Calcium in PDB 1lu2: Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide

The structure of Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide, PDB code: 1lu2 was solved by T.W.Hamelryck, R.Loris, J.Bouckaert, G.Strecker, A.Imberty, E.Fernandez, L.Wyns, M.E.Etzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.730, 108.000, 80.960, 90.00, 124.67, 90.00
R / Rfree (%)	19.1 / 21.9

The structure of Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide (pdb code 1lu2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide, PDB code: 1lu2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:36.8 occ:1.00 OD1 A:ASN129 2.3 41.1 1.0 OD1 A:ASP125 2.4 27.9 1.0 OD2 A:ASP133 2.4 29.7 1.0 O A:LEU127 2.4 32.3 1.0 OD2 A:ASP125 2.5 27.6 1.0 CG A:ASP125 2.7 26.9 1.0 CG A:ASN129 3.4 37.0 1.0 CG A:ASP133 3.5 32.4 1.0 C A:LEU127 3.6 32.6 1.0 OD1 A:ASP133 4.0 34.8 1.0 N A:ASN129 4.1 37.6 1.0 CB A:ASP125 4.2 24.9 1.0 CB A:ASN129 4.3 35.6 1.0 ND2 A:ASN129 4.3 36.0 1.0 O A:GLY103 4.4 26.4 1.0 OD1 A:ASP85 4.4 30.6 1.0 NE1 A:TRP132 4.5 37.1 1.0 O A:ASP85 4.5 28.2 1.0 CA A:LEU127 4.5 31.8 1.0 N A:LEU127 4.6 29.9 1.0 N A:SER128 4.6 33.4 1.0 CA A:SER128 4.6 35.7 1.0 MN A:MN302 4.7 70.6 1.0 C A:SER128 4.7 37.1 1.0 CA A:GLY103 4.7 24.0 1.0 CB A:LEU127 4.7 32.2 1.0 CB A:ASP133 4.8 32.0 1.0 CA A:ASN129 4.8 36.4 1.0 CD2 A:LEU127 4.9 29.2 1.0 CA A:ASP125 5.0 26.5 1.0

Calcium binding site 2 out of 2 in the Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dolichos Biflorus Seed Lectin in Complex with the Blood Group A Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:28.6 occ:1.00 OD1 B:ASN129 2.2 43.6 1.0 OD1 B:ASP125 2.4 32.4 1.0 OD2 B:ASP133 2.4 27.0 1.0 O B:LEU127 2.5 31.6 1.0 OD2 B:ASP125 2.5 30.0 1.0 CG B:ASP125 2.8 29.3 1.0 CG B:ASN129 3.4 38.3 1.0 CG B:ASP133 3.6 31.0 1.0 C B:LEU127 3.7 31.3 1.0 OD1 B:ASP133 4.0 31.8 1.0 N B:ASN129 4.1 35.1 1.0 CB B:ASP125 4.3 26.0 1.0 CB B:ASN129 4.3 35.4 1.0 ND2 B:ASN129 4.3 36.7 1.0 O B:GLY103 4.3 25.4 1.0 OD1 B:ASP85 4.4 25.7 1.0 NE1 B:TRP132 4.5 37.3 1.0 O B:ASP85 4.5 28.7 1.0 CA B:LEU127 4.6 31.0 1.0 N B:LEU127 4.6 29.4 1.0 N B:SER128 4.6 32.2 1.0 CA B:GLY103 4.6 23.1 1.0 CA B:SER128 4.7 34.1 1.0 MN B:MN302 4.7 74.1 1.0 CB B:LEU127 4.7 31.8 1.0 C B:SER128 4.7 34.8 1.0 CB B:ASP133 4.8 32.6 1.0 CA B:ASN129 4.8 34.2 1.0 CD2 B:LEU127 4.9 29.7 1.0 C B:GLY103 5.0 23.8 1.0 CA B:ASP125 5.0 27.1 1.0

T.W.Hamelryck, R.Loris, J.Bouckaert, M.H.Dao-Thi, G.Strecker, A.Imberty, E.Fernandez, L.Wyns, M.E.Etzler. Carbohydrate Binding, Quaternary Structure and A Novel Hydrophobic Binding Site in Two Legume Lectin Oligomers From Dolichos Biflorus. J.Mol.Biol. V. 286 1161 1999.
ISSN: ISSN 0022-2836
PubMed: 10047489
DOI: 10.1006/JMBI.1998.2534