Calcium in PDB 3wcs: Crystal Structure of Plant Lectin (Ligand-Bound Form)

The structure of Crystal Structure of Plant Lectin (Ligand-Bound Form), PDB code: 3wcs 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)	98.10 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.579, 196.193, 98.655, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 25.5

The structure of Crystal Structure of Plant Lectin (Ligand-Bound Form) also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Plant Lectin (Ligand-Bound Form) (pdb code 3wcs). 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 of Plant Lectin (Ligand-Bound Form), PDB code: 3wcs:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Plant Lectin (Ligand-Bound Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Plant Lectin (Ligand-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:17.4 occ:1.00 O A:HOH1105 2.3 17.6 1.0 OD2 A:ASP155 2.3 16.5 1.0 O A:HOH1104 2.3 19.8 1.0 OD1 A:ASN151 2.3 18.7 1.0 O A:LEU149 2.3 16.4 1.0 OD1 A:ASP147 2.4 19.0 1.0 OD2 A:ASP147 2.4 19.1 1.0 CG A:ASP147 2.7 19.1 1.0 CG A:ASP155 3.4 17.4 1.0 CG A:ASN151 3.5 18.2 1.0 C A:LEU149 3.6 16.5 1.0 OD1 A:ASP155 3.8 17.7 1.0 CB A:ASN151 4.1 17.8 1.0 N A:ASN151 4.1 16.7 1.0 MN A:MN1002 4.1 15.9 1.0 CB A:ASP147 4.3 19.6 1.0 O A:HOH1103 4.3 19.2 1.0 NE1 A:TRP154 4.3 18.8 1.0 CA A:LEU149 4.4 17.2 1.0 N A:LEU149 4.4 17.8 1.0 CB A:LEU149 4.5 17.9 1.0 O A:ASP107 4.6 18.1 1.0 N A:TYR150 4.6 16.9 1.0 ND2 A:ASN151 4.6 18.4 1.0 CB A:ASP155 4.6 17.1 1.0 O A:GLY125 4.7 17.3 1.0 C A:TYR150 4.7 17.1 1.0 CA A:ASN151 4.7 17.7 1.0 OD1 A:ASP107 4.7 18.7 1.0 CA A:TYR150 4.7 17.0 1.0 CE1 A:HIS160 4.8 16.0 1.0 CA A:GLY125 4.8 18.2 1.0 CD2 A:LEU149 4.9 19.9 1.0 CZ2 A:TRP154 4.9 19.8 1.0 CE2 A:TRP154 4.9 18.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Plant Lectin (Ligand-Bound Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Plant Lectin (Ligand-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:35.9 occ:1.00 OD2 B:ASP155 2.3 36.6 1.0 O B:HOH1105 2.3 36.8 1.0 O B:LEU149 2.3 35.6 1.0 O B:HOH1104 2.3 39.4 1.0 OD1 B:ASP147 2.3 33.3 1.0 OD1 B:ASN151 2.3 39.4 1.0 OD2 B:ASP147 2.4 32.1 1.0 CG B:ASP147 2.7 30.1 1.0 CG B:ASP155 3.4 34.5 1.0 CG B:ASN151 3.4 44.1 1.0 C B:LEU149 3.5 34.5 1.0 OD1 B:ASP155 3.9 32.8 1.0 MN B:MN1002 4.0 32.4 1.0 N B:ASN151 4.1 39.9 1.0 CB B:ASN151 4.1 41.6 1.0 O B:HOH1101 4.2 36.1 1.0 CB B:ASP147 4.2 31.3 1.0 CA B:LEU149 4.3 36.8 1.0 N B:LEU149 4.4 35.2 1.0 NE1 B:TRP154 4.5 43.7 1.0 ND2 B:ASN151 4.5 43.1 1.0 N B:TYR150 4.6 37.1 1.0 CB B:LEU149 4.6 37.1 1.0 O B:ASP107 4.6 40.6 1.0 CB B:ASP155 4.6 36.3 1.0 OD1 B:ASP107 4.7 40.0 1.0 O B:GLY125 4.7 38.2 1.0 CE1 B:HIS160 4.7 33.6 1.0 C B:TYR150 4.7 40.1 1.0 CA B:ASN151 4.7 41.3 1.0 CA B:TYR150 4.8 38.0 1.0 CZ2 B:TRP154 4.9 45.7 1.0 CA B:GLY125 4.9 38.6 1.0 NE2 B:HIS160 4.9 33.4 1.0 CE2 B:TRP154 4.9 44.8 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