Manganese in PDB 1g8w: Improved Structure of Phytohemagglutinin-L From the Kidney Bean

The structure of Improved Structure of Phytohemagglutinin-L From the Kidney Bean, PDB code: 1g8w was solved by L.Buts, T.W.Hamelryck, M.Dao-Thi, R.Loris, L.Wyns, M.E.Etzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.479, 121.278, 89.957, 90.00, 93.18, 90.00
R / Rfree (%)	18.1 / 21.2

The structure of Improved Structure of Phytohemagglutinin-L From the Kidney Bean also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean (pdb code 1g8w). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean, PDB code: 1g8w:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn253 b:41.4 occ:1.00 OE2 A:GLU122 1.9 39.3 1.0 O A:HOH1255 2.1 45.6 1.0 O A:HOH1254 2.2 25.8 1.0 NE2 A:HIS137 2.3 20.4 1.0 OD2 A:ASP124 2.3 29.0 1.0 OD1 A:ASP132 2.3 50.9 1.0 CD A:GLU122 3.1 31.9 1.0 CD2 A:HIS137 3.1 24.1 1.0 CG A:ASP124 3.2 31.6 1.0 CE1 A:HIS137 3.3 24.6 1.0 CG A:ASP132 3.4 46.6 1.0 CB A:ASP124 3.5 27.0 1.0 OE1 A:GLU122 3.6 32.8 1.0 OD2 A:ASP132 3.8 46.7 1.0 OG A:SER147 3.9 29.3 1.0 CG A:GLU122 4.3 26.8 1.0 CG A:HIS137 4.3 27.2 1.0 O A:HOH1257 4.4 30.4 1.0 ND1 A:HIS137 4.4 28.0 1.0 OD1 A:ASP124 4.4 35.5 1.0 O A:ILE145 4.4 29.9 1.0 CB A:ASP132 4.6 40.7 1.0 CD A:PRO133 4.6 32.0 1.0 CA A:CA256 4.7 37.2 1.0 CA A:ASP132 4.9 39.8 1.0 CA A:ASP124 4.9 26.4 1.0 CD1 A:TRP131 5.0 33.4 1.0 CB A:SER147 5.0 21.9 1.0

Manganese binding site 2 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn253 b:46.0 occ:1.00 OE2 B:GLU122 1.9 26.9 1.0 O B:HOH2254 2.1 23.3 1.0 O B:HOH2255 2.2 35.4 1.0 NE2 B:HIS137 2.2 13.7 1.0 OD1 B:ASP132 2.3 37.6 1.0 OD2 B:ASP124 2.3 32.1 1.0 CD2 B:HIS137 3.1 19.6 1.0 CD B:GLU122 3.1 23.6 1.0 CG B:ASP124 3.3 25.8 1.0 CE1 B:HIS137 3.3 17.3 1.0 CG B:ASP132 3.4 35.7 1.0 CB B:ASP124 3.5 21.2 1.0 OE1 B:GLU122 3.6 29.0 1.0 OG B:SER147 3.8 26.6 1.0 OD2 B:ASP132 3.9 37.6 1.0 CG B:HIS137 4.3 20.1 1.0 CG B:GLU122 4.3 23.2 1.0 O B:HOH2258 4.3 7.9 1.0 ND1 B:HIS137 4.4 18.2 1.0 OD1 B:ASP124 4.4 27.9 1.0 O B:ILE145 4.4 28.5 1.0 CB B:ASP132 4.6 34.6 1.0 CD B:PRO133 4.6 29.4 1.0 CA B:CA256 4.7 22.1 1.0 CA B:ASP132 4.9 33.7 1.0 CB B:SER147 4.9 26.5 1.0 CA B:ASP124 5.0 23.8 1.0 CD1 B:TRP131 5.0 35.0 1.0

Manganese binding site 3 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn253 b:44.1 occ:1.00 OE2 C:GLU122 2.1 39.8 1.0 OD1 C:ASP132 2.2 54.1 1.0 NE2 C:HIS137 2.2 25.0 1.0 O C:HOH3254 2.2 26.8 1.0 OD2 C:ASP124 2.3 18.7 1.0 O C:HOH3255 2.3 32.0 1.0 CD2 C:HIS137 3.1 25.9 1.0 CD C:GLU122 3.2 30.2 1.0 CG C:ASP132 3.2 43.9 1.0 CE1 C:HIS137 3.2 25.9 1.0 CG C:ASP124 3.3 24.6 1.0 CB C:ASP124 3.6 21.8 1.0 OD2 C:ASP132 3.7 42.6 1.0 OE1 C:GLU122 3.7 29.5 1.0 OG C:SER147 3.9 30.4 1.0 O C:HOH3257 4.2 35.4 1.0 CG C:HIS137 4.3 20.7 1.0 ND1 C:HIS137 4.3 22.1 1.0 OD1 C:ASP124 4.4 31.0 1.0 CB C:ASP132 4.4 37.1 1.0 CG C:GLU122 4.4 26.3 1.0 O C:ILE145 4.5 31.9 1.0 CD C:PRO133 4.5 35.7 1.0 CA C:CA256 4.6 33.9 1.0 CA C:ASP132 4.7 38.2 1.0 CD1 C:TRP131 4.9 32.6 1.0 NE1 C:TRP131 5.0 36.5 1.0 CA C:ASP124 5.0 27.7 1.0

Manganese binding site 4 out of 4 in the Improved Structure of Phytohemagglutinin-L From the Kidney Bean


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Improved Structure of Phytohemagglutinin-L From the Kidney Bean within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn253 b:48.8 occ:1.00 OE2 D:GLU122 2.0 46.7 1.0 O D:HOH4254 2.1 50.9 1.0 OD1 D:ASP132 2.2 46.5 1.0 OD2 D:ASP124 2.2 23.2 1.0 O D:HOH4255 2.2 52.4 1.0 NE2 D:HIS137 2.4 14.2 1.0 CD D:GLU122 3.1 41.1 1.0 CG D:ASP132 3.2 41.6 1.0 CG D:ASP124 3.2 27.1 1.0 CD2 D:HIS137 3.3 25.9 1.0 CE1 D:HIS137 3.4 19.1 1.0 CB D:ASP124 3.6 25.9 1.0 OE1 D:GLU122 3.6 42.3 1.0 OD2 D:ASP132 3.6 41.7 1.0 O D:HOH4258 3.8 26.1 1.0 OG D:SER147 4.0 31.9 1.0 O D:ILE145 4.3 37.0 1.0 OD1 D:ASP124 4.3 22.0 1.0 CG D:GLU122 4.4 32.1 1.0 CB D:ASP132 4.4 40.2 1.0 CG D:HIS137 4.5 24.0 1.0 CA D:CA256 4.5 34.7 1.0 ND1 D:HIS137 4.5 25.1 1.0 CD D:PRO133 4.7 42.7 1.0 CD1 D:TRP131 4.8 41.8 1.0 CA D:ASP132 4.8 41.6 1.0 NE1 D:TRP131 4.8 40.0 1.0 CA D:ASP124 5.0 28.1 1.0

L.Buts, M.H.Dao-Thi, R.Loris, L.Wyns, M.Etzler, T.Hamelryck. Weak Protein-Protein Interactions in Lectins: the Crystal Structure of A Vegetative Lectin From the Legume Dolichos Biflorus. J.Mol.Biol. V. 309 193 2001.
ISSN: ISSN 0022-2836
PubMed: 11491289
DOI: 10.1006/JMBI.2001.4639