Calcium in PDB 3hdl: Crystal Structure of Highly Glycosylated Peroxidase From Royal Palm Tree

The structure of Crystal Structure of Highly Glycosylated Peroxidase From Royal Palm Tree, PDB code: 3hdl was solved by L.Watanabe, P.R.Moura, L.Bleicher, A.S.Nascimento, L.S.Zamorano, J.J.Calvete, S.Bursakov, M.G.Roig, V.L.Shnyrov, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.78 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.821, 117.821, 93.447, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 18.7

The structure of Crystal Structure of Highly Glycosylated Peroxidase From Royal Palm Tree also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Highly Glycosylated Peroxidase From Royal Palm Tree (pdb code 3hdl). 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 Highly Glycosylated Peroxidase From Royal Palm Tree, PDB code: 3hdl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Highly Glycosylated Peroxidase From Royal Palm Tree


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 Highly Glycosylated Peroxidase From Royal Palm Tree within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:25.6 occ:1.00 OD2 A:ASP223 2.4 24.6 1.0 O A:THR226 2.4 21.8 1.0 O A:VAL229 2.4 22.3 1.0 O A:SER170 2.5 21.5 1.0 OG A:SER170 2.5 24.1 1.0 OG1 A:THR226 2.5 26.0 1.0 OD1 A:ASP231 2.6 23.6 1.0 C A:THR226 3.4 24.4 1.0 C A:SER170 3.4 23.1 1.0 CG A:ASP223 3.5 24.8 1.0 CB A:SER170 3.5 26.6 1.0 CG A:ASP231 3.6 27.9 1.0 CB A:THR226 3.6 28.5 1.0 C A:VAL229 3.6 25.1 1.0 CA A:SER170 3.7 22.3 1.0 CA A:THR226 3.9 23.0 1.0 OD2 A:ASP231 3.9 26.3 1.0 CB A:ASP223 4.0 23.5 1.0 N A:ASP231 4.1 27.4 1.0 N A:THR226 4.2 25.4 1.0 N A:VAL229 4.2 25.8 1.0 CA A:VAL229 4.3 23.2 1.0 CB A:MET233 4.3 25.1 0.4 CB A:MET233 4.4 24.8 0.6 N A:PRO227 4.5 24.8 1.0 CB A:VAL229 4.5 22.8 1.0 OD1 A:ASP223 4.5 25.2 1.0 O A:ASP231 4.6 25.5 1.0 N A:ILE171 4.6 21.5 1.0 N A:LEU230 4.7 22.6 1.0 CB A:ASP231 4.8 27.8 1.0 CA A:PRO227 4.8 23.0 1.0 N A:TYR234 4.8 25.0 1.0 CA A:ASP231 4.8 28.5 1.0 CA A:LEU230 4.8 23.5 1.0 C A:ASP231 4.9 29.5 1.0 N A:MET233 4.9 23.8 1.0 C A:PRO227 4.9 26.2 1.0 CG2 A:THR226 4.9 24.3 1.0 CG2 A:ILE171 4.9 21.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Highly Glycosylated Peroxidase From Royal Palm Tree


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 Highly Glycosylated Peroxidase From Royal Palm Tree within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca307 b:27.5 occ:1.00 O A:VAL46 2.3 23.4 1.0 OD1 A:ASP43 2.5 23.1 1.0 O A:ASP43 2.5 25.2 1.0 OD1 A:ASP50 2.5 27.2 1.0 O A:GLY48 2.5 28.2 1.0 OG A:SER52 2.5 25.4 1.0 O A:HOH594 2.6 25.4 1.0 C A:ASP43 3.3 24.0 1.0 C A:VAL46 3.5 29.5 1.0 CG A:ASP43 3.6 30.3 1.0 CB A:SER52 3.6 27.9 1.0 CG A:ASP50 3.6 31.2 1.0 CA A:ASP43 3.7 22.9 1.0 C A:GLY48 3.7 26.1 1.0 N A:SER52 3.9 24.1 1.0 N A:ASP50 3.9 24.2 1.0 C A:ARG47 4.1 30.8 1.0 N A:GLY48 4.2 26.8 1.0 O A:ARG47 4.2 28.7 1.0 CB A:ASP43 4.3 21.8 1.0 CA A:SER52 4.3 25.8 1.0 OD2 A:ASP50 4.3 28.6 1.0 CA A:VAL46 4.3 25.5 1.0 CB A:ARG47 4.4 35.8 1.0 OE2 A:GLU64 4.4 27.2 1.0 N A:VAL46 4.4 26.0 1.0 N A:VAL53 4.4 25.2 1.0 CB A:VAL46 4.5 27.3 1.0 N A:ARG47 4.5 24.7 1.0 N A:ALA51 4.5 24.6 1.0 N A:CYS44 4.5 25.5 1.0 OD2 A:ASP43 4.5 25.6 1.0 CA A:ARG47 4.6 29.6 1.0 CA A:GLY48 4.6 24.4 1.0 O A:HIS42 4.6 24.6 1.0 N A:CYS49 4.6 25.0 1.0 CB A:ASP50 4.6 25.0 1.0 CA A:ASP50 4.6 24.8 1.0 OE1 A:GLU64 4.6 26.8 1.0 CA A:CYS49 4.7 24.8 1.0 C A:ASP50 4.7 27.0 1.0 C A:SER52 4.8 29.0 1.0 C A:CYS49 4.8 26.1 1.0 C A:ALA51 4.9 23.3 1.0 N A:ASP43 5.0 21.2 1.0 CD A:GLU64 5.0 28.4 1.0 CA A:CYS44 5.0 24.2 1.0

L.Watanabe, P.R.De Moura, L.Bleicher, A.S.Nascimento, L.S.Zamorano, J.J.Calvete, L.Sanz, A.Perez, S.Bursakov, M.G.Roig, V.L.Shnyrov, I.Polikarpov. Crystal Structure and Statistical Coupling Analysis of Highly Glycosylated Peroxidase From Royal Palm Tree (Roystonea Regia). J.Struct.Biol. V. 169 226 2010.
ISSN: ISSN 1047-8477
PubMed: 19854274
DOI: 10.1016/J.JSB.2009.10.009