Calcium in PDB 1qgj: Arabidopsis Thaliana Peroxidase N

The structure of Arabidopsis Thaliana Peroxidase N, PDB code: 1qgj was solved by O.Mirza, L.Oestergaard, K.G.Welinder, A.Henriksen, M.Gajhede, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.989, 87.457, 91.371, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.5

The structure of Arabidopsis Thaliana Peroxidase N also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

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

Calcium binding site 1 out of 4 in the Arabidopsis Thaliana Peroxidase N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Arabidopsis Thaliana Peroxidase N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:6.1 occ:1.00 O A:VAL46 2.3 6.6 1.0 OD1 A:ASP43 2.4 2.9 1.0 O A:ASP43 2.4 4.1 1.0 OD1 A:ASP50 2.4 6.6 1.0 O A:GLY48 2.5 5.4 1.0 O A:HOH2012 2.5 4.0 1.0 OG A:SER52 2.5 5.6 1.0 C A:ASP43 3.3 3.6 1.0 CG A:ASP43 3.4 3.4 1.0 C A:VAL46 3.5 5.7 1.0 CG A:ASP50 3.6 6.1 1.0 CB A:SER52 3.7 4.6 1.0 CA A:ASP43 3.7 3.9 1.0 C A:GLY48 3.7 5.4 1.0 N A:SER52 3.8 4.1 1.0 N A:ASP50 3.9 4.7 1.0 C A:ASN47 4.1 5.7 1.0 CB A:ASP43 4.2 3.5 1.0 N A:GLY48 4.2 5.3 1.0 CA A:SER52 4.3 3.9 1.0 OD2 A:ASP50 4.3 6.1 1.0 O A:ASN47 4.3 6.5 1.0 CA A:VAL46 4.3 5.2 1.0 OD2 A:ASP43 4.3 2.1 1.0 N A:ALA51 4.4 3.9 1.0 CB A:ASN47 4.4 5.7 1.0 N A:CYS44 4.4 3.6 1.0 CB A:VAL46 4.4 5.3 1.0 N A:VAL46 4.4 5.3 1.0 N A:ASN47 4.4 5.5 1.0 N A:LEU53 4.4 3.4 1.0 CA A:GLY48 4.5 5.4 1.0 CA A:ASN47 4.5 5.5 1.0 CA A:ASP50 4.6 4.4 1.0 C A:ASP50 4.6 4.4 1.0 N A:CYS49 4.6 5.2 1.0 CB A:ASP50 4.6 4.7 1.0 OE1 A:GLU61 4.7 5.4 1.0 CA A:CYS49 4.7 5.1 1.0 O A:HIS42 4.8 4.1 1.0 OE2 A:GLU61 4.8 4.7 1.0 C A:ALA51 4.8 3.9 1.0 C A:SER52 4.8 3.7 1.0 C A:CYS49 4.9 5.2 1.0 CA A:CYS44 4.9 4.4 1.0 CG1 A:VAL46 4.9 4.3 1.0 N A:ASP43 5.0 4.2 1.0 CA A:ALA51 5.0 4.2 1.0

Calcium binding site 2 out of 4 in the Arabidopsis Thaliana Peroxidase N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Arabidopsis Thaliana Peroxidase N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:4.9 occ:1.00 OD2 A:ASP217 2.3 7.2 1.0 O A:THR166 2.3 4.3 1.0 O A:THR220 2.4 8.9 1.0 OG1 A:THR220 2.4 6.7 1.0 O A:THR223 2.4 6.6 1.0 OG1 A:THR166 2.5 5.4 1.0 OD2 A:ASP225 2.5 5.1 1.0 CG A:ASP217 3.3 8.0 1.0 C A:THR166 3.3 4.1 1.0 CG A:ASP225 3.4 6.2 1.0 C A:THR220 3.4 9.2 1.0 CB A:THR220 3.5 8.6 1.0 C A:THR223 3.6 7.7 1.0 CB A:THR166 3.7 4.4 1.0 OD1 A:ASP225 3.7 5.6 1.0 CA A:THR166 3.8 4.0 1.0 CB A:ASP217 3.9 7.6 1.0 CA A:THR220 4.0 8.9 1.0 N A:ASP225 4.2 6.4 1.0 N A:THR223 4.3 8.0 1.0 N A:THR220 4.3 9.9 1.0 CA A:THR223 4.4 8.0 1.0 OD1 A:ASP217 4.4 8.0 1.0 CG2 A:THR166 4.4 4.5 1.0 CB A:ASN227 4.4 7.1 1.0 N A:PHE167 4.5 3.5 1.0 N A:THR221 4.6 8.8 1.0 N A:PHE224 4.6 7.2 1.0 CB A:THR223 4.6 7.8 1.0 O A:ASP225 4.7 6.6 1.0 CB A:ASP225 4.7 5.6 1.0 CA A:PHE224 4.8 6.7 1.0 CG2 A:THR220 4.8 8.3 1.0 C A:THR221 4.9 8.9 1.0 CA A:ASP225 4.9 6.2 1.0 C A:PHE224 4.9 6.7 1.0 CA A:PHE167 5.0 4.0 1.0

Calcium binding site 3 out of 4 in the Arabidopsis Thaliana Peroxidase N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Arabidopsis Thaliana Peroxidase N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:5.2 occ:1.00 O B:VAL46 2.3 5.1 1.0 OD1 B:ASP43 2.3 3.1 1.0 O B:ASP43 2.4 4.7 1.0 OD1 B:ASP50 2.4 4.9 1.0 O B:HOH2335 2.4 4.4 1.0 O B:GLY48 2.5 6.2 1.0 OG B:SER52 2.6 5.4 1.0 C B:ASP43 3.2 4.7 1.0 C B:VAL46 3.5 5.2 1.0 CG B:ASP43 3.5 3.4 1.0 CG B:ASP50 3.6 6.2 1.0 CB B:SER52 3.6 4.8 1.0 CA B:ASP43 3.6 4.6 1.0 C B:GLY48 3.7 5.9 1.0 N B:SER52 3.8 5.0 1.0 N B:ASP50 3.9 5.7 1.0 C B:ASN47 4.2 5.7 1.0 CB B:ASP43 4.2 4.4 1.0 N B:GLY48 4.2 5.6 1.0 OD2 B:ASP50 4.2 6.0 1.0 CA B:SER52 4.3 4.9 1.0 CA B:VAL46 4.3 5.4 1.0 CB B:VAL46 4.3 5.4 1.0 N B:CYS44 4.3 4.7 1.0 N B:VAL46 4.4 4.6 1.0 OD2 B:ASP43 4.4 2.9 1.0 N B:ALA51 4.4 5.0 1.0 O B:ASN47 4.4 5.9 1.0 CB B:ASN47 4.4 6.0 1.0 N B:ASN47 4.4 5.5 1.0 N B:LEU53 4.5 4.1 1.0 CA B:GLY48 4.5 6.2 1.0 CA B:ASN47 4.6 5.3 1.0 CA B:ASP50 4.6 5.5 1.0 N B:CYS49 4.6 5.7 1.0 C B:ASP50 4.6 5.4 1.0 CB B:ASP50 4.6 5.6 1.0 CA B:CYS49 4.7 5.7 1.0 O B:HIS42 4.7 4.8 1.0 OE2 B:GLU61 4.7 6.6 1.0 OE1 B:GLU61 4.8 7.4 1.0 C B:CYS49 4.8 6.1 1.0 CA B:CYS44 4.8 5.0 1.0 C B:ALA51 4.8 5.0 1.0 C B:SER52 4.8 4.8 1.0 CG1 B:VAL46 4.9 5.8 1.0 N B:ASP43 5.0 4.4 1.0

Calcium binding site 4 out of 4 in the Arabidopsis Thaliana Peroxidase N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Arabidopsis Thaliana Peroxidase N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:5.7 occ:1.00 OD2 B:ASP217 2.3 9.5 1.0 O B:THR166 2.3 5.4 1.0 O B:THR220 2.4 9.1 1.0 O B:THR223 2.4 6.4 1.0 OG1 B:THR220 2.4 7.2 1.0 OD2 B:ASP225 2.5 8.5 1.0 OG1 B:THR166 2.5 5.7 1.0 CG B:ASP217 3.3 9.7 1.0 C B:THR166 3.3 5.4 1.0 CG B:ASP225 3.5 8.0 1.0 C B:THR220 3.5 9.0 1.0 CB B:THR220 3.6 8.7 1.0 C B:THR223 3.6 6.6 1.0 CB B:THR166 3.7 6.0 1.0 OD1 B:ASP225 3.8 7.7 1.0 CA B:THR166 3.8 5.2 1.0 CB B:ASP217 3.8 8.7 1.0 CA B:THR220 4.0 8.7 1.0 N B:ASP225 4.2 6.2 1.0 N B:THR220 4.3 9.7 1.0 OD1 B:ASP217 4.3 9.1 1.0 CG2 B:THR166 4.4 5.1 1.0 N B:THR223 4.4 7.6 1.0 CA B:THR223 4.4 7.2 1.0 CB B:ASN227 4.5 7.6 1.0 N B:PHE167 4.5 4.9 1.0 N B:PHE224 4.6 6.4 1.0 N B:THR221 4.7 8.5 1.0 CB B:THR223 4.7 7.1 1.0 CA B:PHE224 4.7 6.0 1.0 CB B:ASP225 4.8 6.8 1.0 O B:ASP225 4.8 6.5 1.0 CG2 B:THR220 4.8 8.7 1.0 C B:THR221 4.9 8.4 1.0 C B:PHE224 4.9 5.9 1.0 CA B:ASP225 4.9 6.4 1.0 OG B:SER219 4.9 10.8 0.3 O B:THR221 4.9 8.0 1.0 CA B:PHE167 4.9 4.7 1.0

O.Mirza, A.Henriksen, L.Ostergaard, K.G.Welinder, M.Gajhede. Arabidopsis Thaliana Peroxidase N: Structure of A Novel Neutral Peroxidase. Acta Crystallogr.,Sect.D V. 56 372 2000.
ISSN: ISSN 0907-4449
PubMed: 10713531
DOI: 10.1107/S0907444999016340