Calcium in PDB 1v6i: Peanut Lectin-Lactose Complex in Acidic pH

The structure of Peanut Lectin-Lactose Complex in Acidic pH, PDB code: 1v6i 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 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.609, 125.749, 76.049, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.8

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin-Lactose Complex in Acidic pH (pdb code 1v6i). 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 in Acidic pH, PDB code: 1v6i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Peanut Lectin-Lactose Complex in 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 in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1237 b:21.8 occ:1.00 O A:TYR125 2.5 23.7 1.0 OD2 A:ASP132 2.5 25.7 1.0 OD1 A:ASN127 2.6 20.4 1.0 O A:HOH1239 2.6 20.0 1.0 O A:HOH1240 2.6 21.9 1.0 OD1 A:ASP123 2.6 22.2 1.0 OD2 A:ASP123 2.6 19.2 1.0 CG A:ASP123 2.9 20.9 1.0 CG A:ASP132 3.5 25.2 1.0 CG A:ASN127 3.6 25.0 1.0 C A:TYR125 3.6 24.6 1.0 N A:ASN127 3.9 24.9 1.0 OD1 A:ASP132 4.0 23.8 1.0 CB A:ASN127 4.1 24.4 1.0 MN A:MN1238 4.1 37.9 1.0 O A:HOH1241 4.3 14.1 1.0 CB A:ASP123 4.4 20.9 1.0 N A:TYR125 4.4 22.1 1.0 CA A:TYR125 4.5 23.8 1.0 CA A:GLY104 4.5 21.1 1.0 N A:SER126 4.6 22.9 1.0 CA A:SER126 4.6 24.6 1.0 CA A:ASN127 4.6 25.9 1.0 CB A:TYR125 4.6 25.8 1.0 C A:SER126 4.7 25.4 1.0 O A:GLY104 4.7 22.0 1.0 CB A:ASP132 4.7 25.3 1.0 CD1 A:TYR125 4.7 29.4 1.0 OD1 A:ASP83 4.7 18.7 1.0 ND2 A:ASN127 4.8 21.8 1.0 CE1 A:HIS137 4.9 20.1 1.0 O A:ASP83 4.9 20.8 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin-Lactose Complex in 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 in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2237 b:18.7 occ:1.00 O B:TYR125 2.5 24.1 1.0 OD2 B:ASP132 2.5 22.8 1.0 O B:HOH2239 2.5 17.2 1.0 OD2 B:ASP123 2.6 19.1 1.0 O B:HOH2240 2.6 17.6 1.0 OD1 B:ASN127 2.6 21.1 1.0 OD1 B:ASP123 2.6 20.2 1.0 CG B:ASP123 2.9 20.1 1.0 CG B:ASP132 3.5 22.8 1.0 CG B:ASN127 3.6 24.2 1.0 C B:TYR125 3.6 24.6 1.0 N B:ASN127 3.9 24.0 1.0 OD1 B:ASP132 4.0 24.3 1.0 CB B:ASN127 4.0 24.3 1.0 MN B:MN2238 4.2 34.0 1.0 O B:HOH2241 4.3 19.4 1.0 CB B:ASP123 4.4 18.9 1.0 CA B:TYR125 4.5 24.4 1.0 N B:TYR125 4.5 23.9 1.0 CA B:GLY104 4.5 21.1 1.0 N B:SER126 4.5 24.8 1.0 CA B:SER126 4.6 25.4 1.0 CA B:ASN127 4.6 25.9 1.0 CB B:TYR125 4.6 25.9 1.0 C B:SER126 4.7 24.8 1.0 CB B:ASP132 4.7 23.7 1.0 O B:GLY104 4.7 19.4 1.0 ND2 B:ASN127 4.7 18.9 1.0 OD1 B:ASP83 4.8 21.0 1.0 CD1 B:TYR125 4.8 29.5 1.0 CE1 B:HIS137 4.8 19.1 1.0 O B:ASP83 4.9 18.3 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin-Lactose Complex in 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 in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3237 b:26.7 occ:1.00 O C:TYR125 2.4 29.8 1.0 OD2 C:ASP132 2.5 25.5 1.0 O C:HOH3240 2.6 26.7 1.0 OD2 C:ASP123 2.6 23.2 1.0 OD1 C:ASN127 2.7 26.6 1.0 OD1 C:ASP123 2.7 24.1 1.0 O C:HOH3239 2.7 25.4 1.0 CG C:ASP123 3.0 22.5 1.0 CG C:ASP132 3.5 27.3 1.0 C C:TYR125 3.6 29.7 1.0 CG C:ASN127 3.6 29.6 1.0 N C:ASN127 3.8 30.8 1.0 OD1 C:ASP132 4.0 26.1 1.0 CB C:ASN127 4.1 28.2 1.0 MN C:MN3238 4.2 42.0 1.0 O C:HOH3241 4.3 20.8 1.0 CA C:SER126 4.5 30.5 1.0 CA C:TYR125 4.5 29.4 1.0 N C:SER126 4.5 29.9 1.0 CB C:ASP123 4.5 21.8 1.0 N C:TYR125 4.5 27.8 1.0 CA C:GLY104 4.5 24.7 1.0 C C:SER126 4.6 31.3 1.0 CA C:ASN127 4.6 28.8 1.0 CB C:TYR125 4.6 31.6 1.0 CB C:ASP132 4.7 28.0 1.0 OD1 C:ASP83 4.7 27.1 1.0 CD1 C:TYR125 4.7 35.5 1.0 ND2 C:ASN127 4.8 28.9 1.0 O C:GLY104 4.8 25.0 1.0 CE1 C:HIS137 4.9 22.4 1.0 O C:ASP83 5.0 24.4 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin-Lactose Complex in 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 in Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4237 b:23.7 occ:1.00 O D:TYR125 2.5 26.2 1.0 OD2 D:ASP132 2.5 25.8 1.0 O D:HOH4240 2.6 24.1 1.0 O D:HOH4239 2.6 24.6 1.0 OD1 D:ASN127 2.6 25.3 1.0 OD2 D:ASP123 2.6 21.9 1.0 OD1 D:ASP123 2.6 22.7 1.0 CG D:ASP123 3.0 22.1 1.0 CG D:ASP132 3.6 27.1 1.0 CG D:ASN127 3.6 28.1 1.0 C D:TYR125 3.7 26.6 1.0 N D:ASN127 3.9 28.8 1.0 OD1 D:ASP132 4.0 28.4 1.0 CB D:ASN127 4.0 27.4 1.0 MN D:MN4238 4.2 37.1 1.0 O D:HOH4241 4.4 26.5 1.0 CB D:ASP123 4.5 20.6 1.0 CA D:GLY104 4.5 22.1 1.0 N D:TYR125 4.5 25.2 1.0 CA D:TYR125 4.5 26.1 1.0 N D:SER126 4.6 27.3 1.0 CA D:SER126 4.6 28.8 1.0 CA D:ASN127 4.6 29.0 1.0 C D:SER126 4.7 29.4 1.0 CB D:TYR125 4.7 28.5 1.0 O D:GLY104 4.7 22.4 1.0 CB D:ASP132 4.7 27.9 1.0 CD1 D:TYR125 4.7 31.6 1.0 ND2 D:ASN127 4.8 25.9 1.0 OD1 D:ASP83 4.8 22.1 1.0 O D:ASP83 4.9 21.6 1.0 CE1 D:HIS137 4.9 19.2 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