Calcium in PDB 5t54: Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen

The structure of Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen, PDB code: 5t54 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)	38.81 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.829, 44.820, 65.771, 90.00, 100.05, 90.00
R / Rfree (%)	15 / 17.7

The binding sites of Calcium atom in the Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen (pdb code 5t54). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen, PDB code: 5t54:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:8.5 occ:1.00 OE2 A:GLU118 2.2 10.4 1.0 OD2 A:ASP120 2.2 9.8 1.0 O A:HOH447 2.3 12.1 1.0 O A:HOH417 2.3 11.8 1.0 OE1 A:GLU129 2.3 12.9 1.0 NE2 A:HIS134 2.4 11.0 1.0 CD A:GLU129 3.3 12.9 1.0 CD A:GLU118 3.3 10.2 1.0 CG A:ASP120 3.3 9.4 1.0 CD2 A:HIS134 3.3 10.6 1.0 CE1 A:HIS134 3.4 11.0 1.0 OE1 A:GLU118 3.6 10.3 1.0 O A:HOH463 3.7 9.1 1.0 CB A:ASP120 3.7 9.1 1.0 OE2 A:GLU129 3.8 12.4 1.0 CB A:GLU129 4.1 14.2 1.0 CA A:CA302 4.1 9.2 1.0 CG A:GLU129 4.3 13.5 1.0 OG A:SER144 4.3 9.9 1.0 O A:ILE142 4.3 11.6 1.0 OD1 A:ASP120 4.4 9.3 1.0 CG A:HIS134 4.5 10.4 1.0 ND1 A:HIS134 4.5 11.2 1.0 CG A:GLU118 4.6 9.3 1.0 O A:HOH492 4.6 12.5 1.0 NE1 A:TRP127 4.9 12.3 1.0

Calcium binding site 2 out of 4 in the Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:9.2 occ:1.00 OD1 A:ASN124 2.3 10.4 1.0 O A:TRP122 2.4 10.5 1.0 OE2 A:GLU129 2.4 12.4 1.0 OD2 A:ASP120 2.4 9.8 1.0 O A:HOH441 2.4 9.0 1.0 O A:HOH463 2.4 9.1 1.0 OD1 A:ASP120 2.6 9.3 1.0 CG A:ASP120 2.8 9.4 1.0 CD A:GLU129 3.3 12.9 1.0 OE1 A:GLU129 3.4 12.9 1.0 CG A:ASN124 3.4 11.4 1.0 C A:TRP122 3.6 11.3 1.0 N A:ASN124 4.0 12.0 1.0 CB A:ASN124 4.0 12.0 1.0 CA A:CA301 4.1 8.5 1.0 CB A:ASP120 4.3 9.1 1.0 CA A:TRP122 4.4 10.7 1.0 N A:TRP122 4.5 10.0 1.0 ND2 A:ASN124 4.5 11.6 1.0 N A:VAL123 4.6 11.8 1.0 CB A:TRP122 4.6 10.7 1.0 CA A:VAL123 4.6 12.4 1.0 C A:VAL123 4.6 12.5 1.0 O A:HOH447 4.7 12.1 1.0 O A:GLY96 4.7 9.1 1.0 CA A:ASN124 4.7 12.7 1.0 OD1 A:ASP78 4.7 9.9 1.0 CE1 A:HIS134 4.7 11.0 1.0 CA A:GLY96 4.7 9.7 1.0 CD1 A:TRP122 4.7 11.0 1.0 CZ2 A:TRP127 4.7 11.6 1.0 CG A:GLU129 4.8 13.5 1.0 O A:ASP78 4.8 9.4 1.0 NE1 A:TRP127 4.8 12.3 1.0 NE2 A:HIS134 4.9 11.0 1.0

Calcium binding site 3 out of 4 in the Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:9.8 occ:1.00 OE1 B:GLU129 2.2 12.8 1.0 OE2 B:GLU118 2.2 9.5 1.0 O B:HOH456 2.2 11.6 1.0 OD2 B:ASP120 2.3 11.0 1.0 NE2 B:HIS134 2.4 12.2 1.0 O B:HOH416 2.4 14.7 1.0 CG B:ASP120 3.2 11.4 1.0 CD B:GLU118 3.3 9.3 1.0 CD2 B:HIS134 3.3 13.0 1.0 CD B:GLU129 3.3 14.1 1.0 CE1 B:HIS134 3.4 12.9 1.0 OE1 B:GLU118 3.6 9.0 1.0 CB B:ASP120 3.7 10.9 1.0 O B:HOH436 3.8 11.1 1.0 OE2 B:GLU129 3.9 13.8 1.0 CA B:CA302 4.1 11.7 1.0 CB B:GLU129 4.2 16.6 1.0 OD1 B:ASP120 4.3 12.2 1.0 OG B:SER144 4.3 10.8 1.0 O B:ILE142 4.3 10.2 1.0 CG B:GLU129 4.4 15.1 1.0 CG B:HIS134 4.5 12.9 1.0 ND1 B:HIS134 4.5 13.3 1.0 CG B:GLU118 4.6 8.4 1.0 O B:HOH470 4.7 17.6 1.0 NE1 B:TRP127 4.9 12.8 1.0

Calcium binding site 4 out of 4 in the Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lectin From Bauhinia Forficata in Complex with Blood Group A Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:11.7 occ:1.00 OD2 B:ASP120 2.4 11.0 1.0 OD1 B:ASN124 2.4 13.3 1.0 O B:TRP122 2.4 12.5 1.0 O B:HOH465 2.4 11.5 1.0 O B:HOH436 2.4 11.1 1.0 OE2 B:GLU129 2.5 13.8 1.0 OD1 B:ASP120 2.5 12.2 1.0 CG B:ASP120 2.8 11.4 1.0 CD B:GLU129 3.3 14.1 1.0 OE1 B:GLU129 3.4 12.8 1.0 CG B:ASN124 3.5 13.7 1.0 C B:TRP122 3.6 14.0 1.0 CB B:ASN124 4.1 13.9 1.0 CA B:CA301 4.1 9.8 1.0 N B:ASN124 4.1 15.7 1.0 CB B:ASP120 4.3 10.9 1.0 N B:TRP122 4.4 13.1 1.0 CA B:TRP122 4.4 14.0 1.0 N B:VAL123 4.5 15.7 1.0 CB B:TRP122 4.6 14.0 1.0 ND2 B:ASN124 4.6 13.8 1.0 O B:HOH456 4.6 11.6 1.0 O B:GLY96 4.7 9.7 1.0 CA B:VAL123 4.7 16.6 1.0 OD1 B:ASP78 4.7 12.4 1.0 CE1 B:HIS134 4.7 12.9 1.0 C B:VAL123 4.7 16.6 1.0 CD1 B:TRP122 4.7 15.4 1.0 CA B:ASN124 4.7 15.1 1.0 O B:ASP78 4.7 11.2 1.0 CG B:GLU129 4.8 15.1 1.0 CA B:GLY96 4.8 11.0 1.0 NE2 B:HIS134 4.8 12.2 1.0 CZ2 B:TRP127 4.8 13.1 1.0 NE1 B:TRP127 4.9 12.8 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