Calcium in PDB 2phr: Pterocarpus Angolensis Lectin (Pal) in Complex with Man-7D1

The structure of Pterocarpus Angolensis Lectin (Pal) in Complex with Man-7D1, PDB code: 2phr 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 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.804, 83.269, 123.133, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.7

The structure of Pterocarpus Angolensis Lectin (Pal) in Complex with Man-7D1 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-7D1 (pdb code 2phr). 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-7D1, PDB code: 2phr:
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-7D1


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-7D1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:17.4 occ:1.00 OD2 A:ASP141 2.3 18.7 1.0 O A:PHE132 2.4 19.0 1.0 OD1 A:ASN138 2.4 19.7 1.0 O A:HOH304 2.4 16.6 1.0 O A:HOH303 2.4 14.6 1.0 OD1 A:ASP130 2.4 18.8 1.0 OD2 A:ASP130 2.4 17.0 1.0 CG A:ASP130 2.8 16.1 1.0 CG A:ASP141 3.4 17.8 1.0 CG A:ASN138 3.4 21.8 1.0 C A:PHE132 3.6 19.8 1.0 OD1 A:ASP141 3.9 16.7 1.0 CB A:ASN138 4.0 17.2 1.0 MN A:MN301 4.2 17.3 1.0 CB A:ASP130 4.3 16.2 1.0 N A:PHE132 4.4 19.3 1.0 CA A:PHE132 4.4 20.1 1.0 NE1 A:TRP140 4.5 24.9 1.0 O A:HOH306 4.5 17.5 1.0 N A:TYR133 4.5 18.7 1.0 ND2 A:ASN138 4.5 20.4 1.0 CA A:TYR133 4.6 19.9 1.0 O A:GLY106 4.6 21.4 1.0 CB A:PHE132 4.6 19.1 1.0 CA A:GLY106 4.6 20.9 1.0 CB A:ASP141 4.6 19.7 1.0 O A:ASP86 4.7 15.9 1.0 OD1 A:ASP86 4.8 18.9 1.0 CE1 A:HIS146 4.9 17.4 1.0

Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Lectin (Pal) in Complex with Man-7D1


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-7D1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:18.1 occ:1.00 O B:HOH303 2.3 17.9 1.0 O B:PHE132 2.3 20.6 1.0 OD2 B:ASP141 2.4 19.6 1.0 O B:HOH304 2.4 17.1 1.0 OD2 B:ASP130 2.4 16.2 1.0 OD1 B:ASP130 2.4 15.3 1.0 OD1 B:ASN138 2.5 23.6 1.0 CG B:ASP130 2.8 16.8 1.0 CG B:ASP141 3.5 18.2 1.0 CG B:ASN138 3.5 25.0 1.0 C B:PHE132 3.5 21.9 1.0 OD1 B:ASP141 4.0 17.0 1.0 CB B:ASN138 4.0 26.1 1.0 MN B:MN301 4.2 17.9 1.0 CB B:ASP130 4.3 18.2 1.0 CA B:PHE132 4.4 20.1 1.0 N B:PHE132 4.4 19.2 1.0 NE1 B:TRP140 4.5 22.2 1.0 CB B:PHE132 4.5 19.4 1.0 N B:TYR133 4.5 22.3 1.0 O B:HOH305 4.6 18.2 1.0 CA B:TYR133 4.6 23.6 1.0 O B:ASP86 4.6 16.2 1.0 O B:GLY106 4.7 21.1 1.0 CA B:GLY106 4.7 17.9 1.0 CB B:ASP141 4.7 19.1 1.0 ND2 B:ASN138 4.7 26.1 1.0 OD1 B:ASP86 4.8 19.1 1.0 CE1 B:HIS146 4.9 18.1 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