Manganese in PDB 3wog: Crystal Structure Plant Lectin in Complex with Ligand

The structure of Crystal Structure Plant Lectin in Complex with Ligand, PDB code: 3wog was solved by M.Nagae, Y.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.74 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.780, 195.481, 97.829, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 26.3

The structure of Crystal Structure Plant Lectin in Complex with Ligand also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Crystal Structure Plant Lectin in Complex with Ligand (pdb code 3wog). 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 Plant Lectin in Complex with Ligand, PDB code: 3wog:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure Plant Lectin in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure Plant Lectin in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:19.0 occ:1.00 O A:HOH1102 1.9 20.5 1.0 O A:HOH1101 1.9 22.1 1.0 NE2 A:HIS160 2.0 22.8 1.0 OE2 A:GLU145 2.0 21.8 1.0 OD2 A:ASP147 2.0 21.4 1.0 OD1 A:ASP155 2.0 22.3 1.0 CE1 A:HIS160 2.9 20.6 1.0 CG A:ASP147 3.0 21.8 1.0 CD2 A:HIS160 3.1 20.9 1.0 CD A:GLU145 3.1 21.9 1.0 CG A:ASP155 3.1 21.5 1.0 CB A:ASP147 3.4 22.6 1.0 OE1 A:GLU145 3.5 22.6 1.0 OD2 A:ASP155 3.7 21.3 1.0 O A:HOH1103 3.8 21.3 1.0 ND1 A:HIS160 4.1 20.9 1.0 CA A:CA1003 4.1 22.3 1.0 OD1 A:ASP147 4.1 21.6 1.0 CG A:HIS160 4.2 21.1 1.0 OG A:SER170 4.2 23.0 1.0 CB A:ASP155 4.3 22.3 1.0 CG A:GLU145 4.4 21.8 1.0 NE1 A:TRP154 4.5 21.3 1.0 O A:ILE168 4.5 24.7 1.0 O A:HOH1112 4.6 23.7 1.0 CD1 A:TRP154 4.6 22.6 1.0 CA A:ASP155 4.8 22.6 1.0 CD A:PRO156 4.8 23.5 1.0 CA A:ASP147 5.0 22.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure Plant Lectin in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure Plant Lectin in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:37.5 occ:1.00 O B:HOH1104 1.9 33.9 1.0 O B:HOH1105 1.9 34.8 1.0 NE2 B:HIS160 1.9 37.1 1.0 OD2 B:ASP147 2.0 34.9 1.0 OE2 B:GLU145 2.0 36.2 1.0 OD1 B:ASP155 2.0 41.6 1.0 CE1 B:HIS160 2.9 35.8 1.0 CG B:ASP147 3.0 34.7 1.0 CG B:ASP155 3.0 44.2 1.0 CD2 B:HIS160 3.0 36.2 1.0 CD B:GLU145 3.1 35.0 1.0 CB B:ASP147 3.4 35.2 1.0 OD2 B:ASP155 3.5 42.9 1.0 OE1 B:GLU145 3.6 37.0 1.0 O B:HOH1106 3.9 41.0 1.0 CA B:CA1003 4.0 39.9 1.0 ND1 B:HIS160 4.0 33.8 1.0 OD1 B:ASP147 4.1 34.7 1.0 CG B:HIS160 4.1 34.9 1.0 CB B:ASP155 4.2 45.2 1.0 OG B:SER170 4.3 36.8 1.0 CG B:GLU145 4.4 34.6 1.0 O B:ILE168 4.5 37.9 1.0 NE1 B:TRP154 4.5 56.9 1.0 CD1 B:TRP154 4.7 55.9 1.0 CA B:ASP155 4.7 47.3 1.0 CA B:ASP147 4.9 36.6 1.0 CD B:PRO156 4.9 44.7 1.0

M.Nagae, K.Soga, K.Morita-Matsumoto, S.Hanashima, A.Ikeda, K.Yamamoto, Y.Yamaguchi. Phytohemagglutinin From Phaseolus Vulgaris (Pha-E) Displays A Novel Glycan Recognition Mode Using A Common Legume Lectin Fold Glycobiology V. 24 368 2014.
ISSN: ISSN 0959-6658
PubMed: 24436051
DOI: 10.1093/GLYCOB/CWU004