Manganese in PDB 2pel: Peanut Lectin

The structure of Peanut Lectin, PDB code: 2pel was solved by R.Banerjee, K.Das, R.Ravishankar, K.Suguna, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	129.300, 126.900, 76.900, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Peanut Lectin also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Peanut Lectin (pdb code 2pel). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Peanut Lectin, PDB code: 2pel:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:35.6 occ:1.00 OD2 A:ASP123 2.3 19.4 1.0 O A:HOH243 2.3 23.9 1.0 OD1 A:ASP132 2.3 23.4 1.0 OE2 A:GLU121 2.3 20.6 1.0 O A:HOH244 2.3 26.3 1.0 NE2 A:HIS137 2.4 20.9 1.0 CG A:ASP132 3.2 22.9 1.0 CG A:ASP123 3.2 18.0 1.0 CD A:GLU121 3.3 19.6 1.0 CE1 A:HIS137 3.3 17.6 1.0 CD2 A:HIS137 3.3 15.3 1.0 CB A:ASP123 3.6 15.9 1.0 OE1 A:GLU121 3.6 21.7 1.0 OD2 A:ASP132 3.8 18.1 1.0 O A:HOH241 3.9 15.4 1.0 CA A:CA237 4.1 16.1 1.0 O A:HOH249 4.2 20.9 1.0 OD1 A:ASP123 4.3 16.6 1.0 O A:VAL145 4.3 22.4 1.0 CB A:ASP132 4.4 21.1 1.0 OG A:SER147 4.4 14.7 1.0 ND1 A:HIS137 4.4 18.7 1.0 CG A:HIS137 4.5 20.7 1.0 CD A:PRO133 4.5 24.3 1.0 CG A:GLU121 4.6 15.7 1.0 CA A:ASP132 4.7 20.6 1.0

Manganese binding site 2 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:34.8 occ:1.00 O B:HOH244 2.3 22.1 1.0 OE2 B:GLU121 2.3 17.8 1.0 OD2 B:ASP123 2.3 17.5 1.0 O B:HOH243 2.3 16.5 1.0 OD1 B:ASP132 2.3 19.9 1.0 NE2 B:HIS137 2.4 19.8 1.0 CD B:GLU121 3.2 17.6 1.0 CD2 B:HIS137 3.3 15.6 1.0 CG B:ASP123 3.3 18.1 1.0 CE1 B:HIS137 3.4 14.2 1.0 CG B:ASP132 3.4 19.5 1.0 OE1 B:GLU121 3.5 15.1 1.0 CB B:ASP123 3.6 18.3 1.0 OG B:SER147 3.9 9.2 1.0 OD2 B:ASP132 4.0 16.8 1.0 O B:VAL145 4.1 19.3 1.0 O B:HOH241 4.2 15.8 1.0 O B:HOH404 4.3 22.9 1.0 CA B:CA237 4.4 16.8 1.0 OD1 B:ASP123 4.4 17.3 1.0 CG B:HIS137 4.5 17.2 1.0 ND1 B:HIS137 4.5 15.7 1.0 CG B:GLU121 4.5 12.2 1.0 CB B:ASP132 4.6 17.1 1.0 CD B:PRO133 4.7 18.8 1.0 CA B:ASP132 4.9 21.7 1.0 CG2 B:THR150 5.0 11.5 1.0

Manganese binding site 3 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:37.7 occ:1.00 O C:HOH244 2.3 28.8 1.0 OE2 C:GLU121 2.3 24.5 1.0 OD1 C:ASP132 2.3 23.3 1.0 OD2 C:ASP123 2.3 25.3 1.0 O C:HOH243 2.3 23.6 1.0 NE2 C:HIS137 2.3 24.9 1.0 CD2 C:HIS137 3.2 19.9 1.0 CG C:ASP123 3.3 21.1 1.0 CG C:ASP132 3.3 26.9 1.0 CD C:GLU121 3.3 24.5 1.0 CE1 C:HIS137 3.4 21.4 1.0 OE1 C:GLU121 3.6 22.2 1.0 CB C:ASP123 3.7 18.1 1.0 OD2 C:ASP132 3.8 22.8 1.0 OG C:SER147 4.1 22.7 1.0 O C:HOH241 4.2 20.1 1.0 CA C:CA237 4.2 18.7 1.0 OD1 C:ASP123 4.3 23.6 1.0 O C:HOH262 4.3 27.9 1.0 CD C:PRO133 4.3 24.2 1.0 CG C:HIS137 4.4 21.6 1.0 O C:VAL145 4.4 20.4 1.0 ND1 C:HIS137 4.4 23.6 1.0 CB C:ASP132 4.5 24.4 1.0 CG C:GLU121 4.6 22.1 1.0 CA C:ASP132 4.7 27.0 1.0

Manganese binding site 4 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:35.2 occ:1.00 OE2 D:GLU121 2.3 17.4 1.0 O D:HOH244 2.3 25.5 1.0 OD1 D:ASP132 2.3 15.3 1.0 OD2 D:ASP123 2.3 19.6 1.0 O D:HOH243 2.3 21.1 1.0 NE2 D:HIS137 2.3 22.0 1.0 CD2 D:HIS137 3.2 19.1 1.0 CD D:GLU121 3.2 16.4 1.0 CG D:ASP123 3.3 17.9 1.0 CE1 D:HIS137 3.4 17.2 1.0 OE1 D:GLU121 3.4 17.4 1.0 CG D:ASP132 3.4 18.5 1.0 CB D:ASP123 3.7 17.7 1.0 O D:VAL145 4.0 16.6 1.0 OD2 D:ASP132 4.1 20.0 1.0 O D:HOH241 4.1 13.7 1.0 OG D:SER147 4.1 11.3 1.0 O D:HOH338 4.2 27.5 1.0 CA D:CA237 4.4 17.7 1.0 CG D:HIS137 4.4 19.8 1.0 OD1 D:ASP123 4.4 15.6 1.0 ND1 D:HIS137 4.4 20.4 1.0 CB D:ASP132 4.5 18.7 1.0 CD D:PRO133 4.5 22.7 1.0 CG D:GLU121 4.5 14.3 1.0 CA D:ASP132 4.8 21.1 1.0 CG2 D:THR150 4.9 14.8 1.0

R.Banerjee, K.Das, R.Ravishankar, K.Suguna, A.Surolia, M.Vijayan. Conformation, Protein-Carbohydrate Interactions and A Novel Subunit Association in the Refined Structure of Peanut Lectin-Lactose Complex. J.Mol.Biol. V. 259 281 1996.
ISSN: ISSN 0022-2836
PubMed: 8656429
DOI: 10.1006/JMBI.1996.0319