Manganese 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:

Calcium

(Ca)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Winged Bean Acidic Lectin Complexed with Methyl-Alpha-D-Galactose, PDB code: 1f9k:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn300 b:41.0 occ:1.00 O A:HOH523 2.2 42.4 1.0 NE2 A:HIS137 2.2 14.1 1.0 OD1 A:ASP132 2.3 31.9 1.0 OD2 A:ASP125 2.3 23.4 1.0 OE2 A:GLU123 2.3 22.1 1.0 O A:HOH526 2.4 38.1 1.0 CE1 A:HIS137 3.1 14.1 1.0 CG A:ASP132 3.1 31.9 1.0 CG A:ASP125 3.2 23.4 1.0 CD2 A:HIS137 3.4 14.1 1.0 CD A:GLU123 3.4 22.1 1.0 CB A:ASP125 3.5 23.4 1.0 OD2 A:ASP132 3.7 31.9 1.0 OE1 A:GLU123 3.9 22.1 1.0 CB A:ASP132 4.1 31.9 1.0 OG A:SER147 4.1 15.5 1.0 ND1 A:HIS137 4.3 14.1 1.0 OD1 A:ASP125 4.4 23.4 1.0 CA A:CA302 4.4 41.0 1.0 CG A:HIS137 4.4 14.1 1.0 O A:HOH527 4.5 34.9 1.0 CD A:PRO133 4.6 27.3 1.0 CA A:ASP132 4.6 14.7 1.0 CG A:GLU123 4.7 22.1 1.0 O A:ILE145 4.7 23.8 1.0 NE1 A:TRP131 4.7 9.4 1.0 O A:HOH522 4.7 44.8 1.0 CD1 A:TRP131 4.8 9.4 1.0 CA A:ASP125 5.0 24.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:41.0 occ:1.00 NE2 B:HIS137 2.2 57.2 1.0 OD1 B:ASP132 2.3 31.4 1.0 OD2 B:ASP125 2.3 45.0 1.0 OE2 B:GLU123 2.3 46.7 1.0 O B:HOH517 2.5 24.7 1.0 O B:HOH518 2.6 39.1 1.0 CE1 B:HIS137 3.1 57.2 1.0 CG B:ASP132 3.1 31.4 1.0 CG B:ASP125 3.2 45.0 1.0 CD2 B:HIS137 3.4 57.2 1.0 CD B:GLU123 3.4 46.7 1.0 CB B:ASP125 3.5 45.0 1.0 OD2 B:ASP132 3.7 31.4 1.0 OE1 B:GLU123 3.9 46.7 1.0 CB B:ASP132 4.1 31.4 1.0 OG B:SER147 4.1 18.5 1.0 ND1 B:HIS137 4.3 57.2 1.0 OD1 B:ASP125 4.4 45.0 1.0 CG B:HIS137 4.4 57.2 1.0 CA B:CA303 4.4 41.0 1.0 CD B:PRO133 4.6 70.7 1.0 CA B:ASP132 4.6 41.4 1.0 O B:ILE145 4.6 47.1 1.0 CG B:GLU123 4.7 46.7 1.0 NE1 B:TRP131 4.7 72.7 1.0 CD1 B:TRP131 4.8 72.7 1.0 CA B:ASP125 5.0 52.1 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