Calcium in PDB 1wbl: Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose

The structure of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose, PDB code: 1wbl was solved by M.M.Prabu, R.Sankaranarayanan, K.D.Puri, V.Sharma, 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)	100.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.585, 91.908, 73.283, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 25.9

The structure of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose (pdb code 1wbl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose, PDB code: 1wbl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:13.8 occ:1.00 O A:HOH607 2.4 5.1 1.0 OD2 A:ASP131 2.4 2.5 1.0 O A:PHE126 2.5 18.6 1.0 OD1 A:ASN128 2.5 15.2 1.0 OD1 A:ASP124 2.6 13.7 1.0 OD2 A:ASP124 2.6 23.0 1.0 O A:HOH606 2.7 28.0 1.0 CG A:ASP124 2.9 24.2 1.0 CG A:ASP131 3.6 9.3 1.0 CG A:ASN128 3.6 14.2 1.0 C A:PHE126 3.7 13.6 1.0 N A:ASN128 4.0 10.0 1.0 O A:HOH605 4.0 19.2 1.0 OD1 A:ASP131 4.1 16.9 1.0 CB A:ASN128 4.2 6.8 1.0 CB A:ASP124 4.4 18.5 1.0 NE1 A:TRP130 4.4 13.6 1.0 CZ A:PHE107 4.5 2.2 1.0 MN A:MN300 4.5 32.0 1.0 CA A:PHE126 4.6 11.3 1.0 O A:GLY105 4.6 14.7 1.0 N A:ARG127 4.6 10.0 1.0 CA A:GLY105 4.6 4.4 1.0 N A:PHE126 4.6 15.5 1.0 CA A:ARG127 4.7 8.5 1.0 CA A:ASN128 4.7 8.2 1.0 C A:ARG127 4.7 5.6 1.0 OD2 A:ASP87 4.7 19.9 1.0 CB A:PHE126 4.7 12.4 1.0 CD2 A:PHE126 4.8 19.1 1.0 ND2 A:ASN128 4.8 6.5 1.0 O A:ASP87 4.8 5.2 1.0 CB A:ASP131 4.8 10.0 1.0 CZ2 A:TRP130 4.8 16.6 1.0 CE2 A:TRP130 4.9 15.3 1.0

Calcium binding site 2 out of 4 in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:28.3 occ:1.00 OD1 B:ASN128 2.3 18.4 1.0 O B:PHE126 2.3 7.6 1.0 O B:HOH606 2.5 2.0 1.0 OD2 B:ASP124 2.5 17.0 1.0 OD2 B:ASP131 2.6 24.4 1.0 O B:HOH607 2.6 31.4 1.0 OD1 B:ASP124 2.6 22.5 1.0 CG B:ASP124 2.9 15.0 1.0 CG B:ASN128 3.4 13.6 1.0 C B:PHE126 3.5 9.9 1.0 CG B:ASP131 3.7 16.4 1.0 N B:ASN128 4.0 14.4 1.0 CB B:ASN128 4.0 12.2 1.0 OD2 B:ASP87 4.1 22.1 1.0 CA B:PHE126 4.2 11.7 1.0 CB B:PHE126 4.2 18.1 1.0 N B:PHE126 4.2 12.5 1.0 OD1 B:ASP131 4.4 18.1 1.0 CB B:ASP124 4.4 14.7 1.0 ND2 B:ASN128 4.5 19.0 1.0 CA B:GLY105 4.5 8.6 1.0 CZ B:PHE107 4.5 2.0 1.0 N B:ARG127 4.5 4.5 1.0 O B:HOH605 4.6 2.7 1.0 CD2 B:PHE126 4.6 14.3 1.0 MN B:MN300 4.6 13.1 1.0 CA B:ASN128 4.6 10.4 1.0 CB B:ASP131 4.7 10.8 1.0 CA B:ARG127 4.7 7.6 1.0 O B:ASP87 4.7 8.7 1.0 C B:ARG127 4.7 10.6 1.0 NE1 B:TRP130 4.8 14.7 1.0 CE1 B:PHE107 4.8 2.0 1.0 O B:GLY105 4.9 5.4 1.0 CG B:PHE126 4.9 17.4 1.0

Calcium binding site 3 out of 4 in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:22.7 occ:1.00 OD1 C:ASN128 2.3 28.4 1.0 O C:HOH505 2.4 2.3 1.0 OD2 C:ASP124 2.5 38.8 1.0 O C:PHE126 2.5 14.6 1.0 OD2 C:ASP131 2.6 14.4 1.0 O C:HOH506 2.7 21.0 1.0 OD1 C:ASP124 3.0 34.5 1.0 CG C:ASP124 3.0 22.8 1.0 CG C:ASN128 3.3 29.8 1.0 CG C:ASP131 3.4 4.5 1.0 N C:ASN128 3.7 22.9 1.0 C C:PHE126 3.7 18.7 1.0 CB C:ASN128 3.8 30.3 1.0 OD1 C:ASP131 4.0 3.1 1.0 O C:HOH504 4.2 25.3 1.0 NE1 C:TRP130 4.2 24.0 1.0 MN C:MN300 4.3 29.8 1.0 CB C:ASP131 4.4 7.3 1.0 CA C:ASN128 4.4 17.1 1.0 ND2 C:ASN128 4.4 30.1 1.0 CB C:ASP124 4.5 18.7 1.0 CA C:ARG127 4.6 26.0 1.0 C C:ARG127 4.6 27.4 1.0 N C:ARG127 4.6 25.3 1.0 CA C:GLY105 4.6 14.5 1.0 CZ C:PHE107 4.7 13.6 1.0 CE2 C:TRP130 4.7 18.8 1.0 CA C:PHE126 4.7 15.0 1.0 CZ2 C:TRP130 4.7 17.4 1.0 O C:GLY105 4.7 17.6 1.0 CB C:PHE126 4.8 21.5 1.0 N C:PHE126 4.8 14.3 1.0 OD2 C:ASP87 4.9 31.8 1.0 CD2 C:PHE126 4.9 23.4 1.0

Calcium binding site 4 out of 4 in the Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Winged Bean Lectin Complexed with Methyl-Alpha-D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:28.3 occ:1.00 O D:PHE126 2.3 14.7 1.0 OD1 D:ASN128 2.4 10.2 1.0 OD1 D:ASP124 2.5 30.8 1.0 OD2 D:ASP124 2.6 31.7 1.0 OD2 D:ASP131 2.6 4.0 1.0 O D:HOH606 2.7 9.7 1.0 CG D:ASP124 2.9 29.3 1.0 CG D:ASN128 3.4 10.4 1.0 C D:PHE126 3.5 13.6 1.0 CG D:ASP131 3.9 8.8 1.0 N D:ASN128 3.9 25.0 1.0 CB D:ASN128 4.0 15.9 1.0 CA D:PHE126 4.3 8.7 1.0 CB D:ASP124 4.3 16.9 1.0 CB D:PHE126 4.3 5.9 1.0 N D:PHE126 4.3 9.0 1.0 CA D:GLY105 4.4 19.2 1.0 ND2 D:ASN128 4.4 10.1 1.0 O D:HOH604 4.5 15.5 1.0 N D:ARG127 4.5 19.7 1.0 CZ D:PHE107 4.5 11.1 1.0 O D:ASP87 4.6 8.8 1.0 OD2 D:ASP87 4.6 28.8 1.0 CA D:ASN128 4.6 23.8 1.0 MN D:MN300 4.6 34.6 1.0 NE1 D:TRP130 4.6 6.1 1.0 OD1 D:ASP131 4.6 11.8 1.0 CA D:ARG127 4.6 15.5 1.0 CD2 D:PHE126 4.7 14.5 1.0 O D:GLY105 4.7 17.9 1.0 C D:ARG127 4.7 18.9 1.0 CE1 D:PHE107 4.8 9.4 1.0 CB D:ASP131 4.9 9.5 1.0 CZ2 D:TRP130 5.0 4.9 1.0

M.M.Prabu, R.Sankaranarayanan, K.D.Puri, V.Sharma, A.Surolia, M.Vijayan, K.Suguna. Carbohydrate Specificity and Quaternary Association in Basic Winged Bean Lectin: X-Ray Analysis of the Lectin at 2.5 A Resolution. J.Mol.Biol. V. 276 787 1998.
ISSN: ISSN 0022-2836
PubMed: 9500920
DOI: 10.1006/JMBI.1997.1568