Calcium in PDB 1bzw: Peanut Lectin Complexed with C-Lactose

The structure of Peanut Lectin Complexed with C-Lactose, PDB code: 1bzw was solved by R.Ravishankar, A.Surolia, M.Vijayan, S.Lim, Y.Kishi, 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 (°)	129.121, 126.748, 76.900, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.7

The structure of Peanut Lectin Complexed with C-Lactose also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

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

Calcium binding site 1 out of 4 in the Peanut Lectin Complexed with C-Lactose


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 C-Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:10.0 occ:1.00 O A:HOH485 2.1 14.9 1.0 O A:TYR125 2.2 15.7 1.0 OD2 A:ASP132 2.2 25.6 1.0 OD1 A:ASN127 2.3 18.9 1.0 OD1 A:ASP123 2.3 2.0 1.0 O A:HOH486 2.4 6.3 1.0 OD2 A:ASP123 2.5 2.0 1.0 CG A:ASP123 2.8 2.0 1.0 CG A:ASP132 3.4 24.0 1.0 C A:TYR125 3.4 13.2 1.0 CG A:ASN127 3.4 12.0 1.0 N A:ASN127 3.8 12.0 1.0 OD1 A:ASP132 4.0 18.1 1.0 CB A:ASN127 4.0 8.9 1.0 MN A:MN409 4.2 35.8 1.0 CA A:TYR125 4.3 5.8 1.0 CB A:ASP123 4.3 2.0 1.0 N A:TYR125 4.3 12.2 1.0 N A:SER126 4.4 13.4 1.0 CB A:TYR125 4.5 8.5 1.0 O A:HOH487 4.5 6.1 1.0 CA A:SER126 4.5 18.6 1.0 CB A:ASP132 4.5 19.5 1.0 ND2 A:ASN127 4.5 14.2 1.0 CA A:ASN127 4.6 9.6 1.0 C A:SER126 4.6 18.0 1.0 CA A:GLY104 4.6 8.9 1.0 CD1 A:TYR125 4.7 16.2 1.0 O A:ASP83 4.8 9.6 1.0 OD2 A:ASP83 4.9 19.3 1.0 O A:GLY104 4.9 17.7 1.0 CE1 A:HIS137 5.0 19.4 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin Complexed with C-Lactose


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 C-Lactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca410 b:14.8 occ:1.00 OD2 B:ASP132 2.1 10.9 1.0 O B:TYR125 2.2 9.3 1.0 O B:HOH510 2.2 4.8 1.0 OD1 B:ASP123 2.3 19.0 1.0 O B:HOH509 2.4 9.0 1.0 OD1 B:ASN127 2.4 14.3 1.0 OD2 B:ASP123 2.4 19.5 1.0 CG B:ASP123 2.7 17.3 1.0 CG B:ASP132 3.3 15.3 1.0 C B:TYR125 3.4 11.9 1.0 CG B:ASN127 3.5 3.5 1.0 OD1 B:ASP132 3.9 16.7 1.0 N B:ASN127 3.9 15.9 1.0 MN B:MN411 3.9 36.0 1.0 CB B:ASN127 4.1 3.2 1.0 CB B:ASP123 4.2 14.8 1.0 CA B:TYR125 4.3 7.7 1.0 N B:TYR125 4.3 13.9 1.0 N B:SER126 4.3 14.6 1.0 O B:HOH511 4.4 2.6 1.0 CB B:ASP132 4.5 14.5 1.0 CA B:SER126 4.5 14.9 1.0 CB B:TYR125 4.5 20.9 1.0 C B:SER126 4.6 15.6 1.0 CA B:ASN127 4.6 15.3 1.0 ND2 B:ASN127 4.6 2.0 1.0 CA B:GLY104 4.7 5.5 1.0 CD1 B:TYR125 4.7 31.9 1.0 O B:ASP83 4.9 4.9 1.0 CE1 B:HIS137 4.9 13.4 1.0 OD2 B:ASP83 5.0 28.0 1.0 O B:GLY104 5.0 11.1 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin Complexed with C-Lactose


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 C-Lactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca412 b:19.8 occ:1.00 O C:HOH487 2.0 19.4 1.0 OD1 C:ASN127 2.2 25.8 1.0 O C:TYR125 2.3 17.1 1.0 OD2 C:ASP132 2.3 18.7 1.0 O C:HOH486 2.3 19.3 1.0 OD1 C:ASP123 2.5 26.5 1.0 OD2 C:ASP123 2.6 30.4 1.0 CG C:ASP123 2.9 19.2 1.0 CG C:ASN127 3.3 19.4 1.0 C C:TYR125 3.5 18.1 1.0 CG C:ASP132 3.5 21.8 1.0 N C:ASN127 3.8 22.6 1.0 CB C:ASN127 4.0 18.8 1.0 OD1 C:ASP132 4.1 20.3 1.0 MN C:MN413 4.2 39.4 1.0 CA C:TYR125 4.3 10.3 1.0 N C:TYR125 4.4 14.1 1.0 N C:SER126 4.4 31.5 1.0 O C:HOH488 4.4 4.4 1.0 CB C:ASP123 4.4 9.4 1.0 ND2 C:ASN127 4.4 22.7 1.0 CA C:GLY104 4.5 23.0 1.0 CB C:TYR125 4.5 25.2 1.0 CA C:ASN127 4.6 18.1 1.0 CA C:SER126 4.6 34.3 1.0 CB C:ASP132 4.6 21.8 1.0 C C:SER126 4.6 36.2 1.0 CD1 C:TYR125 4.6 39.6 1.0 OD2 C:ASP83 4.8 29.1 1.0 O C:GLY104 4.8 24.6 1.0 O C:ASP83 4.9 25.9 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin Complexed with C-Lactose


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 C-Lactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca414 b:13.6 occ:1.00 OD2 D:ASP132 2.2 27.5 1.0 O D:HOH486 2.3 14.3 1.0 O D:TYR125 2.3 7.9 1.0 OD1 D:ASP123 2.4 17.4 1.0 OD1 D:ASN127 2.4 25.9 1.0 OD2 D:ASP123 2.4 21.8 1.0 O D:HOH487 2.4 21.9 1.0 CG D:ASP123 2.7 16.7 1.0 CG D:ASP132 3.3 28.2 1.0 C D:TYR125 3.5 13.9 1.0 CG D:ASN127 3.5 24.4 1.0 OD1 D:ASP132 3.9 31.0 1.0 N D:ASN127 3.9 18.6 1.0 CB D:ASN127 4.1 19.4 1.0 MN D:MN415 4.1 42.3 1.0 CB D:ASP123 4.2 10.5 1.0 O D:HOH488 4.3 48.8 1.0 CA D:TYR125 4.4 4.0 1.0 N D:TYR125 4.4 9.4 1.0 N D:SER126 4.5 23.2 1.0 CB D:ASP132 4.5 23.3 1.0 CA D:SER126 4.6 28.8 1.0 ND2 D:ASN127 4.6 25.8 1.0 CA D:GLY104 4.6 11.9 1.0 CA D:ASN127 4.6 15.7 1.0 CB D:TYR125 4.6 15.1 1.0 C D:SER126 4.7 31.5 1.0 CD1 D:TYR125 4.8 23.8 1.0 O D:ASP83 4.9 20.9 1.0 O D:GLY104 4.9 15.0 1.0 CE1 D:HIS137 4.9 14.2 1.0 OD2 D:ASP83 5.0 28.2 1.0

R.Ravishankar, A.Surolia, M.Vijayan, S.Lim, Y.Kishi. Preferred Conformation of C-Lactose at the Free and Peanut Lectin Bound States J.Am.Chem.Soc. V. 120 11297 1998.
ISSN: ISSN 0002-7863