Calcium in PDB 2zmk: Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene

The structure of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene, PDB code: 2zmk was solved by K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.63 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	156.921, 89.958, 73.321, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.6

The structure of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene (pdb code 2zmk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene, PDB code: 2zmk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:34.6 occ:1.00 O A:PHE126 2.5 39.3 1.0 OD2 A:ASP131 2.5 38.7 1.0 OD1 A:ASP124 2.6 36.8 1.0 OD2 A:ASP124 2.7 36.8 1.0 OD1 A:ASN128 2.7 45.0 1.0 O A:HOH402 2.7 33.5 1.0 O A:HOH403 2.8 38.0 1.0 CG A:ASP124 3.0 36.5 1.0 CG A:ASP131 3.6 40.5 1.0 C A:PHE126 3.7 39.9 1.0 CG A:ASN128 3.7 44.8 1.0 N A:ASN128 4.0 41.3 1.0 OD1 A:ASP131 4.1 42.3 1.0 CB A:ASN128 4.2 43.4 1.0 CA A:PHE126 4.4 38.6 1.0 O A:HOH401 4.4 17.9 1.0 N A:PHE126 4.4 37.6 1.0 CB A:PHE126 4.4 39.7 1.0 CZ A:PHE107 4.4 30.4 1.0 CB A:ASP124 4.4 36.1 1.0 MN A:MN301 4.5 49.0 1.0 CA A:GLY105 4.5 37.4 1.0 OD2 A:ASP87 4.5 37.4 1.0 NE1 A:TRP130 4.6 43.2 1.0 CD2 A:PHE126 4.6 41.2 1.0 N A:ARG127 4.6 39.8 1.0 O A:GLY105 4.7 35.0 1.0 O A:ASP87 4.7 38.8 1.0 CA A:ARG127 4.7 40.6 1.0 CA A:ASN128 4.8 42.3 1.0 CB A:ASP131 4.8 40.9 1.0 ND2 A:ASN128 4.8 45.0 1.0 C A:ARG127 4.8 40.4 1.0 CE1 A:PHE107 4.9 30.1 1.0

Calcium binding site 2 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:40.0 occ:1.00 O B:PHE126 2.5 36.7 1.0 OD2 B:ASP131 2.5 40.1 1.0 OD1 B:ASP124 2.7 37.7 1.0 O B:HOH404 2.7 41.1 1.0 OD1 B:ASN128 2.7 46.4 1.0 OD2 B:ASP124 2.8 37.4 1.0 O B:HOH403 2.8 21.6 1.0 CG B:ASP124 3.1 36.7 1.0 CG B:ASN128 3.6 44.6 1.0 C B:PHE126 3.6 38.0 1.0 CG B:ASP131 3.7 36.6 1.0 N B:ASN128 3.9 40.0 1.0 CB B:ASN128 4.0 41.8 1.0 MN B:MN301 4.3 40.7 1.0 OD1 B:ASP131 4.4 35.5 1.0 CA B:PHE126 4.4 37.8 1.0 CB B:PHE126 4.4 41.0 1.0 N B:PHE126 4.5 36.4 1.0 CA B:GLY105 4.5 36.6 1.0 NE1 B:TRP130 4.5 41.6 1.0 OD2 B:ASP87 4.5 37.3 1.0 CZ B:PHE107 4.5 31.1 1.0 CB B:ASP124 4.6 35.8 1.0 CD2 B:PHE126 4.6 42.4 1.0 N B:ARG127 4.6 38.0 1.0 CA B:ASN128 4.6 41.6 1.0 O B:HOH402 4.6 19.8 1.0 CA B:ARG127 4.7 38.7 1.0 O B:GLY105 4.7 36.9 1.0 C B:ARG127 4.7 39.2 1.0 CB B:ASP131 4.7 37.0 1.0 ND2 B:ASN128 4.7 46.2 1.0 O B:ASP87 4.8 32.7 1.0 CZ2 B:TRP130 5.0 42.4 1.0 CE1 B:PHE107 5.0 32.5 1.0

Calcium binding site 3 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:40.1 occ:1.00 OD2 C:ASP131 2.3 45.8 1.0 O C:PHE126 2.5 42.9 1.0 OD1 C:ASN128 2.6 49.0 1.0 OD2 C:ASP124 2.7 45.5 1.0 O C:HOH402 2.7 36.6 1.0 OD1 C:ASP124 2.7 41.4 1.0 O C:HOH403 2.8 37.3 1.0 CG C:ASP124 3.0 41.0 1.0 CG C:ASP131 3.4 43.9 1.0 CG C:ASN128 3.5 46.4 1.0 C C:PHE126 3.7 42.1 1.0 N C:ASN128 3.9 43.0 1.0 OD1 C:ASP131 3.9 42.6 1.0 CB C:ASN128 4.0 45.1 1.0 O C:HOH401 4.2 27.7 1.0 MN C:MN301 4.3 50.8 1.0 NE1 C:TRP130 4.4 45.4 1.0 CB C:ASP124 4.5 38.5 1.0 CA C:PHE126 4.5 40.4 1.0 CZ C:PHE107 4.5 34.7 1.0 ND2 C:ASN128 4.6 48.1 1.0 CB C:ASP131 4.6 42.9 1.0 N C:PHE126 4.6 38.6 1.0 CB C:PHE126 4.6 42.7 1.0 CA C:ASN128 4.6 43.9 1.0 CA C:GLY105 4.6 39.3 1.0 N C:ARG127 4.6 42.3 1.0 CA C:ARG127 4.7 41.9 1.0 C C:ARG127 4.7 42.9 1.0 CD2 C:PHE126 4.7 44.4 1.0 O C:GLY105 4.7 40.1 1.0 OD2 C:ASP87 4.7 40.6 1.0 CE2 C:TRP130 4.9 44.5 1.0 CZ2 C:TRP130 4.9 43.2 1.0 O C:ASP87 4.9 38.5 1.0

Calcium binding site 4 out of 4 in the Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystl Structure of Basic Winged Bean Lectin in Complex with Gal- Alpha-1,4-Gal-Beta-Ethylene within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:44.4 occ:1.00 O D:PHE126 2.5 40.6 1.0 OD1 D:ASP124 2.5 41.3 1.0 OD2 D:ASP131 2.6 41.9 1.0 OD2 D:ASP124 2.6 40.7 1.0 O D:HOH403 2.7 22.7 1.0 OD1 D:ASN128 2.7 49.4 1.0 CG D:ASP124 2.9 41.1 1.0 CG D:ASP131 3.5 40.2 1.0 C D:PHE126 3.6 40.9 1.0 CG D:ASN128 3.7 47.2 1.0 OD1 D:ASP131 3.8 40.8 1.0 N D:ASN128 4.1 42.7 1.0 CB D:ASN128 4.2 45.3 1.0 CA D:PHE126 4.4 40.3 1.0 N D:PHE126 4.4 40.3 1.0 CB D:PHE126 4.4 41.6 1.0 CZ D:PHE107 4.4 33.7 1.0 CB D:ASP124 4.4 39.2 1.0 MN D:MN301 4.5 44.9 1.0 OD2 D:ASP87 4.5 44.3 1.0 CA D:GLY105 4.5 38.3 1.0 O D:HOH401 4.6 29.2 1.0 O D:ASP87 4.6 42.0 1.0 CD2 D:PHE126 4.6 43.5 1.0 O D:GLY105 4.6 38.5 1.0 N D:ARG127 4.7 40.7 1.0 NE1 D:TRP130 4.7 41.9 1.0 ND2 D:ASN128 4.7 48.5 1.0 CA D:ARG127 4.8 40.4 1.0 CE1 D:PHE107 4.8 32.0 1.0 CA D:ASN128 4.8 42.9 1.0 CB D:ASP131 4.8 40.4 1.0 C D:ARG127 4.9 41.4 1.0

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Structure and Sugar-Specificity of Basic Winged-Bean Lectin: Structures of New Disaccharide Complexes and A Comparative Study with Other Known Disaccharide Complexes of the Lectin. Acta Crystallogr.,Sect.D V. 64 730 2008.
ISSN: ISSN 0907-4449
PubMed: 18566508
DOI: 10.1107/S0907444908011323