Calcium in PDB 2tep: Peanut Lectin Complexed with T-Antigenic Disaccharide

The structure of Peanut Lectin Complexed with T-Antigenic Disaccharide, PDB code: 2tep was solved by R.Ravishankar, M.Ravindran, 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 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	129.892, 126.676, 76.516, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 25.1

The structure of Peanut Lectin Complexed with T-Antigenic Disaccharide also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

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

Calcium binding site 1 out of 4 in the Peanut Lectin Complexed with T-Antigenic Disaccharide


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 T-Antigenic Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:20.2 occ:1.00 O A:HOH376 1.9 11.9 1.0 O A:TYR125 2.2 2.9 1.0 OD1 A:ASN127 2.2 16.8 1.0 OD2 A:ASP123 2.3 2.0 1.0 OD2 A:ASP132 2.3 21.0 1.0 O A:HOH377 2.4 27.2 1.0 OD1 A:ASP123 2.4 10.9 1.0 CG A:ASP123 2.6 9.3 1.0 C A:TYR125 3.4 4.5 1.0 CG A:ASN127 3.4 11.5 1.0 CG A:ASP132 3.5 14.3 1.0 N A:ASN127 4.0 2.0 1.0 CB A:ASN127 4.0 9.9 1.0 CB A:ASP123 4.1 7.2 1.0 OD1 A:ASP132 4.2 10.2 1.0 CA A:TYR125 4.2 2.1 1.0 MN A:MN238 4.3 32.3 1.0 N A:TYR125 4.3 2.3 1.0 N A:SER126 4.4 2.8 1.0 CB A:TYR125 4.5 5.3 1.0 CA A:GLY104 4.5 2.0 1.0 ND2 A:ASN127 4.5 7.7 1.0 CA A:SER126 4.6 4.1 1.0 O A:HOH378 4.6 2.0 1.0 C A:SER126 4.6 4.2 1.0 CA A:ASN127 4.6 2.9 1.0 CB A:ASP132 4.7 12.7 1.0 O A:ASP83 4.7 10.9 1.0 OD1 A:ASP83 4.7 13.3 1.0 CD1 A:TYR125 4.8 7.3 1.0 O A:GLY104 4.9 6.4 1.0 CE1 A:HIS137 4.9 2.0 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin Complexed with T-Antigenic Disaccharide


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 T-Antigenic Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca237 b:2.0 occ:1.00 O B:HOH391 2.0 32.4 1.0 OD2 B:ASP132 2.2 3.0 1.0 O B:TYR125 2.3 6.7 1.0 OD1 B:ASP123 2.4 9.2 1.0 OD2 B:ASP123 2.4 2.0 1.0 OD1 B:ASN127 2.5 5.3 1.0 O B:HOH390 2.6 19.6 1.0 CG B:ASP123 2.7 4.7 1.0 CG B:ASP132 3.3 11.2 1.0 C B:TYR125 3.6 9.1 1.0 CG B:ASN127 3.6 5.6 1.0 OD1 B:ASP132 3.8 6.4 1.0 MN B:MN238 3.9 29.6 1.0 O B:HOH392 4.0 2.0 1.0 N B:ASN127 4.1 4.5 1.0 CB B:ASN127 4.1 3.6 1.0 CB B:ASP123 4.2 4.9 1.0 CA B:TYR125 4.5 9.8 1.0 N B:SER126 4.5 10.6 1.0 CA B:GLY104 4.5 2.0 1.0 N B:TYR125 4.5 12.4 1.0 CB B:ASP132 4.6 9.6 1.0 CA B:SER126 4.6 10.7 1.0 O B:GLY104 4.7 2.0 1.0 CB B:TYR125 4.7 15.2 1.0 OD1 B:ASP83 4.7 3.8 1.0 ND2 B:ASN127 4.7 9.8 1.0 CA B:ASN127 4.7 5.0 1.0 C B:SER126 4.8 9.4 1.0 O B:ASP83 4.8 5.6 1.0 CE1 B:HIS137 4.8 2.1 1.0 NE2 B:HIS137 4.9 3.1 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin Complexed with T-Antigenic Disaccharide


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 T-Antigenic Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca237 b:18.0 occ:1.00 O C:TYR125 2.0 17.0 1.0 OD1 C:ASN127 2.1 9.0 1.0 O C:HOH340 2.2 35.1 1.0 OD2 C:ASP132 2.3 15.3 1.0 OD2 C:ASP123 2.5 9.7 1.0 OD1 C:ASP123 2.6 12.8 1.0 O C:HOH341 2.8 11.2 1.0 CG C:ASP123 2.9 10.4 1.0 C C:TYR125 3.2 14.7 1.0 CG C:ASN127 3.3 7.1 1.0 CG C:ASP132 3.4 9.6 1.0 N C:ASN127 3.6 12.8 1.0 CB C:ASN127 3.9 10.4 1.0 N C:SER126 4.1 15.1 1.0 CA C:TYR125 4.1 7.5 1.0 OD1 C:ASP132 4.1 8.7 1.0 O C:HOH342 4.1 2.7 1.0 CA C:SER126 4.2 15.4 1.0 C C:SER126 4.2 17.1 1.0 N C:TYR125 4.3 10.1 1.0 CB C:TYR125 4.3 9.9 1.0 CB C:ASP123 4.4 8.6 1.0 CA C:ASN127 4.4 11.2 1.0 ND2 C:ASN127 4.4 9.6 1.0 CB C:ASP132 4.4 8.0 1.0 MN C:MN238 4.5 26.5 1.0 CD1 C:TYR125 4.6 18.2 1.0 CA C:GLY104 4.7 8.3 1.0 CE1 C:HIS137 4.8 8.9 1.0 NE2 C:HIS137 5.0 11.7 1.0 CG C:TYR125 5.0 14.6 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin Complexed with T-Antigenic Disaccharide


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 T-Antigenic Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca237 b:16.1 occ:1.00 OD2 D:ASP123 2.1 4.2 1.0 O D:HOH361 2.2 2.1 1.0 OD2 D:ASP132 2.2 2.0 1.0 OD1 D:ASP123 2.2 9.4 1.0 O D:TYR125 2.3 8.9 1.0 O D:HOH360 2.3 2.0 1.0 CG D:ASP123 2.5 3.9 1.0 OD1 D:ASN127 2.5 20.6 1.0 CG D:ASP132 3.4 4.2 1.0 C D:TYR125 3.5 11.7 1.0 CG D:ASN127 3.6 12.0 1.0 CB D:ASP123 3.9 2.5 1.0 OD1 D:ASP132 3.9 2.0 1.0 N D:ASN127 4.0 15.6 1.0 O D:HOH362 4.0 2.0 1.0 CB D:ASN127 4.1 13.1 1.0 MN D:MN238 4.2 28.3 1.0 CA D:TYR125 4.4 9.7 1.0 N D:TYR125 4.4 13.5 1.0 N D:SER126 4.4 13.9 1.0 CB D:ASP132 4.5 6.0 1.0 CA D:SER126 4.6 14.8 1.0 CB D:TYR125 4.7 10.9 1.0 ND2 D:ASN127 4.7 9.6 1.0 CA D:ASN127 4.7 15.7 1.0 C D:SER126 4.7 15.4 1.0 CE1 D:HIS137 4.7 2.0 1.0 O D:GLY104 4.8 6.3 1.0 O D:ASP83 4.8 8.6 1.0 CA D:GLY104 4.8 8.1 1.0 CA D:ASP123 4.9 5.1 1.0 NE2 D:HIS137 4.9 4.8 1.0

R.Ravishankar, M.Ravindran, K.Suguna, A.Surolia, M.Vijayan. The Specificity of Peanut Agglutinin For Thomsen-Friedenreich Antigen Is Mediated By Water-Bridges Curr.Sci. V. 72 855 1997.
ISSN: ISSN 0011-3891