Calcium in PDB 1wbf: Winged Bean Lectin, Saccharide Free Form

The structure of Winged Bean Lectin, Saccharide Free Form, PDB code: 1wbf was solved by N.Manoj, V.R.Srinivas, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.159, 75.161, 95.772, 90.00, 106.91, 90.00
R / Rfree (%)	19.7 / 25.7

The structure of Winged Bean Lectin, Saccharide Free Form also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Winged Bean Lectin, Saccharide Free Form (pdb code 1wbf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Winged Bean Lectin, Saccharide Free Form, PDB code: 1wbf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Winged Bean Lectin, Saccharide Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Winged Bean Lectin, Saccharide Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:23.1 occ:1.00 O A:HOH666 2.4 24.2 1.0 OD2 A:ASP131 2.4 24.6 1.0 O A:PHE126 2.4 24.9 1.0 OD1 A:ASP124 2.5 29.7 1.0 OD1 A:ASN128 2.6 24.6 1.0 OD2 A:ASP124 2.7 28.3 1.0 O A:HOH665 2.7 19.2 1.0 CG A:ASP124 2.9 22.0 1.0 CG A:ASP131 3.5 21.3 1.0 C A:PHE126 3.5 26.1 1.0 CG A:ASN128 3.8 22.8 1.0 MN A:MN300 4.1 37.7 1.0 N A:ASN128 4.1 28.2 1.0 OD1 A:ASP131 4.1 28.0 1.0 CA A:PHE126 4.3 25.3 1.0 N A:PHE126 4.3 27.7 1.0 CB A:ASN128 4.4 22.9 1.0 CB A:ASP124 4.4 19.9 1.0 CB A:PHE126 4.4 25.6 1.0 CB A:ASP131 4.5 17.6 1.0 N A:ARG127 4.5 24.5 1.0 O A:HOH664 4.6 22.3 1.0 NE1 A:TRP130 4.6 34.9 1.0 CA A:ARG127 4.6 25.4 1.0 CA A:GLY105 4.6 20.1 1.0 CZ A:PHE107 4.6 17.4 1.0 ND2 A:ASN128 4.8 21.2 1.0 OD1 A:ASP87 4.8 20.2 1.0 C A:ARG127 4.9 27.6 1.0 CA A:ASN128 4.9 27.2 1.0 O A:ASP87 4.9 16.5 1.0 O A:GLY105 4.9 20.3 1.0 CD2 A:PHE126 4.9 28.6 1.0

Calcium binding site 2 out of 2 in the Winged Bean Lectin, Saccharide Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Winged Bean Lectin, Saccharide Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:23.6 occ:1.00 O B:PHE126 2.3 18.6 1.0 OD2 B:ASP131 2.4 18.8 1.0 OD1 B:ASN128 2.4 23.8 1.0 O B:HOH681 2.4 38.9 1.0 OD1 B:ASP124 2.7 47.5 1.0 OD2 B:ASP124 2.7 37.8 1.0 O B:HOH680 2.8 14.3 1.0 CG B:ASP124 3.1 30.2 1.0 C B:PHE126 3.4 19.0 1.0 CG B:ASP131 3.5 16.7 1.0 CG B:ASN128 3.5 24.0 1.0 N B:ASN128 3.8 23.1 1.0 CB B:ASN128 4.1 22.8 1.0 OD1 B:ASP131 4.2 14.4 1.0 CA B:PHE126 4.2 18.2 1.0 N B:PHE126 4.3 20.2 1.0 CB B:PHE126 4.3 21.4 1.0 N B:ARG127 4.4 18.0 1.0 CB B:ASP131 4.5 8.9 1.0 MN B:MN300 4.5 39.0 1.0 CA B:ARG127 4.5 17.4 1.0 O B:HOH679 4.6 41.6 1.0 CA B:GLY105 4.6 19.4 1.0 CB B:ASP124 4.6 27.4 1.0 CZ B:PHE107 4.6 13.2 1.0 CA B:ASN128 4.6 25.4 1.0 ND2 B:ASN128 4.6 23.9 1.0 NE1 B:TRP130 4.6 24.3 1.0 C B:ARG127 4.7 23.3 1.0 CD2 B:PHE126 4.7 31.8 1.0 O B:ASP87 4.8 12.9 1.0 OD1 B:ASP87 4.8 27.3 1.0 O B:GLY105 4.9 17.7 1.0 CZ2 B:TRP130 4.9 22.2 1.0

N.Manoj, V.R.Srinivas, K.Suguna. Structure of Basic Winged-Bean Lectin and A Comparison with Its Saccharide-Bound Form. Acta Crystallogr.,Sect.D V. 55 794 1999.
ISSN: ISSN 0907-4449
PubMed: 10089310
DOI: 10.1107/S090744499900044X