Calcium in PDB 1cq9: Peanut Lectin-Triclinic Form

The structure of Peanut Lectin-Triclinic Form, PDB code: 1cq9 was solved by 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 / 3.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.640, 71.790, 86.420, 65.35, 77.66, 72.31
R / Rfree (%)	21.7 / 27.8

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin-Triclinic Form (pdb code 1cq9). 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-Triclinic Form, PDB code: 1cq9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:2.0 occ:1.00 OD1 A:ASN127 2.2 28.1 1.0 OD1 A:ASP123 2.5 8.6 1.0 OD2 A:ASP132 2.6 24.3 1.0 OD2 A:ASP123 2.8 5.9 1.0 O A:TYR125 3.0 8.5 1.0 CG A:ASP123 3.0 7.2 1.0 CG A:ASN127 3.3 27.0 1.0 CG A:ASP132 3.7 29.1 1.0 CA A:GLY104 4.0 23.2 1.0 OD1 A:ASP132 4.0 29.6 1.0 CB A:ASN127 4.1 22.6 1.0 C A:TYR125 4.2 6.0 1.0 N A:ASN127 4.3 28.0 1.0 O A:GLY104 4.4 25.1 1.0 OD1 A:ASP83 4.4 10.3 1.0 MN A:MN238 4.4 32.1 1.0 ND2 A:ASN127 4.4 26.8 1.0 CB A:ASP123 4.5 5.1 1.0 C A:GLY104 4.7 24.4 1.0 CA A:ASN127 4.8 23.0 1.0 N A:TYR125 4.9 9.4 1.0 O A:ASP83 4.9 2.0 1.0 CD2 A:TYR125 5.0 20.0 1.0 CA A:TYR125 5.0 6.3 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:2.0 occ:1.00 OD2 B:ASP132 2.2 29.0 1.0 OD1 B:ASN127 2.2 36.4 1.0 OD1 B:ASP123 2.4 35.5 1.0 O B:TYR125 2.8 3.3 1.0 OD2 B:ASP123 3.0 35.4 1.0 CG B:ASP123 3.1 36.1 1.0 CG B:ASN127 3.4 35.8 1.0 CG B:ASP132 3.4 31.6 1.0 OD1 B:ASP132 3.8 32.0 1.0 CB B:ASN127 4.0 34.5 1.0 C B:TYR125 4.0 3.1 1.0 N B:ASN127 4.1 2.0 1.0 CA B:GLY104 4.2 16.9 1.0 O B:GLY104 4.4 17.6 1.0 ND2 B:ASN127 4.5 34.8 1.0 CB B:ASP123 4.5 36.4 1.0 MN B:MN240 4.6 35.0 1.0 CB B:ASP132 4.7 29.2 1.0 CA B:ASN127 4.7 2.0 1.0 OD1 B:ASP83 4.7 32.6 1.0 C B:GLY104 4.8 20.1 1.0 CA B:SER126 4.9 38.6 1.0 C B:SER126 4.9 38.4 1.0 N B:SER126 4.9 35.6 1.0 CA B:TYR125 5.0 3.8 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca241 b:2.1 occ:1.00 OD1 C:ASN127 1.9 24.9 1.0 OD2 C:ASP132 2.7 29.9 1.0 O C:TYR125 3.0 2.0 1.0 CG C:ASN127 3.0 24.2 1.0 OD1 C:ASP123 3.0 28.3 1.0 OD2 C:ASP123 3.3 26.5 1.0 CG C:ASP123 3.5 24.0 1.0 CA C:GLY104 3.7 39.2 1.0 CB C:ASN127 3.9 24.3 1.0 ND2 C:ASN127 3.9 27.8 1.0 CG C:ASP132 3.9 34.0 1.0 O C:GLY104 4.0 42.4 1.0 N C:ASN127 4.1 18.6 1.0 C C:TYR125 4.2 2.0 1.0 C C:GLY104 4.4 40.5 1.0 OD1 C:ASP132 4.4 30.4 1.0 OD1 C:ASP83 4.6 8.7 1.0 CA C:ASN127 4.6 14.8 1.0 MN C:MN242 4.7 39.8 1.0 N C:GLY104 4.9 40.1 1.0 CB C:TYR125 4.9 65.5 1.0 C C:SER126 4.9 43.9 1.0 CD1 C:TYR130 4.9 33.0 1.0 CA C:TYR125 4.9 2.0 1.0 CB C:ASP123 5.0 21.1 1.0 CD2 C:TYR125 5.0 70.4 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin-Triclinic Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Peanut Lectin-Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca243 b:2.0 occ:1.00 OD1 D:ASN127 2.3 26.2 1.0 OD1 D:ASP123 2.4 2.0 1.0 OD2 D:ASP123 2.4 2.0 1.0 OD2 D:ASP132 2.6 14.8 1.0 CG D:ASP123 2.8 2.0 1.0 O D:TYR125 2.9 12.5 1.0 CG D:ASN127 3.5 24.2 1.0 CG D:ASP132 3.6 13.3 1.0 OD1 D:ASP132 4.0 10.2 1.0 C D:TYR125 4.0 14.7 1.0 CB D:ASN127 4.1 25.9 1.0 CA D:GLY104 4.2 30.5 1.0 CB D:ASP123 4.3 2.0 1.0 N D:ASN127 4.3 15.9 1.0 O D:GLY104 4.3 30.8 1.0 MN D:MN244 4.4 10.8 1.0 O D:ASP83 4.6 2.0 1.0 ND2 D:ASN127 4.6 24.0 1.0 OD1 D:ASP83 4.7 7.6 1.0 N D:TYR125 4.8 11.3 1.0 C D:GLY104 4.8 29.9 1.0 CA D:TYR125 4.8 12.7 1.0 CA D:ASN127 4.9 15.5 1.0 CB D:ASP132 4.9 13.6 1.0 CB D:TYR125 4.9 29.3 1.0 N D:SER126 4.9 15.5 1.0 CD2 D:LEU106 5.0 5.9 1.0 CA D:SER126 5.0 18.8 1.0

R.Ravishankar, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan. Crystal Structures of the Peanut Lectin-Lactose Complex at Acidic pH: Retention of Unusual Quaternary Structure, Empty and Carbohydrate Bound Combining Sites, Molecular Mimicry and Crystal Packing Directed By Interactions at the Combining Site. Proteins V. 43 260 2001.
ISSN: ISSN 0887-3585
PubMed: 11288176
DOI: 10.1002/PROT.1037