Calcium in PDB 3wog: Crystal Structure Plant Lectin in Complex with Ligand

The structure of Crystal Structure Plant Lectin in Complex with Ligand, PDB code: 3wog was solved by M.Nagae, Y.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.74 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.780, 195.481, 97.829, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 26.3

The structure of Crystal Structure Plant Lectin in Complex with Ligand also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure Plant Lectin in Complex with Ligand (pdb code 3wog). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure Plant Lectin in Complex with Ligand, PDB code: 3wog:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure Plant Lectin in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Plant Lectin in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:22.3 occ:1.00 OD1 A:ASN151 2.3 23.5 1.0 OD2 A:ASP155 2.3 21.3 1.0 O A:HOH1104 2.3 23.4 1.0 OD1 A:ASP147 2.3 21.6 1.0 O A:HOH1103 2.3 21.3 1.0 O A:LEU149 2.4 21.9 1.0 OD2 A:ASP147 2.4 21.4 1.0 CG A:ASP147 2.7 21.8 1.0 CG A:ASP155 3.3 21.5 1.0 CG A:ASN151 3.5 22.6 1.0 C A:LEU149 3.6 23.3 1.0 OD1 A:ASP155 3.7 22.3 1.0 CB A:ASN151 4.1 23.0 1.0 MN A:MN1002 4.1 19.0 1.0 N A:ASN151 4.2 23.1 1.0 CB A:ASP147 4.2 22.6 1.0 O A:HOH1102 4.3 20.5 1.0 NE1 A:TRP154 4.4 21.3 1.0 N A:LEU149 4.4 23.6 1.0 CA A:LEU149 4.4 23.3 1.0 ND2 A:ASN151 4.6 21.8 1.0 N A:TYR150 4.6 24.4 1.0 CB A:ASP155 4.6 22.3 1.0 O A:ASP107 4.6 21.7 1.0 OD1 A:ASP107 4.7 24.3 1.0 O A:GLY125 4.7 24.4 1.0 CB A:LEU149 4.7 23.4 1.0 C A:TYR150 4.7 23.9 1.0 CE1 A:HIS160 4.7 20.6 1.0 CA A:ASN151 4.8 23.6 1.0 CA A:TYR150 4.8 23.9 1.0 CA A:GLY125 4.8 22.6 1.0 CD2 A:LEU149 4.9 25.3 1.0 CZ2 A:TRP154 5.0 21.1 1.0 CE2 A:TRP154 5.0 21.5 1.0 CA A:ASP147 5.0 22.9 1.0 NE2 A:HIS160 5.0 22.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure Plant Lectin in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Plant Lectin in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:39.9 occ:1.00 OD2 B:ASP155 2.3 42.9 1.0 O B:LEU149 2.3 38.8 1.0 O B:HOH1106 2.3 41.0 1.0 O B:HOH1107 2.3 46.6 1.0 OD1 B:ASP147 2.3 34.7 1.0 OD1 B:ASN151 2.3 47.9 1.0 OD2 B:ASP147 2.4 34.9 1.0 CG B:ASP147 2.7 34.7 1.0 CG B:ASP155 3.4 44.2 1.0 CG B:ASN151 3.5 52.2 1.0 C B:LEU149 3.5 40.6 1.0 OD1 B:ASP155 3.8 41.6 1.0 MN B:MN1002 4.0 37.5 1.0 N B:ASN151 4.0 46.4 1.0 CB B:ASN151 4.1 48.6 1.0 O B:HOH1105 4.2 34.8 1.0 CB B:ASP147 4.2 35.2 1.0 NE1 B:TRP154 4.4 56.9 1.0 CA B:LEU149 4.4 42.0 1.0 N B:LEU149 4.4 42.5 1.0 N B:TYR150 4.5 42.3 1.0 ND2 B:ASN151 4.6 52.9 1.0 O B:ASP107 4.6 53.0 1.0 CB B:ASP155 4.6 45.2 1.0 C B:TYR150 4.6 45.5 1.0 CE1 B:HIS160 4.6 35.8 1.0 O B:GLY125 4.7 45.8 1.0 CA B:TYR150 4.7 44.5 1.0 CA B:ASN151 4.7 48.1 1.0 CB B:LEU149 4.7 44.1 1.0 CA B:GLY125 4.9 46.6 1.0 CZ2 B:TRP154 4.9 58.0 1.0 NE2 B:HIS160 4.9 37.1 1.0 CE2 B:TRP154 4.9 57.3 1.0

M.Nagae, K.Soga, K.Morita-Matsumoto, S.Hanashima, A.Ikeda, K.Yamamoto, Y.Yamaguchi. Phytohemagglutinin From Phaseolus Vulgaris (Pha-E) Displays A Novel Glycan Recognition Mode Using A Common Legume Lectin Fold Glycobiology V. 24 368 2014.
ISSN: ISSN 0959-6658
PubMed: 24436051
DOI: 10.1093/GLYCOB/CWU004