Manganese in PDB 3wcs: Crystal Structure of Plant Lectin (Ligand-Bound Form)

The structure of Crystal Structure of Plant Lectin (Ligand-Bound Form), PDB code: 3wcs 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)	98.10 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.579, 196.193, 98.655, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 25.5

The structure of Crystal Structure of Plant Lectin (Ligand-Bound Form) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

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

Manganese binding site 1 out of 2 in the Crystal Structure of Plant Lectin (Ligand-Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Plant Lectin (Ligand-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:15.9 occ:1.00 O A:HOH1103 2.0 19.2 1.0 O A:HOH1102 2.0 19.3 1.0 OD1 A:ASP155 2.0 17.7 1.0 OE2 A:GLU145 2.0 17.6 1.0 NE2 A:HIS160 2.0 20.0 1.0 OD2 A:ASP147 2.0 19.1 1.0 CE1 A:HIS160 3.0 16.0 1.0 CG A:ASP155 3.1 17.4 1.0 CG A:ASP147 3.1 19.1 1.0 CD2 A:HIS160 3.1 17.3 1.0 CD A:GLU145 3.2 16.5 1.0 CB A:ASP147 3.5 19.6 1.0 OE1 A:GLU145 3.6 16.5 1.0 OD2 A:ASP155 3.6 16.5 1.0 O A:HOH1104 3.7 19.8 1.0 CA A:CA1003 4.1 17.4 1.0 ND1 A:HIS160 4.2 17.6 1.0 OD1 A:ASP147 4.2 19.0 1.0 CG A:HIS160 4.3 17.7 1.0 OG A:SER170 4.3 18.4 1.0 CB A:ASP155 4.3 17.1 1.0 O A:HOH1107 4.3 16.5 1.0 NE1 A:TRP154 4.5 18.8 1.0 CG A:GLU145 4.5 15.9 1.0 O A:ILE168 4.5 20.0 1.0 CD1 A:TRP154 4.6 20.3 1.0 CA A:ASP155 4.8 18.0 1.0 CD A:PRO156 4.8 18.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Plant Lectin (Ligand-Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Plant Lectin (Ligand-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:32.4 occ:1.00 O B:HOH1102 1.9 31.3 1.0 O B:HOH1101 1.9 36.1 1.0 NE2 B:HIS160 2.0 33.4 1.0 OD2 B:ASP147 2.0 32.1 1.0 OE2 B:GLU145 2.0 32.2 1.0 OD1 B:ASP155 2.0 32.8 1.0 CE1 B:HIS160 2.9 33.6 1.0 CG B:ASP155 2.9 34.5 1.0 CG B:ASP147 3.0 30.1 1.0 CD2 B:HIS160 3.0 32.8 1.0 CD B:GLU145 3.1 31.3 1.0 CB B:ASP147 3.4 31.3 1.0 OD2 B:ASP155 3.4 36.6 1.0 OE1 B:GLU145 3.6 32.5 1.0 O B:HOH1105 3.8 36.8 1.0 CA B:CA1003 4.0 35.9 1.0 ND1 B:HIS160 4.0 33.2 1.0 OD1 B:ASP147 4.1 33.3 1.0 CG B:HIS160 4.2 32.7 1.0 CB B:ASP155 4.2 36.3 1.0 OG B:SER170 4.4 32.2 1.0 CG B:GLU145 4.4 30.4 1.0 NE1 B:TRP154 4.5 43.7 1.0 O B:ILE168 4.6 33.7 1.0 CD1 B:TRP154 4.7 43.8 1.0 CA B:ASP155 4.7 36.9 1.0 CA B:ASP147 4.9 31.7 1.0 CD B:PRO156 5.0 36.2 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