 1.0 CG B:ASP45 3.5 22.4 1.0 CB B:SER54 3.5 18.0 1.0 CA B:ASP45 3.7 23.7 1.0 C B:GLY50 3.8 19.9 1.0 N B:SER54 3.8 23.9 1.0 N B:ASP52 3.9 17.2 1.0 OD2 B:ASP52 4.0 21.2 1.0 CB B:ASP45 4.2 22.1 1.0 CA B:SER54 4.2 20.2 1.0 C B:LEU49 4.2 24.4 1.0 CB B:VAL48 4.2 24.8 1.0 CA B:VAL48 4.2 25.9 1.0 N B:GLY50 4.3 24.3 1.0 O B:LEU49 4.3 26.6 1.0 OD2 B:ASP45 4.4 21.2 1.0 N B:CYS46 4.4 21.2 1.0 N B:VAL48 4.4 21.1 1.0 N B:LEU49 4.5 25.4 1.0 CB B:ASP52 4.5 20.5 1.0 N B:ALA53 4.5 19.8 1.0 N B:ILE55 4.5 19.2 1.0 CA B:ASP52 4.5 22.4 1.0 CA B:GLY50 4.6 20.7 1.0 CB B:LEU49 4.6 29.0 1.0 OE1 B:GLU66 4.6 20.9 1.0 CA B:LEU49 4.7 25.8 1.0 N B:CYS51 4.7 19.6 1.0 OE2 B:GLU66 4.7 20.9 1.0 CA B:CYS51 4.7 18.0 1.0 C B:ASP52 4.7 21.3 1.0 O B:HIS44 4.8 24.6 1.0 C B:CYS51 4.8 24.2 1.0 C B:SER54 4.9 24.0 1.0 CG1 B:VAL48 4.9 23.6 1.0 CA B:CYS46 4.9 18.3 1.0 C B:ALA53 4.9 22.2 1.0 N B:ASP45 4.9 19.6 1.0

Calcium binding site 4 out of 4 in the Raphanus Sativus Anionic Peroxidase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Raphanus Sativus Anionic Peroxidase. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1308 b:22.1 occ:1.00 O B:THR172 2.4 19.9 1.0 O B:ALA229 2.4 20.0 1.0 OD1 B:ASP231 2.5 23.0 1.0 OD2 B:ASP223 2.5 20.1 1.0 OG1 B:THR226 2.5 23.0 1.0 O B:THR226 2.6 21.9 1.0 OG1 B:THR172 2.6 15.8 1.0 CG B:ASP231 3.3 24.4 1.0 C B:THR172 3.4 21.3 1.0 CG B:ASP223 3.5 21.0 1.0 CB B:THR226 3.5 24.5 1.0 C B:THR226 3.6 24.1 1.0 C B:ALA229 3.6 27.0 1.0 OD2 B:ASP231 3.6 24.1 1.0 CB B:THR172 3.6 18.0 1.0 CA B:THR172 3.8 15.5 1.0 CA B:THR226 4.0 23.5 1.0 CB B:ASP223 4.0 19.2 1.0 CG2 B:THR172 4.2 16.4 1.0 N B:ASP231 4.2 20.4 1.0 N B:ALA229 4.2 19.1 1.0 CA B:ALA229 4.3 24.5 1.0 N B:THR226 4.4 20.5 1.0 CB B:ASN233 4.5 22.6 1.0 OD1 B:ASP223 4.5 21.4 1.0 N B:PHE173 4.5 21.6 1.0 N B:PHE230 4.6 23.0 1.0 CB B:ALA229 4.6 22.9 1.0 O B:ASP231 4.6 20.4 1.0 CB B:ASP231 4.6 24.7 1.0 CA B:PHE230 4.7 21.9 1.0 N B:PRO227 4.7 20.3 1.0 CG2 B:THR226 4.8 25.8 1.0 CA B:ASP231 4.8 24.3 1.0 C B:PHE230 4.9 24.2 1.0 C B:ASP231 5.0 23.1 1.0 C B:PRO227 5.0 22.1 1.0 CG B:ASN233 5.0 29.3 1.0

P.Gil-Rodriguez, N.Jimenez-Arroyo, S.P.Rojas-Trejo, E.Rudino-Pinera, B.Valderrama. Crystallographic Structure of the Raphanus Sativus Anionic Peroxidase To Be Published.