Calcium in PDB 1qf3: Peanut Lectin Complexed with Methyl-Beta-Galactose

The structure of Peanut Lectin Complexed with Methyl-Beta-Galactose, PDB code: 1qf3 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 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.953, 126.683, 77.284, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.7

The structure of Peanut Lectin Complexed with Methyl-Beta-Galactose also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin Complexed with Methyl-Beta-Galactose (pdb code 1qf3). 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 Complexed with Methyl-Beta-Galactose, PDB code: 1qf3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca437 b:3.6 occ:1.00 OD2 A:ASP132 2.2 13.2 1.0 O A:TYR125 2.2 3.8 1.0 OD1 A:ASN127 2.4 11.8 1.0 O A:HOH525 2.4 5.3 1.0 OD1 A:ASP123 2.4 8.6 1.0 OD2 A:ASP123 2.4 2.0 1.0 O A:HOH526 2.4 2.0 1.0 CG A:ASP123 2.7 2.2 1.0 CG A:ASP132 3.3 8.2 1.0 C A:TYR125 3.4 10.8 1.0 CG A:ASN127 3.4 7.0 1.0 N A:ASN127 3.8 7.0 1.0 MN A:MN238 3.8 36.0 1.0 CB A:ASN127 3.9 2.0 1.0 OD1 A:ASP132 3.9 11.6 1.0 O A:HOH527 4.2 16.1 1.0 CB A:ASP123 4.2 2.0 1.0 CA A:TYR125 4.3 9.3 1.0 N A:TYR125 4.4 15.1 1.0 N A:SER126 4.4 19.2 1.0 CB A:ASP132 4.5 7.0 1.0 CA A:ASN127 4.5 3.6 1.0 CB A:TYR125 4.5 15.2 1.0 CA A:SER126 4.5 22.9 1.0 C A:SER126 4.6 20.1 1.0 ND2 A:ASN127 4.6 4.4 1.0 CA A:GLY104 4.7 4.3 1.0 CD1 A:TYR125 4.8 21.5 1.0 O A:GLY104 4.8 8.2 1.0 OD2 A:ASP83 4.9 11.8 1.0 O A:ASP83 4.9 14.0 1.0 CE1 A:HIS137 4.9 18.9 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:2.0 occ:1.00 O B:TYR125 2.1 4.5 1.0 OD2 B:ASP132 2.2 4.9 1.0 OD1 B:ASN127 2.3 15.9 1.0 OD1 B:ASP123 2.3 27.0 1.0 O B:HOH552 2.4 2.0 1.0 O B:HOH551 2.6 2.0 1.0 OD2 B:ASP123 2.7 32.1 1.0 CG B:ASP123 2.9 25.4 1.0 C B:TYR125 3.3 4.4 1.0 CG B:ASN127 3.4 3.5 1.0 CG B:ASP132 3.4 6.8 1.0 MN B:MN238 3.6 44.8 1.0 N B:ASN127 3.7 13.9 1.0 CB B:ASN127 3.9 2.0 1.0 OD1 B:ASP132 4.0 7.0 1.0 CA B:TYR125 4.2 3.6 1.0 N B:SER126 4.3 16.1 1.0 O B:HOH553 4.3 2.0 1.0 N B:TYR125 4.3 5.2 1.0 CB B:TYR125 4.4 24.0 1.0 CB B:ASP123 4.4 21.5 1.0 CA B:ASN127 4.4 8.4 1.0 CA B:SER126 4.5 20.6 1.0 C B:SER126 4.5 20.4 1.0 CB B:ASP132 4.5 2.0 1.0 ND2 B:ASN127 4.5 2.0 1.0 CD1 B:TYR125 4.6 29.1 1.0 CA B:GLY104 4.7 2.0 1.0 OD2 B:ASP83 4.8 27.1 1.0 O B:ASP83 4.9 3.6 1.0 O B:GLY104 4.9 11.1 1.0 CE1 B:HIS137 5.0 5.7 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:14.3 occ:1.00 O C:TYR125 2.1 17.0 1.0 O C:HOH516 2.2 2.0 1.0 OD1 C:ASN127 2.3 23.8 1.0 OD1 C:ASP123 2.3 17.3 1.0 OD2 C:ASP132 2.3 28.7 1.0 O C:HOH517 2.4 24.1 1.0 OD2 C:ASP123 2.7 20.9 1.0 CG C:ASP123 2.8 11.5 1.0 C C:TYR125 3.3 17.6 1.0 CG C:ASN127 3.4 20.5 1.0 CG C:ASP132 3.5 34.3 1.0 N C:ASN127 3.8 21.2 1.0 CB C:ASN127 4.0 19.5 1.0 CA C:TYR125 4.1 12.2 1.0 N C:TYR125 4.2 10.7 1.0 OD1 C:ASP132 4.2 29.0 1.0 MN C:MN238 4.2 38.8 1.0 N C:SER126 4.3 23.2 1.0 CB C:TYR125 4.3 21.0 1.0 CB C:ASP123 4.3 8.2 1.0 CA C:SER126 4.5 27.3 1.0 ND2 C:ASN127 4.5 20.8 1.0 C C:SER126 4.6 27.8 1.0 CA C:ASN127 4.6 17.5 1.0 CD1 C:TYR125 4.6 29.4 1.0 O C:HOH518 4.6 10.2 1.0 CB C:ASP132 4.6 28.0 1.0 OD2 C:ASP83 4.7 29.1 1.0 CA C:GLY104 4.7 26.0 1.0 O C:ASP83 4.7 22.6 1.0 O C:GLY104 4.9 29.6 1.0 CG C:TYR125 5.0 21.1 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin Complexed with Methyl-Beta-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Peanut Lectin Complexed with Methyl-Beta-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:13.4 occ:1.00 O D:HOH523 2.1 31.0 1.0 O D:HOH524 2.3 33.4 1.0 O D:TYR125 2.3 2.0 1.0 OD1 D:ASN127 2.3 18.3 1.0 OD2 D:ASP132 2.4 7.8 1.0 OD1 D:ASP123 2.4 13.4 1.0 OD2 D:ASP123 2.5 20.7 1.0 CG D:ASP123 2.8 13.1 1.0 CG D:ASN127 3.4 15.1 1.0 C D:TYR125 3.5 4.1 1.0 CG D:ASP132 3.6 13.9 1.0 N D:ASN127 3.9 16.7 1.0 CB D:ASN127 4.0 11.3 1.0 OD1 D:ASP132 4.1 13.1 1.0 CA D:TYR125 4.3 2.0 1.0 CB D:ASP123 4.3 2.0 1.0 N D:TYR125 4.4 7.3 1.0 O D:HOH525 4.4 24.9 1.0 CB D:TYR125 4.5 5.6 1.0 MN D:MN238 4.5 37.2 1.0 N D:SER126 4.5 17.3 1.0 ND2 D:ASN127 4.5 12.4 1.0 CA D:GLY104 4.6 20.3 1.0 CA D:ASN127 4.6 9.9 1.0 OD2 D:ASP83 4.6 12.7 1.0 CA D:SER126 4.7 25.8 1.0 CB D:ASP132 4.7 10.5 1.0 O D:ASP83 4.7 6.8 1.0 C D:SER126 4.7 27.1 1.0 CD1 D:TYR125 4.7 10.2 1.0 O D:GLY104 4.8 30.1 1.0

R.Ravishankar, K.Suguna, A.Surolia, M.Vijayan. Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N-Acetyllactosamine and A Comparative Study of Carbohydrate Binding in Gal/Galnac-Specific Legume Lectins. Acta Crystallogr.,Sect.D V. 55 1375 1999.
ISSN: ISSN 0907-4449
PubMed: 10417405
DOI: 10.1107/S0907444999006587