Calcium in PDB 2e53: Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide, PDB code: 2e53 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)	29.93 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.367, 91.093, 73.399, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Disaccharide 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 B Blood Group Disaccharide (pdb code 2e53). 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 B Blood Group Disaccharide, PDB code: 2e53:
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 B Blood Group Disaccharide


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:28.9 occ:1.00 O A:HOH1402 2.3 42.3 1.0 O A:PHE126 2.3 31.9 1.0 OD2 A:ASP131 2.4 35.1 1.0 O A:HOH1367 2.4 29.1 1.0 OD1 A:ASP124 2.5 30.5 1.0 OD2 A:ASP124 2.5 28.0 1.0 OD1 A:ASN128 2.8 36.7 1.0 CG A:ASP124 2.8 27.8 1.0 CG A:ASP131 3.5 34.8 1.0 C A:PHE126 3.5 31.5 1.0 CG A:ASN128 3.8 36.9 1.0 N A:ASN128 3.9 33.2 1.0 OD1 A:ASP131 4.0 35.4 1.0 CB A:ASN128 4.1 33.8 1.0 MN A:MN1300 4.3 36.2 1.0 CA A:PHE126 4.3 30.8 1.0 CB A:ASP124 4.3 28.3 1.0 O A:HOH1362 4.4 16.9 1.0 N A:PHE126 4.4 30.4 1.0 CB A:PHE126 4.4 31.9 1.0 CZ A:PHE107 4.5 22.1 1.0 N A:ARG127 4.5 31.5 1.0 CA A:GLY105 4.6 28.8 1.0 NE1 A:TRP130 4.6 37.6 1.0 CB A:ASP131 4.6 34.7 1.0 CA A:ARG127 4.6 32.5 1.0 CD2 A:PHE126 4.6 31.9 1.0 CA A:ASN128 4.7 33.8 1.0 OD2 A:ASP87 4.7 30.1 1.0 C A:ARG127 4.7 31.6 1.0 O A:ASP87 4.7 28.8 1.0 O A:GLY105 4.8 29.0 1.0 CE1 A:PHE107 4.9 25.2 1.0 ND2 A:ASN128 5.0 37.1 1.0

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


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2303 b:25.6 occ:1.00 O B:PHE126 2.3 27.2 1.0 OD2 B:ASP131 2.3 32.1 1.0 O B:HOH2338 2.4 20.2 1.0 O B:HOH2339 2.4 37.0 1.0 OD1 B:ASP124 2.5 26.6 1.0 OD2 B:ASP124 2.5 27.9 1.0 OD1 B:ASN128 2.7 29.9 1.0 CG B:ASP124 2.8 27.8 1.0 C B:PHE126 3.5 28.9 1.0 CG B:ASP131 3.5 31.0 1.0 CG B:ASN128 3.7 32.1 1.0 N B:ASN128 4.0 30.1 1.0 OD1 B:ASP131 4.1 31.6 1.0 CB B:ASN128 4.1 28.9 1.0 MN B:MN2300 4.3 34.6 1.0 CA B:PHE126 4.3 28.5 1.0 CB B:ASP124 4.3 26.3 1.0 N B:PHE126 4.3 28.2 1.0 O B:HOH2341 4.4 13.7 1.0 CB B:PHE126 4.4 29.9 1.0 CZ B:PHE107 4.5 20.4 1.0 CA B:GLY105 4.5 28.4 1.0 N B:ARG127 4.5 29.8 1.0 OD2 B:ASP87 4.5 28.0 1.0 CA B:ARG127 4.6 30.8 1.0 CD2 B:PHE126 4.6 28.1 1.0 CB B:ASP131 4.6 30.2 1.0 NE1 B:TRP130 4.6 34.2 1.0 O B:ASP87 4.7 25.8 1.0 CA B:ASN128 4.7 30.7 1.0 C B:ARG127 4.7 30.5 1.0 O B:GLY105 4.7 26.2 1.0 CE1 B:PHE107 4.9 23.3 1.0 ND2 B:ASN128 4.9 33.2 1.0

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


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3303 b:38.0 occ:1.00 O C:HOH3347 2.3 31.1 1.0 OD2 C:ASP131 2.3 36.2 1.0 OD1 C:ASN128 2.3 34.9 1.0 O C:PHE126 2.5 34.3 1.0 OD2 C:ASP124 2.5 36.5 1.0 O C:HOH3348 2.5 32.3 1.0 OD1 C:ASP124 2.7 36.3 1.0 CG C:ASP124 2.9 34.1 1.0 CG C:ASP131 3.4 36.0 1.0 CG C:ASN128 3.4 34.8 1.0 C C:PHE126 3.7 34.7 1.0 OD1 C:ASP131 3.9 37.2 1.0 N C:ASN128 3.9 33.4 1.0 CB C:ASN128 4.0 34.3 1.0 MN C:MN3300 4.3 43.3 1.0 O C:HOH3349 4.3 31.9 1.0 CZ C:PHE107 4.4 26.4 1.0 CA C:GLY105 4.4 33.3 1.0 CB C:ASP124 4.4 32.0 1.0 NE1 C:TRP130 4.4 39.0 1.0 CA C:PHE126 4.5 34.2 1.0 N C:PHE126 4.5 32.9 1.0 CB C:PHE126 4.5 34.3 1.0 ND2 C:ASN128 4.5 34.4 1.0 O C:GLY105 4.6 33.5 1.0 CB C:ASP131 4.6 35.1 1.0 CA C:ASN128 4.6 33.7 1.0 N C:ARG127 4.6 34.0 1.0 OD2 C:ASP87 4.7 34.9 1.0 CD2 C:PHE126 4.7 34.1 1.0 CA C:ARG127 4.7 33.4 1.0 C C:ARG127 4.8 33.3 1.0 O C:ASP87 4.8 30.8 1.0 CE1 C:PHE107 4.8 27.6 1.0

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


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 B Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4303 b:26.9 occ:1.00 OD2 D:ASP131 2.3 30.6 1.0 OD2 D:ASP124 2.3 29.4 1.0 O D:PHE126 2.4 30.0 1.0 OD1 D:ASP124 2.4 28.5 1.0 OD1 D:ASN128 2.5 30.9 1.0 O D:HOH4350 2.5 19.3 1.0 O D:HOH4349 2.6 30.2 1.0 CG D:ASP124 2.7 27.7 1.0 CG D:ASP131 3.4 32.2 1.0 C D:PHE126 3.6 29.7 1.0 CG D:ASN128 3.6 31.9 1.0 OD1 D:ASP131 4.0 32.0 1.0 N D:ASN128 4.0 30.7 1.0 MN D:MN4300 4.2 39.3 1.0 CB D:ASN128 4.2 31.2 1.0 CB D:ASP124 4.2 28.2 1.0 O D:HOH4351 4.3 29.8 1.0 CZ D:PHE107 4.4 24.7 1.0 CA D:PHE126 4.4 29.1 1.0 N D:PHE126 4.4 30.1 1.0 CB D:PHE126 4.5 29.2 1.0 CB D:ASP131 4.6 32.1 1.0 NE1 D:TRP130 4.6 32.7 1.0 N D:ARG127 4.6 29.3 1.0 CA D:ARG127 4.7 29.5 1.0 CA D:GLY105 4.7 30.3 1.0 ND2 D:ASN128 4.7 31.5 1.0 CD2 D:PHE126 4.8 29.4 1.0 O D:ASP87 4.8 30.3 1.0 O D:GLY105 4.8 29.0 1.0 CA D:ASN128 4.8 31.4 1.0 C D:ARG127 4.8 30.2 1.0 OD2 D:ASP87 4.9 32.0 1.0 CE1 D:PHE107 4.9 26.0 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