Calcium in PDB 1v6j: Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH

The structure of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH, PDB code: 1v6j was solved by S.Kundhavai Natchiar, A.Arockia Jeyaprakash, T.N.C.Ramya, C.J.Thomas, 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)	20.00 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.733, 125.531, 76.050, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 22

The structure of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH (pdb code 1v6j). 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-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH, PDB code: 1v6j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:26.6 occ:1.00 OD1 A:ASP123 2.7 21.8 1.0 OD2 A:ASP132 2.7 36.2 1.0 O A:TYR125 2.7 22.3 1.0 OD1 A:ASN127 2.8 30.9 1.0 OD2 A:ASP123 2.9 24.5 1.0 CG A:ASP123 3.1 23.1 1.0 CG A:ASN127 3.5 29.8 1.0 CB A:ASN127 3.8 25.5 1.0 CG A:ASP132 3.8 41.0 1.0 C A:TYR125 3.9 19.8 1.0 CA A:GLY104 4.0 24.1 1.0 N A:ASN127 4.0 24.2 1.0 O A:GLY104 4.3 26.0 1.0 OD1 A:ASP132 4.3 41.5 1.0 O A:ASP83 4.5 49.4 1.0 OD1 A:ASP83 4.5 24.8 1.0 CA A:ASN127 4.6 19.2 1.0 CB A:ASP123 4.6 21.0 1.0 ND2 A:ASN127 4.6 29.6 1.0 C A:GLY104 4.6 25.4 1.0 CA A:TYR125 4.7 20.1 1.0 N A:TYR125 4.7 23.2 1.0 CB A:TYR125 4.7 29.2 1.0 MN A:MN238 4.8 46.2 1.0 CD1 A:TYR125 4.8 30.3 1.0 N A:SER126 4.8 21.9 1.0 C A:SER126 4.9 29.0 1.0 CA A:SER126 4.9 26.6 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:27.3 occ:1.00 OD1 B:ASN127 2.6 26.2 1.0 OD1 B:ASP123 2.6 26.5 1.0 O B:TYR125 2.7 14.6 1.0 OD2 B:ASP132 2.7 35.0 1.0 OD2 B:ASP123 2.8 26.7 1.0 CG B:ASP123 3.1 27.3 1.0 CG B:ASN127 3.5 25.6 1.0 C B:TYR125 3.8 14.4 1.0 CG B:ASP132 3.9 37.6 1.0 CA B:GLY104 4.0 19.2 1.0 CB B:ASN127 4.1 24.3 1.0 N B:ASN127 4.3 30.1 1.0 O B:GLY104 4.3 19.9 1.0 OD1 B:ASP132 4.3 38.0 1.0 O B:ASP83 4.4 35.2 1.0 CB B:ASP83 4.4 38.5 1.0 ND2 B:ASN127 4.4 24.6 1.0 CB B:ASP123 4.6 27.5 1.0 C B:GLY104 4.6 22.5 1.0 CA B:TYR125 4.7 15.1 1.0 CB B:TYR125 4.7 23.8 1.0 MN B:MN238 4.7 45.3 1.0 N B:TYR125 4.7 17.8 1.0 CD1 B:TYR125 4.8 26.6 1.0 N B:SER126 4.8 28.6 1.0 CA B:ASN127 4.9 27.6 1.0 C B:SER126 4.9 31.4 1.0 CA B:SER126 4.9 31.6 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:29.3 occ:1.00 O C:TYR125 2.7 21.4 1.0 OD1 C:ASP123 2.7 38.5 1.0 OD2 C:ASP132 2.7 39.1 1.0 OD1 C:ASN127 2.8 39.0 1.0 OD2 C:ASP123 2.8 40.2 1.0 CG C:ASP123 3.1 36.0 1.0 CG C:ASN127 3.5 38.3 1.0 C C:TYR125 3.8 22.1 1.0 CB C:ASN127 3.8 38.4 1.0 CG C:ASP132 3.8 43.2 1.0 N C:ASN127 3.9 41.2 1.0 CA C:GLY104 4.3 43.9 1.0 OD1 C:ASP132 4.4 39.6 1.0 O C:GLY104 4.5 47.0 1.0 CA C:ASN127 4.5 37.5 1.0 CB C:TYR125 4.5 48.9 1.0 ND2 C:ASN127 4.6 41.9 1.0 CA C:TYR125 4.6 19.2 1.0 CB C:ASP123 4.6 33.0 1.0 CD1 C:TYR125 4.6 54.4 1.0 O C:ASP83 4.6 62.2 1.0 N C:TYR125 4.7 18.3 1.0 CB C:ASP83 4.7 44.4 1.0 N C:SER126 4.7 38.9 1.0 OD1 C:ASP83 4.7 48.4 1.0 C C:SER126 4.8 45.3 1.0 MN C:MN238 4.8 48.3 1.0 CA C:SER126 4.8 41.3 1.0 C C:GLY104 4.9 45.2 1.0 CB C:ASP132 5.0 40.6 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:28.2 occ:1.00 OD2 D:ASP123 2.8 24.4 1.0 O D:TYR125 2.8 18.3 1.0 OD2 D:ASP132 2.8 37.6 1.0 OD1 D:ASP123 2.8 20.5 1.0 OD1 D:ASN127 3.0 30.5 1.0 CG D:ASP123 3.1 22.8 1.0 CG D:ASN127 3.3 28.5 1.0 CB D:ASN127 3.7 30.2 1.0 CG D:ASP132 3.9 36.2 1.0 C D:TYR125 3.9 20.5 1.0 ND2 D:ASN127 4.0 28.3 1.0 CA D:GLY104 4.0 26.4 1.0 N D:ASN127 4.1 32.1 1.0 O D:GLY104 4.3 26.7 1.0 OD1 D:ASP132 4.3 33.0 1.0 CB D:ASP83 4.4 41.2 1.0 CA D:ASN127 4.6 31.7 1.0 OD1 D:ASP83 4.6 45.4 1.0 O D:ASP83 4.6 71.8 1.0 CB D:ASP123 4.6 22.5 1.0 C D:GLY104 4.7 25.9 1.0 CA D:TYR125 4.7 18.6 1.0 CB D:TYR125 4.7 34.5 1.0 C D:SER126 4.8 41.6 1.0 N D:TYR125 4.8 17.1 1.0 N D:SER126 4.8 35.1 1.0 CD1 D:TYR125 4.8 36.5 1.0 CA D:SER126 4.9 38.4 1.0 MN D:MN238 5.0 45.8 1.0

S.Kundhavai Natchiar, A.Arockia Jeyaprakash, T.N.Ramya, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan. Structural Plasticity of Peanut Lectin: An X-Ray Analysis Involving Variation in pH, Ligand Binding and Crystal Structure. Acta Crystallogr.,Sect.D V. 60 211 2004.
ISSN: ISSN 0907-4449
PubMed: 14747696
DOI: 10.1107/S090744490302849X