Calcium in PDB 2phu: Pterocarpus Angolensis Lectin in Complex with Man-8D1D3

The structure of Pterocarpus Angolensis Lectin in Complex with Man-8D1D3, PDB code: 2phu 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 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.696, 83.348, 122.690, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.9

The structure of Pterocarpus Angolensis Lectin in Complex with Man-8D1D3 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pterocarpus Angolensis Lectin in Complex with Man-8D1D3 (pdb code 2phu). 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 in Complex with Man-8D1D3, PDB code: 2phu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pterocarpus Angolensis Lectin in Complex with Man-8D1D3


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 in Complex with Man-8D1D3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:19.2 occ:1.00 OD2 A:ASP141 2.2 20.9 1.0 O A:HOH304 2.3 17.8 1.0 OD1 A:ASN138 2.3 21.4 1.0 O A:PHE132 2.4 23.6 1.0 OD2 A:ASP130 2.4 18.0 1.0 O A:HOH305 2.5 19.4 1.0 OD1 A:ASP130 2.5 20.9 1.0 CG A:ASP130 2.8 20.4 1.0 CG A:ASP141 3.4 19.8 1.0 CG A:ASN138 3.4 27.6 1.0 C A:PHE132 3.6 24.9 1.0 OD1 A:ASP141 3.9 22.4 1.0 CB A:ASN138 3.9 21.9 1.0 MN A:MN301 4.2 15.7 1.0 CB A:ASP130 4.3 19.5 1.0 NE1 A:TRP140 4.4 24.1 1.0 CA A:PHE132 4.5 24.9 1.0 N A:PHE132 4.5 23.0 1.0 O A:HOH306 4.5 20.5 1.0 N A:TYR133 4.5 24.6 1.0 ND2 A:ASN138 4.5 23.5 1.0 CB A:ASP141 4.6 21.0 1.0 CA A:TYR133 4.6 24.1 1.0 O A:GLY106 4.6 22.1 1.0 CA A:GLY106 4.7 20.7 1.0 CB A:PHE132 4.7 23.9 1.0 O A:ASP86 4.7 17.6 1.0 OD1 A:ASP86 4.8 22.7 1.0 CE1 A:HIS146 4.9 20.6 1.0

Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Lectin in Complex with Man-8D1D3


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 in Complex with Man-8D1D3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:19.7 occ:1.00 O B:PHE132 2.3 20.0 1.0 OD2 B:ASP141 2.4 20.2 1.0 O B:HOH310 2.4 19.1 1.0 OD1 B:ASN138 2.4 22.4 1.0 O B:HOH305 2.5 16.9 1.0 OD2 B:ASP130 2.5 17.8 1.0 OD1 B:ASP130 2.5 21.7 1.0 CG B:ASP130 2.8 19.3 1.0 CG B:ASP141 3.5 20.0 1.0 CG B:ASN138 3.5 28.9 1.0 C B:PHE132 3.5 23.5 1.0 CB B:ASN138 4.0 26.6 1.0 OD1 B:ASP141 4.0 21.2 1.0 MN B:MN301 4.2 16.5 1.0 CB B:ASP130 4.3 15.5 1.0 CA B:PHE132 4.4 21.6 1.0 N B:PHE132 4.4 21.9 1.0 NE1 B:TRP140 4.5 21.9 1.0 CB B:PHE132 4.5 25.4 1.0 N B:TYR133 4.5 24.4 1.0 O B:HOH303 4.6 11.7 1.0 CA B:TYR133 4.6 25.5 1.0 O B:ASP86 4.6 15.8 1.0 O B:GLY106 4.6 21.3 1.0 CA B:GLY106 4.7 19.2 1.0 CB B:ASP141 4.7 21.3 1.0 ND2 B:ASN138 4.7 26.4 1.0 OD1 B:ASP86 4.8 16.7 1.0 CE1 B:HIS146 4.9 18.4 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