Calcium 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:

Manganese

(Mn)

4 atoms

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

Calcium binding site 1 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:16.1 occ:1.00 OD2 A:ASP132 2.4 18.1 1.0 O A:TYR125 2.4 18.4 1.0 OD1 A:ASN127 2.4 18.9 1.0 O A:HOH242 2.4 17.4 1.0 O A:HOH241 2.4 15.4 1.0 OD2 A:ASP123 2.5 19.4 1.0 OD1 A:ASP123 2.5 16.6 1.0 CG A:ASP123 2.8 18.0 1.0 CG A:ASP132 3.4 22.9 1.0 CG A:ASN127 3.6 17.9 1.0 C A:TYR125 3.6 15.9 1.0 OD1 A:ASP132 3.9 23.4 1.0 N A:ASN127 4.0 22.1 1.0 MN A:MN238 4.1 35.6 1.0 CB A:ASN127 4.1 13.5 1.0 O A:HOH243 4.2 23.9 1.0 CB A:ASP123 4.3 15.9 1.0 N A:TYR125 4.4 19.3 1.0 CA A:TYR125 4.5 16.2 1.0 CA A:GLY104 4.5 15.8 1.0 N A:SER126 4.5 15.8 1.0 CA A:SER126 4.5 20.4 1.0 ND2 A:ASN127 4.6 17.7 1.0 CB A:ASP132 4.6 21.1 1.0 CA A:ASN127 4.7 17.1 1.0 CB A:TYR125 4.7 20.4 1.0 OD1 A:ASP83 4.7 16.1 1.0 C A:SER126 4.7 22.9 1.0 O A:GLY104 4.7 17.7 1.0 CD1 A:TYR125 4.8 21.6 1.0 O A:ASP83 4.9 14.1 1.0 CE1 A:HIS137 4.9 17.6 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:16.8 occ:1.00 OD2 B:ASP132 2.4 16.8 1.0 O B:TYR125 2.4 17.0 1.0 OD1 B:ASP123 2.4 17.3 1.0 OD1 B:ASN127 2.4 19.8 1.0 O B:HOH241 2.4 15.8 1.0 O B:HOH242 2.4 11.7 1.0 OD2 B:ASP123 2.4 17.5 1.0 CG B:ASP123 2.8 18.1 1.0 CG B:ASP132 3.4 19.5 1.0 CG B:ASN127 3.6 19.2 1.0 C B:TYR125 3.6 16.8 1.0 OD1 B:ASP132 3.8 19.9 1.0 N B:ASN127 4.0 18.2 1.0 O B:HOH243 4.2 16.5 1.0 CB B:ASN127 4.2 17.9 1.0 CB B:ASP123 4.3 18.3 1.0 MN B:MN238 4.4 34.8 1.0 N B:SER126 4.5 17.6 1.0 CA B:GLY104 4.5 15.1 1.0 CA B:TYR125 4.5 17.5 1.0 CA B:SER126 4.5 20.6 1.0 N B:TYR125 4.6 20.1 1.0 CB B:ASP132 4.6 17.1 1.0 ND2 B:ASN127 4.7 18.2 1.0 C B:SER126 4.7 20.4 1.0 O B:GLY104 4.7 15.8 1.0 CB B:TYR125 4.8 17.3 1.0 CA B:ASN127 4.8 15.7 1.0 CD1 B:TYR125 4.8 20.0 1.0 OD1 B:ASP83 4.8 18.4 1.0 CE1 B:HIS137 4.9 14.2 1.0 O B:ASP83 4.9 13.6 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:18.7 occ:1.00 O C:TYR125 2.4 23.7 1.0 OD2 C:ASP132 2.4 22.8 1.0 O C:HOH242 2.4 18.3 1.0 O C:HOH241 2.4 20.1 1.0 OD1 C:ASP123 2.4 23.6 1.0 OD2 C:ASP123 2.4 25.3 1.0 OD1 C:ASN127 2.5 23.8 1.0 CG C:ASP123 2.8 21.1 1.0 CG C:ASP132 3.5 26.9 1.0 CG C:ASN127 3.6 23.1 1.0 C C:TYR125 3.6 24.4 1.0 OD1 C:ASP132 3.9 23.3 1.0 N C:ASN127 4.0 28.3 1.0 O C:HOH243 4.2 23.6 1.0 MN C:MN238 4.2 37.7 1.0 CB C:ASN127 4.3 23.2 1.0 CB C:ASP123 4.3 18.1 1.0 N C:TYR125 4.4 20.7 1.0 CA C:TYR125 4.4 21.6 1.0 N C:SER126 4.5 22.8 1.0 CA C:GLY104 4.5 27.6 1.0 CA C:SER126 4.5 25.1 1.0 ND2 C:ASN127 4.6 26.7 1.0 CB C:TYR125 4.7 25.8 1.0 O C:GLY104 4.7 30.7 1.0 C C:SER126 4.7 29.1 1.0 CB C:ASP132 4.7 24.4 1.0 CA C:ASN127 4.7 24.5 1.0 O C:ASP83 4.8 18.7 1.0 CE1 C:HIS137 4.9 21.4 1.0 CD2 C:TYR125 4.9 30.7 1.0 OD1 C:ASP83 5.0 23.4 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Peanut Lectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:17.7 occ:1.00 O D:TYR125 2.4 17.7 1.0 O D:HOH241 2.4 13.7 1.0 OD2 D:ASP132 2.4 20.0 1.0 O D:HOH242 2.4 20.2 1.0 OD2 D:ASP123 2.4 19.6 1.0 OD1 D:ASN127 2.4 24.6 1.0 OD1 D:ASP123 2.4 15.6 1.0 CG D:ASP123 2.8 17.9 1.0 CG D:ASP132 3.3 18.5 1.0 CG D:ASN127 3.5 22.5 1.0 C D:TYR125 3.6 19.9 1.0 OD1 D:ASP132 3.7 15.3 1.0 N D:ASN127 3.9 27.5 1.0 CB D:ASN127 4.0 24.2 1.0 O D:HOH243 4.2 21.1 1.0 CB D:ASP123 4.3 17.7 1.0 MN D:MN238 4.4 35.2 1.0 CA D:GLY104 4.5 20.5 1.0 N D:SER126 4.5 21.0 1.0 CA D:SER126 4.5 24.3 1.0 CA D:TYR125 4.5 17.9 1.0 N D:TYR125 4.5 16.5 1.0 CB D:ASP132 4.6 18.7 1.0 CA D:ASN127 4.6 27.1 1.0 C D:SER126 4.7 27.5 1.0 O D:GLY104 4.7 20.8 1.0 O D:ASP83 4.7 18.2 1.0 ND2 D:ASN127 4.7 22.4 1.0 OD1 D:ASP83 4.8 18.1 1.0 CE1 D:HIS137 4.8 17.2 1.0 CB D:TYR125 4.8 17.8 1.0 CD1 D:TYR125 4.9 19.9 1.0 NE2 D:HIS137 5.0 22.0 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