Manganese 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:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of Dioclea Violacea Seed Lectin (pdb code 2gdf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Dioclea Violacea Seed Lectin, PDB code: 2gdf:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Dioclea Violacea Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:38.7 occ:1.00 OD2 B:ASP10 1.9 35.6 1.0 O B:HOH308 2.3 29.5 1.0 NE2 B:HIS24 2.3 34.9 1.0 OE2 B:GLU8 2.5 32.6 1.0 OD1 B:ASP19 2.7 44.4 1.0 CG B:ASP10 3.1 39.0 1.0 CG B:ASP19 3.1 42.1 1.0 CE1 B:HIS24 3.3 38.8 1.0 CD2 B:HIS24 3.3 37.2 1.0 CD B:GLU8 3.3 33.9 1.0 OD2 B:ASP19 3.3 39.5 1.0 OE1 B:GLU8 3.4 33.5 1.0 CB B:ASP10 3.7 38.0 1.0 OG B:SER34 4.0 34.2 1.0 OD1 B:ASP10 4.2 39.1 1.0 CA B:CA302 4.2 42.7 1.0 CB B:ASP19 4.2 41.8 1.0 ND1 B:HIS24 4.4 36.5 1.0 CG B:HIS24 4.4 35.8 1.0 O B:ILE32 4.5 32.6 1.0 CA B:ASP19 4.6 42.1 1.0 CG B:GLU8 4.7 34.8 1.0

Manganese 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 Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Dioclea Violacea Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1301 b:37.4 occ:1.00 OD2 D:ASP10 1.8 35.1 1.0 O D:HOH1304 2.2 29.3 1.0 NE2 D:HIS24 2.3 35.1 1.0 OE2 D:GLU8 2.5 29.8 1.0 OD1 D:ASP19 2.8 41.4 1.0 CG D:ASP10 3.0 37.8 1.0 CG D:ASP19 3.2 40.9 1.0 CD2 D:HIS24 3.2 38.3 1.0 CE1 D:HIS24 3.3 39.8 1.0 OD2 D:ASP19 3.4 36.8 1.0 CD D:GLU8 3.4 31.2 1.0 OE1 D:GLU8 3.6 33.1 1.0 CB D:ASP10 3.6 36.7 1.0 OD1 D:ASP10 4.1 38.0 1.0 OG D:SER34 4.1 33.5 1.0 CA D:CA1302 4.2 42.6 1.0 CB D:ASP19 4.3 42.0 1.0 ND1 D:HIS24 4.4 38.3 1.0 CG D:HIS24 4.4 37.4 1.0 O D:ILE32 4.5 34.2 1.0 CA D:ASP19 4.7 42.3 1.0 CG D:GLU8 4.7 32.7 1.0

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