Calcium in PDB 1f9k: Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose

The structure of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose, PDB code: 1f9k was solved by N.Manoj, V.R.Srinivas, A.Surolia, M.Vijayan, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	182.110, 182.110, 44.990, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 25.1

The structure of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose (pdb code 1f9k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose, PDB code: 1f9k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:41.0 occ:1.00 O A:HOH527 2.2 34.9 1.0 O A:HOH524 2.3 17.9 1.0 OD2 A:ASP132 2.3 31.9 1.0 O A:PHE127 2.4 15.4 1.0 OD1 A:ASN129 2.4 29.0 1.0 OD1 A:ASP125 2.4 23.4 1.0 OD2 A:ASP125 2.5 23.4 1.0 CG A:ASP125 2.8 23.4 1.0 CG A:ASP132 3.4 31.9 1.0 CG A:ASN129 3.4 29.0 1.0 C A:PHE127 3.5 15.4 1.0 N A:ASN129 3.8 21.6 1.0 OD1 A:ASP132 3.9 31.9 1.0 CB A:ASN129 4.0 29.0 1.0 O A:HOH523 4.1 42.4 1.0 CB A:ASP125 4.3 23.4 1.0 CA A:PHE127 4.4 15.4 1.0 MN A:MN300 4.4 41.0 1.0 CB A:PHE127 4.4 14.8 1.0 N A:GLN128 4.5 16.9 1.0 NE1 A:TRP131 4.5 9.4 1.0 CA A:ASN129 4.5 21.6 1.0 ND2 A:ASN129 4.5 29.0 1.0 CA A:GLN128 4.5 16.9 1.0 N A:PHE127 4.6 15.4 1.0 C A:GLN128 4.6 16.9 1.0 CB A:ASP132 4.6 31.9 1.0 O A:GLY106 4.7 22.1 1.0 CD2 A:PHE127 4.7 14.8 1.0 O A:ASP88 4.7 17.9 1.0 CA A:GLY106 4.7 22.1 1.0 OD1 A:ASP88 4.8 25.8 1.0

Calcium binding site 2 out of 2 in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:41.0 occ:1.00 O B:HOH519 2.2 51.7 1.0 OD2 B:ASP132 2.4 31.4 1.0 OD1 B:ASN129 2.4 95.3 1.0 O B:PHE127 2.4 62.0 1.0 OD1 B:ASP125 2.5 45.0 1.0 OD2 B:ASP125 2.6 45.0 1.0 CG B:ASP125 2.9 45.0 1.0 CG B:ASN129 3.4 95.3 1.0 CG B:ASP132 3.5 31.4 1.0 C B:PHE127 3.6 62.0 1.0 N B:ASN129 3.9 55.4 1.0 OD1 B:ASP132 3.9 31.4 1.0 CB B:ASN129 4.0 95.3 1.0 CB B:ASP125 4.4 45.0 1.0 CA B:PHE127 4.4 62.0 1.0 MN B:MN301 4.4 41.0 1.0 CB B:PHE127 4.5 75.5 1.0 NE1 B:TRP131 4.5 72.7 1.0 ND2 B:ASN129 4.5 95.3 1.0 N B:GLN128 4.5 66.8 1.0 CA B:ASN129 4.6 55.4 1.0 O B:GLY106 4.6 35.9 1.0 N B:PHE127 4.6 62.0 1.0 CA B:GLN128 4.6 66.8 1.0 C B:GLN128 4.6 66.8 1.0 CA B:GLY106 4.7 35.9 1.0 CB B:ASP132 4.7 31.4 1.0 CD2 B:PHE127 4.7 75.5 1.0 O B:ASP88 4.7 52.8 1.0 OD1 B:ASP88 4.7 68.5 1.0 O B:HOH518 4.7 39.1 1.0 CZ2 B:TRP131 5.0 72.7 1.0 CE2 B:TRP131 5.0 72.7 1.0

N.Manoj, V.R.Srinivas, A.Surolia, M.Vijayan, K.Suguna. Carbohydrate Specificity and Salt-Bridge Mediated Conformational Change in Acidic Winged Bean Agglutinin. J.Mol.Biol. V. 302 1129 2000.
ISSN: ISSN 0022-2836
PubMed: 11183779
DOI: 10.1006/JMBI.2000.4111