Calcium in PDB 2e51: Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Disaccharide

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with A Blood Group Disaccharide, PDB code: 2e51 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)	30.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.665, 91.112, 73.617, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.8

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with A 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 A Blood Group Disaccharide (pdb code 2e51). 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 Disaccharide, PDB code: 2e51:
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 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 A Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:31.9 occ:1.00 OD2 A:ASP131 2.4 35.5 1.0 O A:HOH632 2.4 21.6 1.0 O A:PHE126 2.4 34.8 1.0 OD1 A:ASN128 2.4 43.0 1.0 OD2 A:ASP124 2.6 27.5 1.0 OD1 A:ASP124 2.6 32.4 1.0 CG A:ASP124 2.9 29.2 1.0 CG A:ASP131 3.5 35.2 1.0 CG A:ASN128 3.5 42.5 1.0 C A:PHE126 3.6 34.9 1.0 N A:ASN128 4.0 36.4 1.0 OD1 A:ASP131 4.0 33.2 1.0 CB A:ASN128 4.2 39.2 1.0 MN A:MN300 4.3 46.1 1.0 CA A:GLY105 4.4 28.4 1.0 CZ A:PHE107 4.4 22.6 1.0 CA A:PHE126 4.4 33.2 1.0 N A:PHE126 4.4 31.7 1.0 CB A:ASP124 4.4 28.0 1.0 CD2 A:PHE126 4.5 34.5 1.0 CB A:PHE126 4.5 35.7 1.0 NE1 A:TRP130 4.5 40.0 1.0 N A:ARG127 4.6 35.1 1.0 ND2 A:ASN128 4.6 40.6 1.0 OD2 A:ASP87 4.6 31.5 1.0 CA A:ARG127 4.7 37.1 1.0 O A:GLY105 4.7 30.0 1.0 CB A:ASP131 4.7 36.6 1.0 CA A:ASN128 4.7 37.5 1.0 O A:ASP87 4.7 33.8 1.0 C A:ARG127 4.8 35.5 1.0 CE1 A:PHE107 4.8 26.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with A 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 A Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1303 b:27.9 occ:1.00 OD2 B:ASP131 2.3 33.3 1.0 O B:PHE126 2.3 27.9 1.0 OD1 B:ASN128 2.4 34.8 1.0 O B:HOH1369 2.4 32.5 1.0 OD2 B:ASP124 2.4 28.5 1.0 O B:HOH1328 2.4 16.3 1.0 OD1 B:ASP124 2.5 28.2 1.0 CG B:ASP124 2.8 27.7 1.0 CG B:ASP131 3.4 31.8 1.0 CG B:ASN128 3.5 34.8 1.0 C B:PHE126 3.5 30.1 1.0 OD1 B:ASP131 4.0 34.6 1.0 N B:ASN128 4.0 34.6 1.0 CB B:ASN128 4.1 34.1 1.0 MN B:MN1300 4.3 34.5 1.0 CB B:ASP124 4.3 27.3 1.0 CA B:PHE126 4.3 29.2 1.0 N B:PHE126 4.3 29.6 1.0 O B:HOH1331 4.4 19.7 1.0 CB B:PHE126 4.4 30.2 1.0 CZ B:PHE107 4.4 21.6 1.0 N B:ARG127 4.5 31.9 1.0 CD2 B:PHE126 4.5 28.8 1.0 OD2 B:ASP87 4.5 30.1 1.0 CA B:GLY105 4.5 29.1 1.0 NE1 B:TRP130 4.6 32.7 1.0 ND2 B:ASN128 4.6 34.2 1.0 CB B:ASP131 4.6 31.4 1.0 CA B:ARG127 4.6 33.9 1.0 O B:ASP87 4.7 32.7 1.0 CA B:ASN128 4.7 34.6 1.0 O B:GLY105 4.7 27.9 1.0 C B:ARG127 4.7 34.1 1.0 CE1 B:PHE107 4.8 23.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with A 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 A Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2303 b:35.2 occ:1.00 OD1 C:ASN128 2.3 37.9 1.0 O C:HOH2327 2.3 17.9 1.0 O C:HOH2322 2.4 32.5 1.0 OD2 C:ASP131 2.4 42.4 1.0 OD2 C:ASP124 2.5 39.8 1.0 O C:PHE126 2.5 34.5 1.0 OD1 C:ASP124 2.6 38.2 1.0 CG C:ASP124 2.9 35.8 1.0 CG C:ASN128 3.3 37.6 1.0 CG C:ASP131 3.6 41.9 1.0 C C:PHE126 3.7 35.6 1.0 N C:ASN128 3.9 36.1 1.0 CB C:ASN128 4.0 37.0 1.0 O C:HOH2326 4.1 22.8 1.0 MN C:MN2300 4.2 37.4 1.0 NE1 C:TRP130 4.4 47.5 1.0 ND2 C:ASN128 4.4 37.8 1.0 CB C:ASP124 4.4 33.6 1.0 CA C:GLY105 4.4 32.4 1.0 OD1 C:ASP131 4.4 45.3 1.0 CZ C:PHE107 4.4 30.2 1.0 CA C:PHE126 4.5 34.3 1.0 CB C:ASP131 4.6 40.5 1.0 N C:PHE126 4.6 32.7 1.0 CA C:ASN128 4.6 36.7 1.0 O C:GLY105 4.6 32.8 1.0 CB C:PHE126 4.6 36.6 1.0 N C:ARG127 4.6 36.2 1.0 CA C:ARG127 4.7 35.7 1.0 C C:ARG127 4.7 36.5 1.0 CD2 C:PHE126 4.7 40.0 1.0 OD2 C:ASP87 4.7 41.0 1.0 CE1 C:PHE107 4.9 30.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with A 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 A Blood Group Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3303 b:29.4 occ:1.00 OD2 D:ASP131 2.3 30.9 1.0 OD2 D:ASP124 2.3 28.2 1.0 O D:PHE126 2.4 32.0 1.0 OD1 D:ASN128 2.4 32.3 1.0 O D:HOH3326 2.5 23.0 1.0 O D:HOH3324 2.5 34.3 1.0 OD1 D:ASP124 2.6 29.6 1.0 CG D:ASP124 2.8 28.2 1.0 CG D:ASP131 3.5 34.0 1.0 CG D:ASN128 3.6 32.5 1.0 C D:PHE126 3.6 32.5 1.0 N D:ASN128 4.0 32.7 1.0 OD1 D:ASP131 4.2 37.2 1.0 CB D:ASN128 4.2 32.9 1.0 CB D:ASP124 4.3 29.3 1.0 MN D:MN3300 4.3 42.1 1.0 O D:HOH3327 4.3 22.5 1.0 CZ D:PHE107 4.3 32.7 1.0 CA D:PHE126 4.5 29.7 1.0 N D:PHE126 4.5 29.8 1.0 CA D:GLY105 4.5 30.1 1.0 O D:GLY105 4.6 28.2 1.0 CB D:PHE126 4.6 29.6 1.0 N D:ARG127 4.6 31.8 1.0 CD2 D:PHE126 4.6 28.0 1.0 CB D:ASP131 4.6 33.5 1.0 ND2 D:ASN128 4.6 32.4 1.0 NE1 D:TRP130 4.7 34.3 1.0 CA D:ARG127 4.7 31.3 1.0 CE1 D:PHE107 4.7 31.6 1.0 O D:ASP87 4.8 36.5 1.0 CA D:ASN128 4.8 34.1 1.0 OD2 D:ASP87 4.8 42.7 1.0 C D:ARG127 4.8 31.8 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