Calcium in PDB 1ciw: Peanut Lectin Complexed with N-Acetyllactosamine

The structure of Peanut Lectin Complexed with N-Acetyllactosamine, PDB code: 1ciw 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	129.380, 126.922, 76.065, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.4

The structure of Peanut Lectin Complexed with N-Acetyllactosamine also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

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

Calcium binding site 1 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:17.6 occ:1.00 O A:HOH507 2.1 27.5 1.0 O A:HOH508 2.2 8.2 1.0 OD1 A:ASP123 2.2 12.5 1.0 O A:TYR125 2.3 24.6 1.0 OD2 A:ASP123 2.3 14.0 1.0 OD1 A:ASN127 2.4 20.2 1.0 OD2 A:ASP132 2.4 27.4 1.0 CG A:ASP123 2.6 8.4 1.0 C A:TYR125 3.5 25.8 1.0 CG A:ASP132 3.5 29.9 1.0 CG A:ASN127 3.6 20.2 1.0 MN A:MN238 3.9 40.5 1.0 OD1 A:ASP132 4.0 25.8 1.0 N A:ASN127 4.1 17.3 1.0 CB A:ASP123 4.1 7.9 1.0 CB A:ASN127 4.2 20.3 1.0 O A:HOH509 4.3 17.4 1.0 CA A:TYR125 4.3 22.2 1.0 N A:TYR125 4.3 25.1 1.0 CB A:TYR125 4.4 21.5 1.0 N A:SER126 4.5 26.7 1.0 O A:ASP83 4.5 19.4 1.0 CA A:GLY104 4.6 13.8 1.0 ND2 A:ASN127 4.6 15.6 1.0 CA A:SER126 4.7 28.6 1.0 CB A:ASP132 4.7 28.1 1.0 C A:SER126 4.8 24.5 1.0 CD2 A:TYR125 4.8 26.4 1.0 CA A:ASN127 4.8 14.8 1.0 O A:GLY104 4.9 14.0 1.0 OD2 A:ASP83 4.9 31.6 1.0 CA A:ASP123 4.9 11.4 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:11.9 occ:1.00 O B:TYR125 2.0 20.7 1.0 OD2 B:ASP132 2.2 22.2 1.0 OD1 B:ASP123 2.3 15.6 1.0 O B:HOH530 2.3 27.8 1.0 OD1 B:ASN127 2.4 15.2 1.0 O B:HOH531 2.5 11.3 1.0 OD2 B:ASP123 2.5 11.0 1.0 CG B:ASP123 2.7 15.1 1.0 C B:TYR125 3.2 17.3 1.0 CG B:ASP132 3.4 21.3 1.0 CG B:ASN127 3.6 13.9 1.0 N B:ASN127 3.9 17.6 1.0 OD1 B:ASP132 3.9 24.6 1.0 CA B:TYR125 4.1 13.7 1.0 CB B:ASN127 4.1 15.8 1.0 N B:TYR125 4.2 16.6 1.0 N B:SER126 4.2 21.8 1.0 CB B:ASP123 4.2 9.4 1.0 O B:HOH532 4.3 22.4 1.0 CB B:TYR125 4.3 32.5 1.0 MN B:MN238 4.4 41.1 1.0 CA B:SER126 4.4 24.8 1.0 CB B:ASP132 4.5 14.8 1.0 C B:SER126 4.5 25.3 1.0 O B:HOH525 4.6 73.8 1.0 CD1 B:TYR125 4.6 42.0 1.0 CA B:ASN127 4.6 13.3 1.0 ND2 B:ASN127 4.7 12.1 1.0 O B:ASP83 4.7 18.8 1.0 CA B:GLY104 4.8 14.0 1.0 CE1 B:HIS137 4.9 11.4 1.0 OD2 B:ASP83 5.0 23.5 1.0 CG B:TYR125 5.0 38.6 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:21.2 occ:1.00 O C:HOH497 2.1 25.7 1.0 OD1 C:ASN127 2.3 25.6 1.0 O C:TYR125 2.3 17.5 1.0 OD2 C:ASP132 2.3 17.7 1.0 O C:HOH496 2.4 12.7 1.0 OD1 C:ASP123 2.4 27.6 1.0 OD2 C:ASP123 2.5 30.3 1.0 CG C:ASP123 2.8 24.0 1.0 CG C:ASN127 3.4 22.0 1.0 CG C:ASP132 3.5 26.5 1.0 C C:TYR125 3.5 18.3 1.0 N C:ASN127 3.9 32.4 1.0 MN C:MN238 4.0 44.7 1.0 OD1 C:ASP132 4.0 28.7 1.0 CB C:ASN127 4.0 23.2 1.0 CA C:TYR125 4.3 12.6 1.0 CB C:ASP123 4.3 15.0 1.0 N C:TYR125 4.4 13.5 1.0 N C:SER126 4.4 41.3 1.0 CB C:TYR125 4.4 29.7 1.0 O C:HOH498 4.4 6.8 1.0 ND2 C:ASN127 4.5 16.8 1.0 CA C:GLY104 4.6 27.4 1.0 CA C:SER126 4.6 44.1 1.0 CB C:ASP132 4.6 19.5 1.0 CA C:ASN127 4.6 27.5 1.0 C C:SER126 4.6 45.5 1.0 O C:ASP83 4.7 18.3 1.0 CD2 C:TYR125 4.7 36.8 1.0 O C:GLY104 4.8 32.1 1.0 OD2 C:ASP83 4.9 29.4 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin Complexed with N-Acetyllactosamine


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 N-Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:20.4 occ:1.00 OD2 D:ASP132 2.1 23.9 1.0 O D:TYR125 2.2 16.5 1.0 OD2 D:ASP123 2.2 23.5 1.0 O D:HOH490 2.3 21.0 1.0 OD1 D:ASP123 2.4 19.2 1.0 OD1 D:ASN127 2.4 28.4 1.0 O D:HOH491 2.5 36.5 1.0 CG D:ASP123 2.6 19.2 1.0 CG D:ASP132 3.3 27.9 1.0 C D:TYR125 3.4 17.1 1.0 CG D:ASN127 3.5 24.1 1.0 OD1 D:ASP132 3.8 25.1 1.0 N D:ASN127 3.9 32.8 1.0 MN D:MN238 4.0 36.5 1.0 CB D:ASN127 4.1 24.1 1.0 CB D:ASP123 4.1 14.8 1.0 O D:HOH492 4.2 19.4 1.0 CA D:TYR125 4.3 11.1 1.0 N D:TYR125 4.4 15.1 1.0 N D:SER126 4.4 41.1 1.0 CB D:ASP132 4.4 20.8 1.0 CA D:SER126 4.5 43.7 1.0 CB D:TYR125 4.6 21.2 1.0 C D:SER126 4.6 44.9 1.0 ND2 D:ASN127 4.6 26.0 1.0 CA D:ASN127 4.7 29.9 1.0 CA D:GLY104 4.7 28.1 1.0 O D:ASP83 4.8 9.2 1.0 CD1 D:TYR125 4.8 26.9 1.0 CE1 D:HIS137 4.9 13.3 1.0 O D:GLY104 4.9 26.0 1.0 NE2 D:HIS137 5.0 12.8 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