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

Protein crystallography data

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

Other elements in 3hdl:

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

Iron (Fe) 1 atom

Calcium Binding Sites:

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 3hdl

Go back to Calcium Binding Sites List in 3hdl
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 3hdl

Go back to Calcium Binding Sites List in 3hdl
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

Reference:

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
Page generated: Sat Dec 12 04:13:58 2020

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