Calcium in PDB 1v6k: Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva)

The structure of Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva), PDB code: 1v6k 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 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.030, 124.030, 75.710, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.9

The structure of Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva) also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva) (pdb code 1v6k). 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 the Presence of Peptide(Iwssagnva), PDB code: 1v6k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva)


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 the Presence of Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca233 b:18.7 occ:1.00 O A:TYR125 2.5 28.1 1.0 OD2 A:ASP132 2.5 31.5 1.0 OD1 A:ASN127 2.6 22.9 1.0 O A:HOH237 2.6 13.6 1.0 OD1 A:ASP123 2.6 24.6 1.0 O A:HOH238 2.7 23.9 1.0 OD2 A:ASP123 2.7 22.3 1.0 CG A:ASP123 3.0 22.6 1.0 CG A:ASN127 3.5 25.2 1.0 CG A:ASP132 3.5 30.3 1.0 C A:TYR125 3.7 27.8 1.0 N A:ASN127 3.8 26.3 1.0 CB A:ASN127 3.8 23.9 1.0 OD1 A:ASP132 4.0 30.2 1.0 MN A:MN234 4.1 39.0 1.0 CA A:GLY104 4.3 20.4 1.0 O A:HOH239 4.4 14.1 1.0 CA A:ASN127 4.4 25.8 1.0 CB A:ASP123 4.5 22.8 1.0 CA A:TYR125 4.5 26.8 1.0 N A:TYR125 4.5 25.7 1.0 N A:SER126 4.6 28.3 1.0 O A:ASP83 4.6 26.4 1.0 CA A:SER126 4.6 27.9 1.0 C A:SER126 4.6 27.3 1.0 CB A:TYR125 4.6 28.2 1.0 CB A:ASP132 4.7 30.1 1.0 ND2 A:ASN127 4.7 25.2 1.0 O A:GLY104 4.7 21.4 1.0 CD1 A:TYR125 4.8 31.4 1.0 OD1 A:ASP83 4.9 22.4 1.0 CE1 A:HIS137 5.0 17.2 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva)


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 the Presence of Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca233 b:18.1 occ:1.00 O B:TYR125 2.5 26.6 1.0 OD2 B:ASP132 2.6 29.6 1.0 OD1 B:ASP123 2.6 21.4 1.0 OD1 B:ASN127 2.6 21.6 1.0 O B:HOH237 2.6 17.4 1.0 O B:HOH238 2.7 20.7 1.0 OD2 B:ASP123 2.8 22.2 1.0 CG B:ASP123 3.0 21.3 1.0 CG B:ASP132 3.4 27.6 1.0 C B:TYR125 3.6 26.2 1.0 CG B:ASN127 3.6 23.8 1.0 N B:ASN127 3.7 24.4 1.0 OD1 B:ASP132 3.8 27.7 1.0 CB B:ASN127 4.0 23.2 1.0 O B:ASP83 4.2 43.9 1.0 O B:HOH239 4.3 13.2 1.0 MN B:MN234 4.4 33.7 1.0 N B:SER126 4.4 26.0 1.0 CA B:SER126 4.4 26.2 1.0 CA B:TYR125 4.4 26.2 1.0 CA B:GLY104 4.5 18.6 1.0 N B:TYR125 4.5 25.1 1.0 CB B:ASP123 4.5 21.7 1.0 CA B:ASN127 4.5 24.5 1.0 C B:SER126 4.5 24.6 1.0 CB B:TYR125 4.5 27.6 1.0 CB B:ASP132 4.5 27.6 1.0 CD1 B:TYR125 4.6 31.7 1.0 O B:GLY104 4.8 19.1 1.0 ND2 B:ASN127 4.8 22.4 1.0 CE1 B:HIS137 4.9 18.5 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva)


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 the Presence of Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca233 b:25.6 occ:1.00 O C:TYR125 2.5 28.2 1.0 OD2 C:ASP132 2.5 29.5 1.0 OD1 C:ASN127 2.6 26.2 1.0 O C:HOH238 2.7 21.1 1.0 OD1 C:ASP123 2.7 24.6 1.0 OD2 C:ASP123 2.7 23.3 1.0 O C:HOH237 2.7 17.4 1.0 CG C:ASP123 3.0 22.2 1.0 CG C:ASP132 3.4 29.9 1.0 CG C:ASN127 3.6 29.2 1.0 C C:TYR125 3.6 28.2 1.0 OD1 C:ASP132 3.7 29.5 1.0 N C:ASN127 3.8 29.4 1.0 CB C:ASN127 4.0 27.6 1.0 MN C:MN234 4.1 40.1 1.0 O C:HOH239 4.2 12.8 1.0 CA C:TYR125 4.4 28.2 1.0 CA C:GLY104 4.4 22.8 1.0 N C:TYR125 4.5 28.2 1.0 CB C:ASP123 4.5 22.7 1.0 N C:SER126 4.5 28.4 1.0 CA C:ASN127 4.5 28.6 1.0 CB C:TYR125 4.5 30.6 1.0 O C:ASP83 4.5 43.2 1.0 CB C:ASP132 4.5 29.8 1.0 CA C:SER126 4.6 29.3 1.0 C C:SER126 4.6 29.5 1.0 O C:GLY104 4.7 24.1 1.0 ND2 C:ASN127 4.7 29.9 1.0 CD1 C:TYR125 4.7 33.7 1.0 CE1 C:HIS137 4.8 20.9 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin-Lactose Complex in the Presence of Peptide(Iwssagnva)


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 the Presence of Peptide(Iwssagnva) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca233 b:22.9 occ:1.00 OD1 D:ASN127 2.6 27.1 1.0 O D:HOH237 2.6 18.0 1.0 OD2 D:ASP132 2.6 29.7 1.0 O D:TYR125 2.6 26.2 1.0 O D:HOH238 2.6 21.2 1.0 OD1 D:ASP123 2.6 24.5 1.0 OD2 D:ASP123 2.6 21.8 1.0 CG D:ASP123 3.0 21.9 1.0 CG D:ASN127 3.5 26.7 1.0 CG D:ASP132 3.5 29.3 1.0 C D:TYR125 3.7 27.0 1.0 N D:ASN127 3.8 28.8 1.0 CB D:ASN127 3.9 26.9 1.0 OD1 D:ASP132 4.0 30.4 1.0 MN D:MN234 4.2 41.8 1.0 O D:HOH239 4.3 18.9 1.0 CA D:GLY104 4.3 20.6 1.0 CB D:ASP123 4.4 22.2 1.0 O D:ASP83 4.5 29.9 1.0 CA D:ASN127 4.5 28.7 1.0 ND2 D:ASN127 4.6 27.9 1.0 N D:SER126 4.6 27.9 1.0 CA D:SER126 4.6 28.9 1.0 O D:GLY104 4.6 21.0 1.0 C D:SER126 4.6 29.4 1.0 CA D:TYR125 4.6 26.5 1.0 N D:TYR125 4.7 25.7 1.0 CB D:ASP132 4.7 29.9 1.0 CB D:TYR125 4.8 28.5 1.0 CD1 D:TYR125 4.8 31.8 1.0 OD1 D:ASP83 4.9 28.8 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