Calcium in PDB 5t50: Ligand-Free Lectin From Bauhinia Forficata

The structure of Ligand-Free Lectin From Bauhinia Forficata, PDB code: 5t50 was solved by J.Lubkowski, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.991, 58.004, 190.546, 90.00, 90.00, 90.00
R / Rfree (%)	11.6 / 16.1

The binding sites of Calcium atom in the Ligand-Free Lectin From Bauhinia Forficata (pdb code 5t50). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ligand-Free Lectin From Bauhinia Forficata, PDB code: 5t50:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ligand-Free Lectin From Bauhinia Forficata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ligand-Free Lectin From Bauhinia Forficata within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:11.3 occ:1.00 OD2 A:ASP120 2.2 11.5 1.0 OE2 A:GLU118 2.2 11.1 1.0 OE1 A:GLU129 2.3 12.5 1.0 O A:HOH429 2.3 14.2 1.0 O A:HOH458 2.3 12.2 1.0 NE2 A:HIS134 2.5 12.7 1.0 CD A:GLU129 3.3 11.7 1.0 CD A:GLU118 3.3 12.1 1.0 CG A:ASP120 3.3 11.0 1.0 CD2 A:HIS134 3.3 13.3 1.0 CE1 A:HIS134 3.5 12.6 1.0 OE1 A:GLU118 3.7 13.6 1.0 O A:HOH455 3.7 11.5 1.0 CB A:ASP120 3.8 9.7 1.0 OE2 A:GLU129 3.9 11.2 1.0 CB A:GLU129 4.1 18.6 1.0 CA A:CA302 4.1 10.6 1.0 OG A:SER144 4.3 12.5 1.0 O A:ILE142 4.3 11.6 1.0 CG A:GLU129 4.3 15.2 1.0 OD1 A:ASP120 4.4 11.4 1.0 CG A:HIS134 4.5 10.4 1.0 ND1 A:HIS134 4.5 12.2 1.0 O A:HOH480 4.6 17.4 1.0 CG A:GLU118 4.6 11.9 1.0 NE1 A:TRP127 4.9 15.8 1.0

Calcium binding site 2 out of 4 in the Ligand-Free Lectin From Bauhinia Forficata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ligand-Free Lectin From Bauhinia Forficata within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:10.6 occ:1.00 O A:TRP122 2.3 10.8 1.0 OD1 A:ASN124 2.3 11.4 1.0 O A:HOH462 2.4 10.2 1.0 O A:HOH455 2.4 11.5 1.0 OD2 A:ASP120 2.4 11.5 1.0 OE2 A:GLU129 2.5 11.2 1.0 OD1 A:ASP120 2.5 11.4 1.0 CG A:ASP120 2.8 11.0 1.0 CD A:GLU129 3.3 11.7 1.0 OE1 A:GLU129 3.5 12.5 1.0 CG A:ASN124 3.5 10.7 1.0 C A:TRP122 3.5 10.5 1.0 N A:ASN124 4.0 12.2 1.0 CB A:ASN124 4.1 10.5 1.0 CA A:CA301 4.1 11.3 1.0 CB A:ASP120 4.3 9.7 1.0 CA A:TRP122 4.4 11.0 1.0 N A:TRP122 4.5 10.0 1.0 N A:VAL123 4.5 10.9 1.0 CB A:TRP122 4.5 11.9 1.0 CA A:VAL123 4.6 12.5 1.0 CD1 A:TRP122 4.6 12.0 1.0 ND2 A:ASN124 4.6 11.0 1.0 C A:VAL123 4.6 11.9 1.0 O A:HOH458 4.6 12.2 1.0 OD1 A:ASP78 4.7 11.5 1.0 CA A:ASN124 4.7 11.2 1.0 CA A:GLY96 4.7 11.8 1.0 O A:GLY96 4.7 11.6 1.0 O A:ASP78 4.8 12.6 1.0 CE1 A:HIS134 4.8 12.6 1.0 CG A:GLU129 4.8 15.2 1.0 CZ2 A:TRP127 4.8 14.3 1.0 NE2 A:HIS134 4.9 12.7 1.0 NE1 A:TRP127 5.0 15.8 1.0

Calcium binding site 3 out of 4 in the Ligand-Free Lectin From Bauhinia Forficata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ligand-Free Lectin From Bauhinia Forficata within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:13.0 occ:1.00 OD2 B:ASP120 2.3 11.8 1.0 OE2 B:GLU118 2.3 12.6 1.0 O B:HOH451 2.3 15.8 1.0 O B:HOH458 2.3 14.2 1.0 OE1 B:GLU129 2.3 13.3 1.0 NE2 B:HIS134 2.5 12.2 1.0 CD B:GLU129 3.3 13.5 1.0 CD B:GLU118 3.3 11.5 1.0 CG B:ASP120 3.3 12.1 1.0 CD2 B:HIS134 3.4 12.7 1.0 CE1 B:HIS134 3.5 13.8 1.0 OE1 B:GLU118 3.7 14.1 1.0 O B:HOH445 3.7 14.0 1.0 CB B:ASP120 3.8 11.8 1.0 OE2 B:GLU129 3.9 14.6 1.0 CB B:GLU129 4.0 17.7 1.0 CA B:CA302 4.1 12.9 1.0 CG B:GLU129 4.2 16.3 1.0 O B:ILE142 4.3 13.9 1.0 OG B:SER144 4.4 13.8 1.0 OD1 B:ASP120 4.4 12.6 1.0 CG B:HIS134 4.6 13.0 1.0 ND1 B:HIS134 4.6 14.4 1.0 O B:HOH484 4.7 16.5 1.0 CG B:GLU118 4.7 11.1 1.0 NE1 B:TRP127 4.9 15.5 1.0

Calcium binding site 4 out of 4 in the Ligand-Free Lectin From Bauhinia Forficata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ligand-Free Lectin From Bauhinia Forficata within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:12.9 occ:1.00 OD1 B:ASN124 2.3 13.8 1.0 O B:TRP122 2.4 13.1 1.0 O B:HOH445 2.4 14.0 1.0 O B:HOH441 2.4 12.6 1.0 OD2 B:ASP120 2.4 11.8 1.0 OE2 B:GLU129 2.4 14.6 1.0 OD1 B:ASP120 2.5 12.6 1.0 CG B:ASP120 2.8 12.1 1.0 CD B:GLU129 3.3 13.5 1.0 OE1 B:GLU129 3.4 13.3 1.0 CG B:ASN124 3.5 14.5 1.0 C B:TRP122 3.6 13.8 1.0 N B:ASN124 4.0 13.7 1.0 CB B:ASN124 4.1 14.4 1.0 CA B:CA301 4.1 13.0 1.0 CB B:ASP120 4.3 11.8 1.0 CA B:TRP122 4.4 13.2 1.0 N B:TRP122 4.4 13.2 1.0 N B:VAL123 4.5 15.7 1.0 CD1 B:TRP122 4.6 16.1 1.0 ND2 B:ASN124 4.6 14.1 1.0 CA B:VAL123 4.6 15.9 1.0 CB B:TRP122 4.6 13.5 1.0 C B:VAL123 4.6 13.0 1.0 O B:GLY96 4.7 13.3 1.0 CA B:ASN124 4.7 15.1 1.0 OD1 B:ASP78 4.7 14.0 1.0 O B:HOH458 4.7 14.2 1.0 CE1 B:HIS134 4.7 13.8 1.0 CA B:GLY96 4.7 13.1 1.0 CG B:GLU129 4.7 16.3 1.0 O B:ASP78 4.8 14.1 1.0 CZ2 B:TRP127 4.8 16.7 1.0 NE2 B:HIS134 4.9 12.2 1.0 NE1 B:TRP127 5.0 15.5 1.0

J.Lubkowski, S.V.Durbin, M.C.Silva, D.Farnsworth, J.C.Gildersleeve, M.L.Oliva, A.Wlodawer. Structural Analysis and Unique Molecular Recognition Properties of A Bauhinia Forficata Lectin That Inhibits Cancer Cell Growth. Febs J. V. 284 429 2017.
ISSN: ISSN 1742-4658
PubMed: 27973758
DOI: 10.1111/FEBS.13989