Calcium in PDB 2e7t: Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Trisaccharide

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Trisaccharide, PDB code: 2e7t was solved by K.A.Kulkarni, 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)	29.00 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.729, 91.130, 73.718, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.4

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Trisaccharide 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 in Complex with A Blood Group Trisaccharide (pdb code 2e7t). 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 in Complex with A Blood Group Trisaccharide, PDB code: 2e7t:
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 in Complex with A Blood Group Trisaccharide


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 in Complex with A Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:30.4 occ:1.00 OD1 A:ASN128 2.4 40.1 1.0 OD1 A:ASP124 2.5 31.6 1.0 O A:PHE126 2.6 33.9 1.0 OD2 A:ASP124 2.6 30.9 1.0 OD2 A:ASP131 2.7 36.5 1.0 O A:HOH626 2.7 40.9 1.0 CG A:ASP124 2.9 30.4 1.0 CG A:ASN128 3.6 39.0 1.0 C A:PHE126 3.7 33.3 1.0 CG A:ASP131 3.8 37.4 1.0 N A:ASN128 4.2 36.0 1.0 OD1 A:ASP131 4.2 37.6 1.0 CZ A:PHE107 4.3 20.6 1.0 CB A:ASN128 4.3 38.4 1.0 CA A:GLY105 4.4 31.2 1.0 MN A:MN300 4.4 46.8 1.0 CD2 A:PHE126 4.5 32.9 1.0 CB A:ASP124 4.5 29.7 1.0 CB A:PHE126 4.5 32.4 1.0 N A:PHE126 4.5 31.1 1.0 CA A:PHE126 4.5 32.0 1.0 OD2 A:ASP87 4.6 32.6 1.0 ND2 A:ASN128 4.6 40.6 1.0 NE1 A:TRP130 4.7 41.4 1.0 O A:GLY105 4.7 32.5 1.0 O A:ASP87 4.7 32.9 1.0 N A:ARG127 4.7 34.1 1.0 CE1 A:PHE107 4.8 22.9 1.0 CA A:ARG127 4.8 35.4 1.0 CA A:ASN128 4.9 36.7 1.0 C A:ARG127 4.9 35.3 1.0 CZ2 A:TRP130 4.9 41.7 1.0 CB A:ASP131 5.0 36.5 1.0 CG A:PHE126 5.0 32.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Trisaccharide


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 in Complex with A Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1303 b:27.9 occ:1.00 OD1 B:ASN128 2.3 36.4 1.0 O B:PHE126 2.4 27.6 1.0 OD2 B:ASP124 2.4 26.9 1.0 O B:HOH1347 2.5 34.1 1.0 OD2 B:ASP131 2.5 30.8 1.0 OD1 B:ASP124 2.5 29.6 1.0 CG B:ASP124 2.8 28.2 1.0 O B:HOH1321 2.8 25.6 1.0 CG B:ASN128 3.5 36.2 1.0 C B:PHE126 3.5 29.7 1.0 CG B:ASP131 3.7 29.9 1.0 N B:ASN128 4.0 33.5 1.0 MN B:MN1300 4.3 35.5 1.0 CB B:ASP124 4.3 28.8 1.0 N B:PHE126 4.3 28.6 1.0 CB B:ASN128 4.3 35.3 1.0 CA B:PHE126 4.3 28.7 1.0 OD1 B:ASP131 4.4 34.4 1.0 CB B:PHE126 4.4 29.0 1.0 ND2 B:ASN128 4.4 39.2 1.0 N B:ARG127 4.5 32.1 1.0 O B:HOH1323 4.5 26.3 1.0 CZ B:PHE107 4.5 21.9 1.0 CA B:ARG127 4.5 32.6 1.0 OD2 B:ASP87 4.6 31.6 1.0 CD2 B:PHE126 4.7 27.6 1.0 CB B:ASP131 4.7 30.3 1.0 CA B:GLY105 4.7 30.8 1.0 C B:ARG127 4.7 32.7 1.0 O B:ASP87 4.7 31.0 1.0 NE1 B:TRP130 4.8 35.4 1.0 CA B:ASN128 4.8 35.3 1.0 CE1 B:PHE107 4.9 22.9 1.0 O B:GLY105 4.9 29.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Trisaccharide


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 in Complex with A Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2303 b:31.4 occ:1.00 OD1 C:ASN128 2.2 41.3 1.0 O C:PHE126 2.4 33.9 1.0 OD2 C:ASP131 2.5 39.3 1.0 OD1 C:ASP124 2.5 38.1 1.0 OD2 C:ASP124 2.6 38.2 1.0 O C:HOH2315 2.6 30.3 1.0 O C:HOH2320 2.7 19.7 1.0 CG C:ASP124 2.9 36.5 1.0 CG C:ASN128 3.4 40.3 1.0 C C:PHE126 3.6 35.3 1.0 CG C:ASP131 3.7 38.0 1.0 N C:ASN128 4.0 37.1 1.0 CB C:ASN128 4.3 40.1 1.0 CB C:ASP124 4.3 34.4 1.0 ND2 C:ASN128 4.3 43.7 1.0 CA C:PHE126 4.4 34.3 1.0 MN C:MN2300 4.4 40.3 1.0 N C:PHE126 4.4 32.2 1.0 OD1 C:ASP131 4.4 39.6 1.0 CB C:PHE126 4.4 36.3 1.0 O C:HOH2319 4.4 17.0 1.0 CZ C:PHE107 4.5 29.9 1.0 N C:ARG127 4.5 36.4 1.0 CA C:ARG127 4.6 36.2 1.0 CA C:GLY105 4.6 33.9 1.0 NE1 C:TRP130 4.6 45.1 1.0 CD2 C:PHE126 4.7 37.2 1.0 C C:ARG127 4.7 36.9 1.0 CB C:ASP131 4.7 37.5 1.0 CA C:ASN128 4.7 37.6 1.0 O C:ASP87 4.8 33.8 1.0 O C:GLY105 4.9 34.4 1.0 OD2 C:ASP87 4.9 33.2 1.0 CE1 C:PHE107 5.0 32.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Trisaccharide


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 in Complex with A Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3303 b:32.0 occ:1.00 OD1 D:ASN128 2.4 31.6 1.0 O D:PHE126 2.5 33.9 1.0 OD1 D:ASP124 2.5 28.5 1.0 OD2 D:ASP131 2.5 32.8 1.0 OD2 D:ASP124 2.6 29.0 1.0 O D:HOH3323 2.6 22.4 1.0 O D:HOH3321 2.8 63.0 1.0 CG D:ASP124 2.9 28.9 1.0 CG D:ASN128 3.5 33.5 1.0 CG D:ASP131 3.6 32.4 1.0 C D:PHE126 3.7 32.7 1.0 N D:ASN128 4.1 34.0 1.0 OD1 D:ASP131 4.2 31.9 1.0 CB D:ASP124 4.3 28.5 1.0 CZ D:PHE107 4.4 24.9 1.0 MN D:MN3300 4.4 41.7 1.0 O D:HOH3324 4.4 26.0 1.0 CB D:ASN128 4.4 33.5 1.0 N D:PHE126 4.4 30.1 1.0 ND2 D:ASN128 4.4 34.8 1.0 CA D:PHE126 4.4 31.1 1.0 CB D:PHE126 4.5 31.7 1.0 N D:ARG127 4.6 32.9 1.0 CA D:ARG127 4.6 32.5 1.0 CA D:GLY105 4.7 32.4 1.0 O D:GLY105 4.7 30.8 1.0 CB D:ASP131 4.7 32.0 1.0 O D:ASP87 4.7 32.7 1.0 CE1 D:PHE107 4.8 26.1 1.0 NE1 D:TRP130 4.8 33.0 1.0 CD2 D:PHE126 4.8 29.8 1.0 C D:ARG127 4.8 32.3 1.0 CA D:ASN128 4.9 34.6 1.0 OD2 D:ASP87 5.0 35.1 1.0

K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, K.Suguna. Generation of Blood Group Specificity: New Insights From Structural Studies on the Complexes of A- and B-Reactive Saccharides with Basic Winged Bean Agglutinin Proteins V. 68 762 2007.
ISSN: ISSN 0887-3585
PubMed: 17510954
DOI: 10.1002/PROT.21428