Calcium in PDB 1q8p: Pterocarpus Angolensis Lectin Pal in Complex with the Dimannoside Man(ALPHA1-3)Man

The structure of Pterocarpus Angolensis Lectin Pal in Complex with the Dimannoside Man(ALPHA1-3)Man, PDB code: 1q8p was solved by R.Loris, I.Van Walle, H.De Greve, S.Beeckmans, F.Deboeck, L.Wyns, J.Bouckaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.880, 83.030, 122.940, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 20.6

The structure of Pterocarpus Angolensis Lectin Pal in Complex with the Dimannoside Man(ALPHA1-3)Man 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 Dimannoside Man(ALPHA1-3)Man (pdb code 1q8p). 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 Dimannoside Man(ALPHA1-3)Man, PDB code: 1q8p:
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 Dimannoside Man(ALPHA1-3)Man


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 Dimannoside Man(ALPHA1-3)Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca262 b:14.9 occ:1.00 OD2 A:ASP141 2.3 17.5 1.0 O A:PHE132 2.3 15.8 1.0 OD1 A:ASN138 2.4 17.4 1.0 OD2 A:ASP130 2.4 15.1 1.0 O A:HOH267 2.4 16.6 1.0 O A:HOH263 2.4 14.6 1.0 OD1 A:ASP130 2.5 16.1 1.0 CG A:ASP130 2.8 14.3 1.0 CG A:ASP141 3.4 15.4 1.0 CG A:ASN138 3.4 23.3 1.0 C A:PHE132 3.6 17.1 1.0 OD1 A:ASP141 3.9 13.7 1.0 CB A:ASN138 4.0 16.1 1.0 MN A:MN261 4.2 14.9 1.0 CB A:ASP130 4.3 13.2 1.0 CA A:PHE132 4.4 18.2 1.0 NE1 A:TRP140 4.4 18.1 1.0 N A:PHE132 4.5 17.9 1.0 N A:TYR133 4.5 16.2 1.0 CA A:TYR133 4.6 14.4 1.0 O A:GLY106 4.6 19.5 1.0 ND2 A:ASN138 4.6 19.8 1.0 CB A:ASP141 4.6 16.6 1.0 CB A:PHE132 4.6 16.3 1.0 O A:HOH264 4.6 14.7 1.0 CA A:GLY106 4.7 18.8 1.0 O A:ASP86 4.7 15.4 1.0 OD1 A:ASP86 4.8 19.3 1.0 CE1 A:HIS146 4.9 15.9 1.0

Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Lectin Pal in Complex with the Dimannoside Man(ALPHA1-3)Man


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 Dimannoside Man(ALPHA1-3)Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1262 b:15.7 occ:1.00 O B:PHE132 2.3 16.6 1.0 OD2 B:ASP141 2.3 18.4 1.0 O B:HOH1268 2.4 15.8 1.0 OD1 B:ASN138 2.4 22.2 1.0 OD2 B:ASP130 2.4 13.3 1.0 O B:HOH1265 2.4 16.9 1.0 OD1 B:ASP130 2.4 14.5 1.0 CG B:ASP130 2.8 16.8 1.0 CG B:ASP141 3.4 17.3 1.0 CG B:ASN138 3.5 24.1 1.0 C B:PHE132 3.5 21.4 1.0 OD1 B:ASP141 3.9 13.4 1.0 CB B:ASN138 4.0 23.5 1.0 MN B:MN261 4.2 15.6 1.0 CB B:ASP130 4.3 17.0 1.0 CA B:PHE132 4.4 16.8 1.0 N B:PHE132 4.4 16.7 1.0 NE1 B:TRP140 4.4 20.8 1.0 N B:TYR133 4.5 20.8 1.0 CB B:PHE132 4.6 18.5 1.0 CA B:TYR133 4.6 20.7 1.0 O B:HOH1267 4.6 16.7 1.0 CB B:ASP141 4.6 17.3 1.0 ND2 B:ASN138 4.6 21.4 1.0 O B:GLY106 4.7 17.4 1.0 O B:ASP86 4.7 14.3 1.0 CA B:GLY106 4.7 17.0 1.0 OD1 B:ASP86 4.9 17.6 1.0 CE1 B:HIS146 4.9 15.0 1.0

R.Loris, I.Van Walle, H.De Greve, S.Beeckmans, F.Deboeck, L.Wyns, J.Bouckaert. Structural Basis of Oligomannose Recognition By the Pterocarpus Angolensis Seed Lectin J.Mol.Biol. V. 335 1227 2004.
ISSN: ISSN 0022-2836
PubMed: 14729339
DOI: 10.1016/J.JMB.2003.11.043