Calcium in PDB 1h9w: Native Dioclea Guianensis Seed Lectin

The structure of Native Dioclea Guianensis Seed Lectin, PDB code: 1h9w was solved by A.Romero, D.A.Wah, F.G.D.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)	22.54 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.163, 90.163, 106.755, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.7

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

Manganese

(Mn)

7 atoms

The binding sites of Calcium atom in the Native Dioclea Guianensis Seed Lectin (pdb code 1h9w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Native Dioclea Guianensis Seed Lectin, PDB code: 1h9w:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Native Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Dioclea Guianensis Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:20.9 occ:1.00 O A:HOH2007 2.2 22.2 1.0 OD1 A:ASP10 2.2 18.9 1.0 O A:TYR12 2.2 23.2 1.0 OD2 A:ASP19 2.3 24.3 1.0 O A:HOH2138 2.4 21.6 1.0 OD2 A:ASP10 2.4 16.9 1.0 OD1 A:ASN14 2.6 25.7 1.0 CG A:ASP10 2.7 14.1 1.0 C A:TYR12 3.5 24.1 1.0 CG A:ASP19 3.5 24.7 1.0 CG A:ASN14 3.7 27.4 1.0 N A:ASN14 4.0 25.0 1.0 OD1 A:ASP19 4.0 22.9 1.0 CB A:ASP10 4.2 19.0 1.0 MN A:MN238 4.2 11.1 1.0 CB A:ASN14 4.2 25.2 1.0 CA A:TYR12 4.3 23.4 1.0 N A:TYR12 4.4 22.7 1.0 N A:PRO13 4.4 24.1 1.0 CB A:TYR12 4.4 24.5 1.0 O A:ASP208 4.5 17.4 1.0 CA A:PRO13 4.6 24.7 1.0 CB A:ASP19 4.6 25.2 1.0 C A:PRO13 4.7 25.0 1.0 O A:HOH2146 4.7 21.7 1.0 CA A:ASN14 4.8 26.3 1.0 OD1 A:ASP208 4.8 19.9 1.0 CE1 A:HIS24 4.8 18.0 1.0 O A:ARG228 4.8 24.7 1.0 ND2 A:ASN14 4.8 25.3 1.0 CB A:ARG228 4.9 27.6 1.0 CA A:ARG228 4.9 26.0 1.0 CA A:ASP10 4.9 18.4 1.0

Calcium binding site 2 out of 3 in the Native Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Native Dioclea Guianensis Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:27.1 occ:1.00 OD1 B:ASP10 2.2 24.9 1.0 O B:HOH2004 2.2 27.9 1.0 O B:TYR12 2.3 29.1 1.0 OD1 B:ASN14 2.4 25.5 1.0 O B:HOH2108 2.4 24.4 1.0 OD2 B:ASP19 2.5 29.0 1.0 OD2 B:ASP10 2.6 22.6 1.0 CG B:ASP10 2.7 23.6 1.0 CG B:ASN14 3.5 29.9 1.0 C B:TYR12 3.5 30.0 1.0 CG B:ASP19 3.6 28.9 1.0 N B:ASN14 3.9 32.2 1.0 CB B:ASN14 4.0 29.1 1.0 CB B:ASP10 4.2 23.6 1.0 OD1 B:ASP19 4.2 27.6 1.0 MN B:MN238 4.2 16.4 1.0 CA B:TYR12 4.4 30.1 1.0 N B:TYR12 4.5 28.8 1.0 O B:ASP208 4.5 23.5 1.0 N B:PRO13 4.5 30.7 1.0 CE1 B:HIS24 4.5 33.1 1.0 CB B:TYR12 4.6 31.5 1.0 CA B:ASN14 4.6 32.8 1.0 CA B:PRO13 4.6 30.7 1.0 C B:PRO13 4.6 32.0 1.0 ND2 B:ASN14 4.6 27.0 1.0 O B:ARG228 4.7 31.0 1.0 CB B:ASP19 4.7 30.3 1.0 CB B:ARG228 4.7 30.8 1.0 CA B:ARG228 4.8 29.9 1.0 OD1 B:ASP208 4.9 25.8 1.0 CA B:ASP10 4.9 24.6 1.0 NE2 B:HIS24 5.0 31.5 1.0

Calcium binding site 3 out of 3 in the Native Dioclea Guianensis Seed Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Native Dioclea Guianensis Seed Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca243 b:6.5 occ:1.00 OE1 A:GLU183 2.4 33.5 1.0 OE2 A:GLU87 2.4 28.4 1.0 OE1 A:GLU87 2.4 23.2 1.0 CD A:GLU87 2.7 22.0 1.0 CD A:GLU183 3.1 31.4 1.0 OE2 A:GLU183 3.2 31.3 1.0 O A:HOH2114 3.9 10.0 1.0 CG A:GLU87 4.2 23.1 1.0 N A:LYS184 4.3 29.1 1.0 CG A:GLU183 4.6 30.4 1.0 CA A:GLU183 4.7 26.9 1.0 CB A:LYS184 4.9 33.7 1.0 CB A:GLU87 5.0 17.6 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