Manganese in PDB 2phu: Pterocarpus Angolensis Lectin in Complex with Man-8D1D3

The structure of Pterocarpus Angolensis Lectin in Complex with Man-8D1D3, PDB code: 2phu was solved by A.Garcia-Pino, L.Buts, L.Wyns, A.Imberty, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.696, 83.348, 122.690, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.9

The structure of Pterocarpus Angolensis Lectin in Complex with Man-8D1D3 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Pterocarpus Angolensis Lectin in Complex with Man-8D1D3 (pdb code 2phu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Pterocarpus Angolensis Lectin in Complex with Man-8D1D3, PDB code: 2phu:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Pterocarpus Angolensis Lectin in Complex with Man-8D1D3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pterocarpus Angolensis Lectin in Complex with Man-8D1D3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:15.7 occ:1.00 O A:HOH303 2.2 11.3 1.0 OE1 A:GLU128 2.2 17.9 1.0 OD1 A:ASP141 2.2 22.4 1.0 OD2 A:ASP130 2.3 18.0 1.0 NE2 A:HIS146 2.3 20.9 1.0 O A:HOH306 2.3 20.5 1.0 CG A:ASP141 3.1 19.8 1.0 CD A:GLU128 3.2 16.6 1.0 CE1 A:HIS146 3.2 20.6 1.0 CG A:ASP130 3.2 20.4 1.0 CD2 A:HIS146 3.3 19.5 1.0 OD2 A:ASP141 3.5 20.9 1.0 OE2 A:GLU128 3.5 21.7 1.0 CB A:ASP130 3.5 19.5 1.0 O A:HOH305 3.9 19.4 1.0 CA A:CA302 4.2 19.2 1.0 OG A:SER156 4.3 24.1 1.0 CB A:ASP141 4.3 21.0 1.0 OD1 A:ASP130 4.3 20.9 1.0 ND1 A:HIS146 4.3 20.7 1.0 CG A:HIS146 4.4 19.4 1.0 CG A:GLU128 4.5 13.2 1.0 O A:HOH307 4.5 20.9 1.0 O A:ILE154 4.6 20.5 1.0 CD1 A:TRP140 4.6 20.8 1.0 NE1 A:TRP140 4.7 24.1 1.0 CA A:ASP141 4.8 23.1 1.0 CD A:PRO142 4.8 25.9 1.0

Manganese binding site 2 out of 2 in the Pterocarpus Angolensis Lectin in Complex with Man-8D1D3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pterocarpus Angolensis Lectin in Complex with Man-8D1D3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:16.5 occ:1.00 OD1 B:ASP141 2.2 21.2 1.0 O B:HOH303 2.2 11.7 1.0 OE1 B:GLU128 2.2 16.0 1.0 OD2 B:ASP130 2.2 17.8 1.0 O B:HOH306 2.3 14.4 1.0 NE2 B:HIS146 2.3 12.9 1.0 CG B:ASP141 3.1 20.0 1.0 CE1 B:HIS146 3.1 18.4 1.0 CG B:ASP130 3.2 19.3 1.0 CD B:GLU128 3.2 15.7 1.0 CD2 B:HIS146 3.4 18.8 1.0 OE2 B:GLU128 3.5 14.6 1.0 OD2 B:ASP141 3.5 20.2 1.0 CB B:ASP130 3.5 15.5 1.0 O B:HOH305 3.9 16.9 1.0 CA B:CA302 4.2 19.7 1.0 OG B:SER156 4.2 19.4 1.0 CB B:ASP141 4.3 21.3 1.0 ND1 B:HIS146 4.3 13.2 1.0 OD1 B:ASP130 4.3 21.7 1.0 CG B:HIS146 4.4 16.1 1.0 O B:HOH316 4.5 20.2 1.0 NE1 B:TRP140 4.6 21.9 1.0 O B:ILE154 4.6 20.7 1.0 CD1 B:TRP140 4.6 20.3 1.0 CG B:GLU128 4.6 14.2 1.0 CA B:ASP141 4.8 21.4 1.0 CD B:PRO142 4.9 21.5 1.0

A.Garcia-Pino, L.Buts, L.Wyns, A.Imberty, R.Loris. How A Plant Lectin Recognizes High Mannose Oligosaccharides Plant Physiol. V. 144 1733 2007.
ISSN: ISSN 0032-0889
PubMed: 17556509
DOI: 10.1104/PP.107.100867