Calcium in PDB 2arb: Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide

The structure of Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide, PDB code: 2arb was solved by L.Buts, A.Garcia-Pino, A.Imberty, N.Amiot, G.-J.Boons, W.Versees, J.Lah, S.Beeckmans, L.Wyns, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.877, 83.478, 123.077, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.2

The structure of Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide (pdb code 2arb). 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 Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide, PDB code: 2arb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca263 b:19.3 occ:1.00 OD2 A:ASP141 2.2 18.9 1.0 O A:HOH265 2.4 19.2 1.0 OD1 A:ASP130 2.4 17.6 1.0 O A:PHE132 2.4 18.3 1.0 O A:HOH264 2.4 18.0 1.0 OD1 A:ASN138 2.4 23.0 1.0 OD2 A:ASP130 2.5 17.5 1.0 CG A:ASP130 2.8 16.0 1.0 CG A:ASP141 3.4 19.0 1.0 CG A:ASN138 3.5 23.6 1.0 C A:PHE132 3.6 19.2 1.0 OD1 A:ASP141 3.8 17.7 1.0 CB A:ASN138 4.0 20.3 1.0 MN A:MN261 4.2 17.9 1.0 CB A:ASP130 4.3 16.1 1.0 NE1 A:TRP140 4.5 23.1 1.0 O A:HOH267 4.5 19.4 1.0 N A:PHE132 4.5 20.2 1.0 CA A:PHE132 4.5 21.6 1.0 CA A:TYR133 4.6 19.0 1.0 N A:TYR133 4.6 19.0 1.0 ND2 A:ASN138 4.6 22.5 1.0 CA A:GLY106 4.6 21.6 1.0 CB A:ASP141 4.6 18.8 1.0 O A:GLY106 4.6 22.5 1.0 CB A:PHE132 4.8 20.6 1.0 O A:ASP86 4.8 19.1 1.0 OD2 A:ASP86 4.8 21.3 1.0 CE1 A:HIS146 4.8 22.2 1.0

Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pterocarpus Angolensis Lectin (Pal) in Complex with the Glcnac(BETA1- 2)Man Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca264 b:17.4 occ:1.00 OD2 B:ASP141 2.3 20.9 1.0 O B:PHE132 2.3 17.1 1.0 O B:HOH266 2.4 16.5 1.0 OD1 B:ASN138 2.4 21.6 1.0 O B:HOH265 2.4 18.8 1.0 OD1 B:ASP130 2.4 16.1 1.0 OD2 B:ASP130 2.5 14.5 1.0 CG B:ASP130 2.8 19.2 1.0 CG B:ASP141 3.4 19.4 1.0 CG B:ASN138 3.5 25.1 1.0 C B:PHE132 3.6 21.5 1.0 OD1 B:ASP141 3.9 16.1 1.0 CB B:ASN138 4.0 24.8 1.0 MN B:MN262 4.2 15.5 1.0 CB B:ASP130 4.3 15.4 1.0 N B:PHE132 4.4 17.0 1.0 CA B:PHE132 4.4 19.0 1.0 O B:HOH267 4.5 19.4 1.0 NE1 B:TRP140 4.5 25.6 1.0 N B:TYR133 4.5 21.6 1.0 CA B:TYR133 4.6 22.3 1.0 ND2 B:ASN138 4.6 23.6 1.0 CB B:PHE132 4.6 19.6 1.0 CB B:ASP141 4.6 19.2 1.0 CA B:GLY106 4.7 16.0 1.0 O B:ASP86 4.7 14.7 1.0 O B:GLY106 4.7 20.5 1.0 OD2 B:ASP86 4.8 18.3 1.0 CE1 B:HIS146 4.8 17.8 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