Cadmium in PDB 1h9p: Crystal Structure of Dioclea Guianensis Seed Lectin

The structure of Crystal Structure of Dioclea Guianensis Seed Lectin, PDB code: 1h9p was solved by A.Romero, D.A.Wah, F.Gallego Del Sol, B.S.Cavada, M.V.Ramos, T.B.Grangeiro, A.H.Sampaio, J.J.Calvete, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.68 / 2.00
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.314, 90.314, 108.276, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 28.9

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

Manganese

(Mn)

3 atoms

The binding sites of Cadmium atom in the Crystal Structure of Dioclea Guianensis Seed Lectin (pdb code 1h9p). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Dioclea Guianensis Seed Lectin, PDB code: 1h9p:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Dioclea Guianensis Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd238 b:39.9 occ:1.00 O A:HOH2009 1.8 14.0 1.0 OD2 A:ASP10 2.0 20.2 1.0 O A:HOH2023 2.1 31.8 1.0 OE2 A:GLU8 2.3 28.2 1.0 NE2 A:HIS24 2.3 32.9 1.0 OD1 A:ASP19 2.9 55.8 1.0 CG A:ASP10 3.0 27.8 1.0 OD2 A:ASP19 3.0 55.5 1.0 CE1 A:HIS24 3.1 34.4 1.0 CG A:ASP19 3.1 55.7 1.0 CD A:GLU8 3.2 29.6 1.0 CD2 A:HIS24 3.4 33.5 1.0 CB A:ASP10 3.4 27.5 1.0 OE1 A:GLU8 3.4 28.4 1.0 OD1 A:ASP10 4.0 29.9 1.0 O A:HOH2115 4.1 21.6 1.0 CD A:CD239 4.2 44.2 1.0 OG A:SER34 4.2 35.4 1.0 ND1 A:HIS24 4.2 35.3 1.0 CB A:ASP19 4.3 56.1 1.0 CG A:HIS24 4.4 34.4 1.0 CG A:GLU8 4.6 25.4 1.0 O A:ILE32 4.7 40.5 1.0 CA A:ASP19 4.7 55.9 1.0 CD A:PRO20 4.9 54.9 1.0 CA A:ASP10 4.9 30.5 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Dioclea Guianensis Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd239 b:44.2 occ:1.00 O A:HOH2011 1.9 16.2 1.0 O A:HOH2115 2.1 21.6 1.0 OD1 A:ASP10 2.3 29.9 1.0 OD2 A:ASP19 2.4 55.5 1.0 O A:TYR12 2.4 43.5 1.0 OD1 A:ASN14 2.4 44.9 1.0 OD2 A:ASP10 2.7 20.2 1.0 CG A:ASP10 2.8 27.8 1.0 CG A:ASN14 3.4 48.1 1.0 CG A:ASP19 3.5 55.7 1.0 C A:TYR12 3.6 44.9 1.0 N A:ASN14 3.9 47.9 1.0 CB A:ASN14 4.0 48.0 1.0 CD A:CD238 4.2 39.9 1.0 OD1 A:ASP19 4.2 55.8 1.0 CB A:ASP10 4.3 27.5 1.0 CA A:TYR12 4.5 44.2 1.0 ND2 A:ASN14 4.5 49.0 1.0 N A:TYR12 4.5 41.0 1.0 O A:ARG228 4.5 39.8 1.0 N A:PRO13 4.5 45.7 1.0 CB A:ASP19 4.6 56.1 1.0 CE1 A:HIS24 4.6 34.4 1.0 CA A:PRO13 4.6 46.8 1.0 CA A:ASN14 4.6 49.0 1.0 O A:ASP208 4.6 41.5 1.0 CB A:ARG228 4.6 42.8 1.0 C A:PRO13 4.6 46.8 1.0 CA A:ARG228 4.7 39.9 1.0 O A:HOH2009 4.7 14.0 1.0 CB A:TYR12 4.7 46.9 1.0 OD1 A:ASP208 4.7 40.8 1.0 CD1 A:TYR12 5.0 49.9 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Dioclea Guianensis Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd501 b:46.0 occ:0.50 OE1 A:GLU183 2.2 46.9 1.0 OE2 A:GLU87 2.3 43.8 1.0 OE1 A:GLU87 2.5 36.3 1.0 CD A:GLU87 2.7 37.8 1.0 OE2 A:GLU183 2.8 49.1 1.0 CD A:GLU183 2.9 46.0 1.0 CG A:GLU87 4.2 37.3 1.0 N A:LYS184 4.3 40.9 1.0 CG A:GLU183 4.3 44.1 1.0 CA A:GLU183 4.6 39.0 1.0 CB A:LYS184 4.9 44.0 1.0 O A:HOH2096 5.0 22.2 1.0

D.A.Wah, A.Romero, F.Gallego, B.S.Cavada, M.V.Ramos, T.B.Grangeiro, A.H.Sampaio, J.J.Calvete. Crystal Structure of Native and Cd/Cd-Substituted Dioclea Guianensis Seed Lectin. A Novel Manganese-Binding Site and Structural Basis of Dimer-Tetramer Association J.Mol.Biol. V. 310 885 2001.
ISSN: ISSN 0022-2836
PubMed: 11453695
DOI: 10.1006/JMBI.2001.4814