Calcium in PDB 2d3s: Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen

The structure of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen, PDB code: 2d3s was solved by K.A.Kulkarni, S.Sinha, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.866, 91.897, 73.503, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.4

The structure of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen (pdb code 2d3s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen, PDB code: 2d3s:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:34.6 occ:1.00 O A:PHE126 2.5 35.1 1.0 OD2 A:ASP131 2.5 38.6 1.0 O A:HOH652 2.6 28.5 1.0 OD2 A:ASP124 2.7 36.4 1.0 ND2 A:ASN128 2.7 39.8 1.0 OD1 A:ASP124 2.7 36.5 1.0 O A:HOH653 2.7 40.0 1.0 CG A:ASP124 3.0 35.1 1.0 CG A:ASP131 3.5 39.9 1.0 C A:PHE126 3.7 36.4 1.0 CG A:ASN128 3.7 43.7 1.0 N A:ASN128 3.9 40.1 1.0 CB A:ASN128 3.9 41.6 1.0 OD1 A:ASP131 3.9 39.4 1.0 O A:HOH651 4.3 20.1 1.0 MN A:MN300 4.3 43.8 1.0 CA A:PHE126 4.5 35.0 1.0 CZ A:PHE107 4.5 25.3 1.0 N A:PHE126 4.5 32.1 1.0 CB A:ASP124 4.5 35.5 1.0 NE1 A:TRP130 4.5 47.3 1.0 CA A:ASN128 4.5 42.2 1.0 CB A:PHE126 4.5 36.3 1.0 CA A:GLY105 4.6 30.9 1.0 CD2 A:PHE126 4.6 37.5 1.0 N A:ARG127 4.6 37.9 1.0 O A:GLY105 4.7 29.7 1.0 C A:ARG127 4.7 39.4 1.0 CA A:ARG127 4.7 40.9 1.0 CB A:ASP131 4.7 41.5 1.0 OD2 A:ASP87 4.8 31.7 1.0 OD1 A:ASN128 4.8 44.4 1.0 CZ2 A:TRP130 4.8 47.1 1.0 O A:ASP87 4.9 33.8 1.0 CE1 A:PHE107 4.9 26.9 1.0 CE2 A:TRP130 4.9 47.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1303 b:34.2 occ:1.00 OD2 B:ASP131 2.5 26.1 1.0 O B:PHE126 2.5 31.1 1.0 ND2 B:ASN128 2.6 24.5 1.0 OD1 B:ASP124 2.6 29.8 1.0 O B:HOH1441 2.6 28.0 1.0 OD2 B:ASP124 2.6 30.4 1.0 O B:HOH1442 2.7 30.2 1.0 CG B:ASP124 3.0 30.5 1.0 CG B:ASP131 3.5 27.7 1.0 C B:PHE126 3.7 31.8 1.0 CG B:ASN128 3.7 34.6 1.0 OD1 B:ASP131 4.0 24.9 1.0 N B:ASN128 4.0 32.6 1.0 CB B:ASN128 4.1 31.5 1.0 MN B:MN1300 4.2 35.2 1.0 O B:HOH1440 4.3 18.3 1.0 CZ B:PHE107 4.4 25.9 1.0 CB B:ASP124 4.5 27.9 1.0 CA B:GLY105 4.5 29.6 1.0 N B:PHE126 4.5 29.8 1.0 CA B:PHE126 4.5 31.0 1.0 CB B:PHE126 4.6 34.3 1.0 NE1 B:TRP130 4.6 36.7 1.0 N B:ARG127 4.6 32.9 1.0 OD2 B:ASP87 4.7 31.8 1.0 CB B:ASP131 4.7 26.3 1.0 CA B:ARG127 4.7 32.0 1.0 CA B:ASN128 4.7 32.3 1.0 O B:ASP87 4.8 28.2 1.0 O B:GLY105 4.8 29.7 1.0 OD1 B:ASN128 4.8 35.4 1.0 C B:ARG127 4.8 31.8 1.0 CD2 B:PHE126 4.8 35.3 1.0 CE1 B:PHE107 4.9 30.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2303 b:43.8 occ:1.00 O C:PHE126 2.5 41.5 1.0 ND2 C:ASN128 2.6 41.6 1.0 OD2 C:ASP131 2.6 52.1 1.0 OD2 C:ASP124 2.7 45.4 1.0 O C:HOH2437 2.7 32.2 1.0 O C:HOH2438 2.7 33.5 1.0 OD1 C:ASP124 2.8 44.9 1.0 CG C:ASP124 3.1 40.8 1.0 CG C:ASP131 3.5 51.1 1.0 CG C:ASN128 3.6 42.8 1.0 C C:PHE126 3.6 43.2 1.0 N C:ASN128 3.6 42.2 1.0 CB C:ASN128 3.7 42.8 1.0 OD1 C:ASP131 4.0 51.7 1.0 CA C:ASN128 4.3 42.2 1.0 CB C:PHE126 4.4 41.7 1.0 MN C:MN2300 4.4 49.9 1.0 CA C:PHE126 4.4 42.5 1.0 NE1 C:TRP130 4.4 54.0 1.0 CD2 C:PHE126 4.5 42.9 1.0 N C:ARG127 4.5 43.4 1.0 N C:PHE126 4.5 40.5 1.0 C C:ARG127 4.5 41.5 1.0 CA C:GLY105 4.5 39.8 1.0 CB C:ASP131 4.5 50.6 1.0 O C:HOH2436 4.5 35.2 1.0 CA C:ARG127 4.6 41.9 1.0 CZ C:PHE107 4.6 31.4 1.0 CB C:ASP124 4.6 39.6 1.0 OD2 C:ASP87 4.6 42.7 1.0 OD1 C:ASN128 4.7 44.2 1.0 O C:GLY105 4.7 41.5 1.0 CG C:PHE126 5.0 43.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Basic Winged Bean Lectin with Tn-Antigen within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3303 b:38.8 occ:1.00 O D:PHE126 2.5 41.8 1.0 OD1 D:ASP124 2.6 42.9 1.0 OD2 D:ASP131 2.6 33.3 1.0 O D:HOH3429 2.6 26.0 1.0 ND2 D:ASN128 2.6 42.2 1.0 OD2 D:ASP124 2.7 42.1 1.0 O D:HOH3425 2.8 47.7 1.0 CG D:ASP124 3.0 41.0 1.0 CG D:ASN128 3.6 45.1 1.0 C D:PHE126 3.6 42.9 1.0 CG D:ASP131 3.7 34.3 1.0 N D:ASN128 3.8 43.6 1.0 CB D:ASN128 3.9 42.9 1.0 OD1 D:ASP131 4.2 35.8 1.0 MN D:MN3300 4.3 49.7 1.0 O D:HOH3427 4.3 33.3 1.0 CA D:PHE126 4.4 42.5 1.0 CZ D:PHE107 4.4 28.4 1.0 CB D:ASP124 4.5 40.0 1.0 CB D:PHE126 4.5 42.4 1.0 CA D:GLY105 4.5 42.3 1.0 N D:PHE126 4.5 41.9 1.0 CA D:ASN128 4.5 42.7 1.0 NE1 D:TRP130 4.5 43.9 1.0 N D:ARG127 4.6 43.0 1.0 CA D:ARG127 4.6 42.4 1.0 OD1 D:ASN128 4.6 46.9 1.0 C D:ARG127 4.6 43.4 1.0 CD2 D:PHE126 4.7 45.1 1.0 O D:GLY105 4.7 41.0 1.0 CB D:ASP131 4.8 35.6 1.0 CE1 D:PHE107 4.9 30.3 1.0 OD2 D:ASP87 4.9 47.2 1.0 O D:ASP87 4.9 45.7 1.0

K.A.Kulkarni, S.Sinha, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structural Basis For the Specificity of Basic Winged Bean Lectin For the Tn-Antigen: A Crystallographic, Thermodynamic and Modelling Study Febs Lett. V. 579 6775 2005.
ISSN: ISSN 0014-5793
PubMed: 16310781
DOI: 10.1016/J.FEBSLET.2005.11.011