Calcium in PDB 2e7q: Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Trisaccharide

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group Trisaccharide, PDB code: 2e7q 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)	29.74 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.410, 90.545, 73.324, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.8

The structure of Crystal Structure of Basic Winged Bean Lectin in Complex with B 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 B Blood Group Trisaccharide (pdb code 2e7q). 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 Trisaccharide, PDB code: 2e7q:
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 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 B Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:26.1 occ:1.00 OD2 A:ASP131 2.3 35.3 1.0 O A:PHE126 2.5 26.0 1.0 OD1 A:ASP124 2.5 21.4 1.0 OD1 A:ASN128 2.6 35.6 1.0 OD2 A:ASP124 2.7 21.8 1.0 O A:HOH631 2.7 18.9 1.0 CG A:ASP124 2.9 20.7 1.0 C A:PHE126 3.5 26.7 1.0 CG A:ASP131 3.6 35.1 1.0 CG A:ASN128 3.7 34.5 1.0 N A:ASN128 4.0 30.8 1.0 CD2 A:PHE126 4.0 23.3 1.0 CB A:PHE126 4.2 24.0 1.0 CB A:ASN128 4.2 33.7 1.0 OD1 A:ASP131 4.2 36.3 1.0 CA A:PHE126 4.3 25.1 1.0 OD2 A:ASP87 4.3 27.3 1.0 N A:PHE126 4.4 25.3 1.0 CA A:GLY105 4.4 26.4 1.0 CB A:ASP124 4.4 20.7 1.0 N A:ARG127 4.4 27.4 1.0 CA A:ARG127 4.6 29.1 1.0 CZ A:PHE107 4.6 14.0 1.0 CG A:PHE126 4.6 24.2 1.0 O A:ASP87 4.6 26.4 1.0 CB A:ASP131 4.6 32.0 1.0 C A:ARG127 4.7 29.4 1.0 O A:HOH632 4.7 33.2 1.0 MN A:MN300 4.7 29.3 1.0 CA A:ASN128 4.7 32.0 1.0 ND2 A:ASN128 4.8 36.1 1.0 NE1 A:TRP130 4.8 34.9 1.0 O A:GLY105 4.8 27.3 1.0 CE1 A:PHE107 5.0 15.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with B Blood Group 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 B Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1303 b:19.3 occ:1.00 OD1 B:ASN128 2.2 31.4 1.0 O B:PHE126 2.5 23.5 1.0 OD2 B:ASP131 2.5 23.3 1.0 O B:HOH1328 2.6 6.5 1.0 OD1 B:ASP124 2.6 22.6 1.0 OD2 B:ASP124 2.8 22.2 1.0 CG B:ASP124 3.1 20.7 1.0 CG B:ASN128 3.3 28.5 1.0 C B:PHE126 3.6 24.2 1.0 CG B:ASP131 3.7 20.6 1.0 N B:ASN128 3.9 25.0 1.0 CB B:ASN128 3.9 26.6 1.0 OD2 B:ASP87 4.1 31.6 1.0 CD2 B:PHE126 4.3 24.3 1.0 CA B:GLY105 4.3 24.4 1.0 OD1 B:ASP131 4.4 23.5 1.0 CA B:PHE126 4.4 23.4 1.0 ND2 B:ASN128 4.5 29.7 1.0 CB B:PHE126 4.5 23.5 1.0 CA B:ASN128 4.5 25.3 1.0 N B:PHE126 4.5 22.4 1.0 N B:ARG127 4.6 25.1 1.0 CB B:ASP124 4.6 18.1 1.0 C B:ARG127 4.6 23.6 1.0 CZ B:PHE107 4.6 19.4 1.0 CA B:ARG127 4.6 23.6 1.0 NE1 B:TRP130 4.6 21.2 1.0 MN B:MN1300 4.7 27.1 1.0 O B:GLY105 4.7 25.2 1.0 O B:HOH1329 4.7 6.9 1.0 CB B:ASP131 4.8 18.6 1.0 O B:ASP87 4.8 24.1 1.0 CE1 B:PHE107 4.9 20.6 1.0 CG B:PHE126 4.9 24.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with B 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 B Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2303 b:22.6 occ:1.00 OD1 C:ASN128 2.4 34.8 1.0 OD2 C:ASP131 2.4 34.0 1.0 O C:HOH2326 2.6 24.4 1.0 O C:HOH2325 2.6 32.4 1.0 O C:PHE126 2.7 31.7 1.0 OD2 C:ASP124 2.7 25.7 1.0 OD1 C:ASP124 2.8 26.4 1.0 CG C:ASP124 3.1 26.7 1.0 CG C:ASP131 3.4 35.2 1.0 CG C:ASN128 3.5 33.6 1.0 C C:PHE126 3.8 32.1 1.0 OD1 C:ASP131 3.8 35.7 1.0 N C:ASN128 4.0 30.8 1.0 CB C:ASN128 4.0 32.2 1.0 NE1 C:TRP130 4.2 38.3 1.0 O C:HOH2327 4.2 23.4 1.0 CZ C:PHE107 4.3 23.9 1.0 CA C:GLY105 4.4 28.0 1.0 CB C:PHE126 4.5 34.6 1.0 CA C:PHE126 4.6 32.0 1.0 CB C:ASP124 4.6 27.1 1.0 O C:GLY105 4.6 29.9 1.0 MN C:MN2300 4.6 38.5 1.0 ND2 C:ASN128 4.6 37.2 1.0 CA C:ASN128 4.6 31.0 1.0 CB C:ASP131 4.6 34.1 1.0 N C:PHE126 4.6 31.4 1.0 OD2 C:ASP87 4.7 29.2 1.0 N C:ARG127 4.8 32.2 1.0 CD2 C:PHE126 4.8 38.2 1.0 CE2 C:TRP130 4.8 37.5 1.0 C C:ARG127 4.8 31.0 1.0 CA C:ARG127 4.9 31.6 1.0 O C:ASP87 4.9 25.2 1.0 CZ2 C:TRP130 4.9 37.2 1.0 CE2 C:PHE107 5.0 23.0 1.0 CE1 C:PHE107 5.0 25.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Basic Winged Bean Lectin in Complex with B 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 B Blood Group Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3303 b:21.5 occ:1.00 O D:HOH3320 2.4 38.5 1.0 O D:PHE126 2.4 26.9 1.0 OD2 D:ASP131 2.4 31.2 1.0 OD1 D:ASN128 2.4 25.7 1.0 OD1 D:ASP124 2.5 30.3 1.0 O D:HOH3321 2.6 10.4 1.0 OD2 D:ASP124 2.7 30.7 1.0 CG D:ASP124 2.9 30.7 1.0 CG D:ASN128 3.5 26.4 1.0 C D:PHE126 3.5 25.9 1.0 CG D:ASP131 3.5 33.0 1.0 OD1 D:ASP131 4.0 34.6 1.0 N D:ASN128 4.1 27.4 1.0 O D:HOH3338 4.3 22.3 1.0 CA D:PHE126 4.3 25.5 1.0 CB D:PHE126 4.3 25.0 1.0 N D:PHE126 4.3 24.9 1.0 ND2 D:ASN128 4.3 25.7 1.0 CB D:ASP124 4.4 29.1 1.0 CB D:ASN128 4.4 26.4 1.0 MN D:MN3300 4.5 42.5 1.0 CZ D:PHE107 4.5 20.2 1.0 N D:ARG127 4.5 26.2 1.0 CA D:ARG127 4.5 25.1 1.0 CA D:GLY105 4.6 27.5 1.0 C D:ARG127 4.7 25.5 1.0 CB D:ASP131 4.7 30.0 1.0 O D:GLY105 4.7 27.2 1.0 CD2 D:PHE126 4.8 24.4 1.0 OD2 D:ASP87 4.8 27.3 1.0 O D:ASP87 4.8 27.6 1.0 NE1 D:TRP130 4.8 26.7 1.0 CA D:ASN128 4.9 27.4 1.0 CE1 D:PHE107 4.9 20.2 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