Calcium in PDB 2arx: Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F

The structure of Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F, PDB code: 2arx was solved by L.Buts, A.Garcia-Pino, A.Imberty, N.Amiot, G.-J.Boons, J.Lah, W.Versees, L.Wyns, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.780, 83.320, 122.380, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.6

The structure of Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F (pdb code 2arx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F, PDB code: 2arx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca253 b:18.4 occ:1.00 OD2 A:ASP141 2.2 16.2 1.0 OD1 A:ASN138 2.3 17.6 1.0 O A:PHE132 2.4 19.5 1.0 O A:HOH904 2.4 16.5 1.0 OD2 A:ASP130 2.4 16.5 1.0 OD1 A:ASP130 2.5 16.5 1.0 O A:HOH907 2.5 16.5 1.0 CG A:ASP130 2.8 18.1 1.0 CG A:ASP141 3.4 17.8 1.0 CG A:ASN138 3.4 21.9 1.0 C A:PHE132 3.6 20.9 1.0 OD1 A:ASP141 3.9 16.1 1.0 CB A:ASN138 4.0 19.6 1.0 MN A:MN903 4.2 17.1 1.0 CB A:ASP130 4.3 20.9 1.0 NE1 A:TRP140 4.4 21.3 1.0 CA A:PHE132 4.5 21.2 1.0 N A:PHE132 4.5 20.4 1.0 ND2 A:ASN138 4.5 17.6 1.0 N A:TYR133 4.5 19.6 1.0 CB A:ASP141 4.6 20.8 1.0 CA A:TYR133 4.6 21.1 1.0 CB A:PHE132 4.6 22.9 1.0 O A:GLY106 4.6 19.3 1.0 O A:HOH906 4.6 16.3 1.0 CA A:GLY106 4.6 20.6 1.0 OD1 A:ASP86 4.8 19.3 1.0 O A:ASP86 4.8 18.6 1.0 CE1 A:HIS146 4.9 20.2 1.0

Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pterocarpus Angolensis Seed Lectin in Complex with the Decasaccharide NA2F within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca254 b:18.1 occ:1.00 OD2 B:ASP141 2.3 20.3 1.0 O B:PHE132 2.3 20.4 1.0 O B:HOH922 2.4 15.1 1.0 OD1 B:ASN138 2.4 20.2 1.0 O B:HOH921 2.4 16.4 1.0 OD1 B:ASP130 2.4 15.6 1.0 OD2 B:ASP130 2.5 16.0 1.0 CG B:ASP130 2.8 13.4 1.0 CG B:ASP141 3.5 20.3 1.0 CG B:ASN138 3.5 28.1 1.0 C B:PHE132 3.6 22.5 1.0 CB B:ASN138 4.0 30.0 1.0 OD1 B:ASP141 4.0 21.9 1.0 MN B:MN919 4.2 19.1 1.0 CB B:ASP130 4.3 15.3 1.0 CA B:PHE132 4.4 21.8 1.0 NE1 B:TRP140 4.4 23.2 1.0 N B:PHE132 4.5 20.0 1.0 N B:TYR133 4.5 22.2 1.0 CB B:PHE132 4.5 22.1 1.0 O B:HOH923 4.6 15.9 1.0 O B:GLY106 4.6 19.2 1.0 CB B:ASP141 4.6 23.9 1.0 CA B:TYR133 4.6 23.5 1.0 ND2 B:ASN138 4.6 23.1 1.0 CA B:GLY106 4.6 17.4 1.0 O B:ASP86 4.7 17.4 1.0 OD1 B:ASP86 4.8 18.5 1.0 CE1 B:HIS146 4.8 16.9 1.0

L.Buts, A.Garcia-Pino, A.Imberty, N.Amiot, G.J.Boons, S.Beeckmans, W.Versees, L.Wyns, R.Loris. Structural Basis For the Recognition of Complex-Type Biantennary Oligosaccharides By Pterocarpus Angolensis Lectin. Febs J. V. 273 2407 2006.
ISSN: ISSN 1742-464X
PubMed: 16704415
DOI: 10.1111/J.1742-4658.2006.05248.X