Calcium in PDB 2phx: Pterocarpus Angolensis Lectin (Pal) in Complex with Man-5

The structure of Pterocarpus Angolensis Lectin (Pal) in Complex with Man-5, PDB code: 2phx was solved by A.Garcia-Pino, L.Buts, L.Wyns, A.Imberty, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.830, 83.570, 122.810, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.7

The structure of Pterocarpus Angolensis Lectin (Pal) in Complex with Man-5 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 Man-5 (pdb code 2phx). 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 Man-5, PDB code: 2phx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pterocarpus Angolensis Lectin (Pal) in Complex with Man-5


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 Man-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:16.7 occ:1.00 OD2 A:ASP141 2.3 19.4 1.0 OD1 A:ASN138 2.4 20.2 1.0 O A:PHE132 2.4 18.2 1.0 O A:HOH303 2.4 16.3 1.0 O A:HOH304 2.4 18.1 1.0 OD1 A:ASP130 2.4 18.0 1.0 OD2 A:ASP130 2.6 17.5 1.0 CG A:ASP130 2.8 12.7 1.0 CG A:ASP141 3.4 21.0 1.0 CG A:ASN138 3.4 24.8 1.0 C A:PHE132 3.6 18.9 1.0 OD1 A:ASP141 3.8 15.5 1.0 CB A:ASN138 4.0 20.6 1.0 MN A:MN301 4.2 16.0 1.0 CB A:ASP130 4.4 13.1 1.0 NE1 A:TRP140 4.4 22.1 1.0 N A:PHE132 4.5 19.2 1.0 CA A:PHE132 4.5 20.2 1.0 CA A:TYR133 4.5 17.7 1.0 ND2 A:ASN138 4.5 20.9 1.0 N A:TYR133 4.5 16.1 1.0 O A:HOH305 4.6 16.2 1.0 O A:GLY106 4.6 21.0 1.0 CA A:GLY106 4.6 20.6 1.0 CB A:ASP141 4.6 19.3 1.0 O A:ASP86 4.7 18.7 1.0 CB A:PHE132 4.7 19.1 1.0 OD1 A:ASP86 4.8 20.3 1.0 CE1 A:HIS146 4.9 21.1 1.0

Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Lectin (Pal) in Complex with Man-5


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 Man-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:17.5 occ:1.00 OD2 B:ASP141 2.3 19.7 1.0 O B:PHE132 2.4 16.7 1.0 O B:HOH306 2.4 15.9 1.0 O B:HOH305 2.4 15.2 1.0 OD1 B:ASN138 2.4 20.3 1.0 OD1 B:ASP130 2.4 14.1 1.0 OD2 B:ASP130 2.5 14.9 1.0 CG B:ASP130 2.8 17.7 1.0 CG B:ASP141 3.4 20.7 1.0 CG B:ASN138 3.5 22.0 1.0 C B:PHE132 3.6 21.8 1.0 OD1 B:ASP141 3.9 15.8 1.0 CB B:ASN138 4.1 21.0 1.0 MN B:MN301 4.2 15.9 1.0 CB B:ASP130 4.3 16.9 1.0 N B:PHE132 4.4 16.9 1.0 NE1 B:TRP140 4.4 20.9 1.0 CA B:PHE132 4.4 15.8 1.0 N B:TYR133 4.5 19.8 1.0 CA B:TYR133 4.6 19.8 1.0 O B:HOH304 4.6 17.0 1.0 ND2 B:ASN138 4.6 21.2 1.0 CB B:PHE132 4.7 17.7 1.0 O B:GLY106 4.7 20.9 1.0 CA B:GLY106 4.7 17.3 1.0 CB B:ASP141 4.7 19.4 1.0 O B:ASP86 4.7 15.5 1.0 OD1 B:ASP86 4.8 16.5 1.0 CE1 B:HIS146 4.9 17.9 1.0

A.Garcia-Pino, L.Buts, L.Wyns, A.Imberty, R.Loris. How A Plant Lectin Recognizes High Mannose Oligosaccharides Plant Physiol. V. 144 1733 2007.
ISSN: ISSN 0032-0889
PubMed: 17556509
DOI: 10.1104/PP.107.100867