Calcium in PDB 1n3p: Pterocarpus Angolensis Lectin in Complex with Sucrose

The structure of Pterocarpus Angolensis Lectin in Complex with Sucrose, PDB code: 1n3p was solved by R.Loris, A.Imberty, S.Beeckmans, E.Van Driessche, J.S.Read, J.Bouckaert, H.De Greve, L.Buts, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.830, 83.550, 123.390, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.7

The structure of Pterocarpus Angolensis Lectin in Complex with Sucrose also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pterocarpus Angolensis Lectin in Complex with Sucrose (pdb code 1n3p). 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 Sucrose, PDB code: 1n3p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pterocarpus Angolensis Lectin in Complex with Sucrose


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 Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca272 b:17.6 occ:1.00 O A:HOH273 2.3 17.6 1.0 O A:PHE132 2.3 17.9 1.0 OD2 A:ASP141 2.3 20.1 1.0 OD1 A:ASN138 2.4 23.9 1.0 OD1 A:ASP130 2.4 20.5 1.0 O A:HOH276 2.4 21.6 1.0 OD2 A:ASP130 2.5 14.6 1.0 CG A:ASP130 2.8 18.8 1.0 CG A:ASN138 3.5 28.5 1.0 CG A:ASP141 3.5 19.1 1.0 C A:PHE132 3.5 24.7 1.0 CB A:ASN138 4.0 19.4 1.0 OD1 A:ASP141 4.1 21.8 1.0 MN A:MN271 4.2 20.0 1.0 CB A:ASP130 4.3 18.0 1.0 CA A:PHE132 4.3 23.5 1.0 N A:PHE132 4.4 22.6 1.0 N A:TYR133 4.5 24.4 1.0 CB A:PHE132 4.5 29.4 1.0 O A:GLY106 4.6 25.3 1.0 NE1 A:TRP140 4.6 28.8 1.0 CA A:TYR133 4.6 23.2 1.0 ND2 A:ASN138 4.6 21.2 1.0 OD1 A:ASP86 4.6 20.8 1.0 CB A:ASP141 4.6 20.6 1.0 CA A:GLY106 4.7 18.9 1.0 O A:HOH275 4.7 15.4 1.0 O A:ASP86 4.7 20.2 1.0 CE1 A:HIS146 4.9 21.4 1.0

Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Lectin in Complex with Sucrose


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 Sucrose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca274 b:16.9 occ:1.00 OD2 B:ASP141 2.3 20.4 1.0 O B:PHE132 2.4 17.6 1.0 O B:HOH275 2.4 17.2 1.0 OD1 B:ASN138 2.4 26.1 1.0 O B:HOH276 2.4 16.1 1.0 OD2 B:ASP130 2.4 18.6 1.0 OD1 B:ASP130 2.5 18.0 1.0 CG B:ASP130 2.8 17.4 1.0 CG B:ASP141 3.4 14.0 1.0 CG B:ASN138 3.4 26.0 1.0 C B:PHE132 3.6 23.6 1.0 CB B:ASN138 3.8 23.8 1.0 OD1 B:ASP141 3.9 18.2 1.0 MN B:MN273 4.2 17.3 1.0 CB B:ASP130 4.3 16.9 1.0 NE1 B:TRP140 4.4 25.2 1.0 CA B:PHE132 4.5 18.2 1.0 O B:HOH278 4.5 14.3 1.0 N B:PHE132 4.5 16.7 1.0 O B:GLY106 4.5 20.3 1.0 CB B:PHE132 4.6 15.9 1.0 N B:TYR133 4.6 19.9 1.0 CB B:ASP141 4.6 12.8 1.0 ND2 B:ASN138 4.6 16.4 1.0 CA B:TYR133 4.6 27.0 1.0 CA B:GLY106 4.7 11.7 1.0 O B:ASP86 4.7 15.4 1.0 OD1 B:ASP86 4.9 25.5 1.0 CE1 B:HIS146 5.0 14.5 1.0

R.Loris, A.Imberty, S.Beeckmans, E.Van Driessche, J.S.Read, J.Bouckaert, H.De Greve, L.Buts, L.Wyns. Crystal Structure of Pterocarpus Angolensis Lectin in Complex with Glucose, Sucrose, and Turanose J.Biol.Chem. V. 278 16297 2003.
ISSN: ISSN 0021-9258
PubMed: 12595543
DOI: 10.1074/JBC.M211148200