Calcium in PDB 2gdf: Crystal Structure of Dioclea Violacea Seed Lectin

The structure of Crystal Structure of Dioclea Violacea Seed Lectin, PDB code: 2gdf was solved by F.Gallego Del Sol, J.J.C.Chornet, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.40
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	72.938, 72.938, 161.362, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 25.8

The structure of Crystal Structure of Dioclea Violacea Seed Lectin also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Dioclea Violacea Seed Lectin (pdb code 2gdf). 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 Dioclea Violacea Seed Lectin, PDB code: 2gdf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Dioclea Violacea Seed Lectin


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 Dioclea Violacea Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:42.7 occ:1.00 O B:TYR12 2.2 39.0 1.0 O B:HOH313 2.4 39.0 1.0 OD2 B:ASP19 2.4 39.5 1.0 OD1 B:ASP10 2.4 39.1 1.0 OD1 B:ASN14 2.5 43.0 1.0 OD2 B:ASP10 2.7 35.6 1.0 CG B:ASP10 2.9 39.0 1.0 CG B:ASN14 3.4 43.4 1.0 C B:TYR12 3.5 40.0 1.0 CG B:ASP19 3.6 42.1 1.0 N B:ASN14 3.9 42.2 1.0 CB B:ASN14 4.0 43.0 1.0 MN B:MN301 4.2 38.7 1.0 OD1 B:ASP19 4.3 44.4 1.0 CA B:TYR12 4.4 40.1 1.0 N B:PRO13 4.4 39.9 1.0 CB B:ASP10 4.4 38.0 1.0 ND2 B:ASN14 4.4 44.1 1.0 N B:TYR12 4.5 40.0 1.0 CA B:PRO13 4.5 40.8 1.0 CE1 B:HIS24 4.5 38.8 1.0 CB B:TYR12 4.6 40.7 1.0 C B:PRO13 4.6 41.5 1.0 CA B:ASN14 4.6 42.7 1.0 O B:ARG228 4.7 37.5 1.0 CB B:ASP19 4.7 41.8 1.0 CB B:ARG228 4.7 36.6 1.0 O B:ASP208 4.7 39.1 1.0 CA B:ARG228 4.8 36.8 1.0 OD1 B:ASP208 4.9 35.5 1.0 NE2 B:HIS24 4.9 34.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Dioclea Violacea Seed Lectin


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 Dioclea Violacea Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1302 b:42.6 occ:1.00 O D:TYR12 2.2 39.1 1.0 OD1 D:ASP10 2.3 38.0 1.0 OD2 D:ASP19 2.4 36.8 1.0 OD1 D:ASN14 2.5 40.8 1.0 O D:HOH1314 2.6 38.2 1.0 OD2 D:ASP10 2.8 35.1 1.0 CG D:ASP10 2.9 37.8 1.0 C D:TYR12 3.5 39.9 1.0 CG D:ASN14 3.5 43.0 1.0 CG D:ASP19 3.6 40.9 1.0 N D:ASN14 3.8 42.1 1.0 CB D:ASN14 4.0 42.7 1.0 MN D:MN1301 4.2 37.4 1.0 OD1 D:ASP19 4.3 41.4 1.0 CA D:TYR12 4.3 39.6 1.0 CB D:ASP10 4.4 36.7 1.0 N D:PRO13 4.4 39.9 1.0 N D:TYR12 4.4 38.8 1.0 CA D:PRO13 4.5 40.8 1.0 ND2 D:ASN14 4.5 44.6 1.0 CB D:TYR12 4.5 40.0 1.0 C D:PRO13 4.5 41.7 1.0 CE1 D:HIS24 4.6 39.8 1.0 CA D:ASN14 4.6 42.6 1.0 O D:ARG228 4.7 35.6 1.0 CB D:ARG228 4.7 35.0 1.0 CB D:ASP19 4.7 42.0 1.0 O D:ASP208 4.7 39.5 1.0 NE2 D:HIS24 4.8 35.1 1.0 CA D:ARG228 4.9 35.1 1.0 OD1 D:ASP208 4.9 37.6 1.0

F.Gallego Del Sol, J.J.C.Chornet, B.S.Cavada. Crystal Structure of Dioclea Violacea Seed Lectin To Be Published.