Calcium in PDB 5t55: Lectin From Bauhinia Forficata in Complex with Globotetraose

The structure of Lectin From Bauhinia Forficata in Complex with Globotetraose, PDB code: 5t55 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)	39.86 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.681, 88.233, 110.782, 90.00, 90.00, 90.00
R / Rfree (%)	10.5 / 14.7

The structure of Lectin From Bauhinia Forficata in Complex with Globotetraose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Lectin From Bauhinia Forficata in Complex with Globotetraose (pdb code 5t55). 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 Globotetraose, PDB code: 5t55:
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 Globotetraose


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 Globotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:12.0 occ:1.00 O A:HOH470 2.1 14.7 1.0 OD2 A:ASP120 2.1 11.7 1.0 OE1 A:GLU129 2.2 17.5 1.0 OE2 A:GLU118 2.2 12.3 1.0 O A:HOH438 2.2 13.3 1.0 NE2 A:HIS134 2.3 13.8 1.0 CD A:GLU129 3.2 13.0 1.0 CG A:ASP120 3.2 10.1 1.0 CD2 A:HIS134 3.2 13.8 1.0 CD A:GLU118 3.2 11.8 1.0 CE1 A:HIS134 3.3 14.7 1.0 OE1 A:GLU118 3.6 12.3 1.0 CB A:ASP120 3.7 9.9 1.0 O A:HOH462 3.7 12.3 1.0 OE2 A:GLU129 3.7 13.3 1.0 CA A:CA302 4.0 10.7 1.0 CG A:GLU129 4.2 18.1 1.0 OG A:SER144 4.3 12.8 1.0 OD1 A:ASP120 4.3 11.2 1.0 O A:ILE142 4.3 12.0 1.0 ND1 A:HIS134 4.4 14.2 1.0 CG A:HIS134 4.4 12.6 1.0 O A:HOH478 4.5 16.2 1.0 CG A:GLU118 4.5 11.2 1.0 CB A:GLU129 4.7 20.7 1.0

Calcium binding site 2 out of 4 in the Lectin From Bauhinia Forficata in Complex with Globotetraose


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 Globotetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:10.7 occ:1.00 OD1 A:ASN124 2.3 11.8 1.0 O A:TRP122 2.3 12.8 1.0 O A:HOH467 2.4 11.0 1.0 O A:HOH462 2.4 12.3 1.0 OE2 A:GLU129 2.4 13.3 1.0 OD2 A:ASP120 2.4 11.7 1.0 OD1 A:ASP120 2.5 11.2 1.0 CG A:ASP120 2.8 10.1 1.0 CD A:GLU129 3.2 13.0 1.0 OE1 A:GLU129 3.4 17.5 1.0 CG A:ASN124 3.5 11.9 1.0 C A:TRP122 3.6 11.9 1.0 N A:ASN124 4.0 11.3 1.0 CA A:CA301 4.0 12.0 1.0 CB A:ASN124 4.1 12.7 1.0 CB A:ASP120 4.3 9.9 1.0 CA A:TRP122 4.4 11.3 1.0 N A:TRP122 4.4 11.0 1.0 O A:HOH490 4.5 42.2 1.0 O A:HOH438 4.5 13.3 1.0 N A:VAL123 4.5 12.6 1.0 ND2 A:ASN124 4.6 11.7 1.0 CE1 A:HIS134 4.6 14.7 1.0 CG A:GLU129 4.6 18.1 1.0 CA A:VAL123 4.6 13.4 1.0 CB A:TRP122 4.6 11.9 1.0 OD1 A:ASP78 4.7 10.9 1.0 CA A:ASN124 4.7 12.0 1.0 CD1 A:TRP122 4.7 12.8 1.0 O A:GLY96 4.7 10.9 1.0 C A:VAL123 4.7 12.2 1.0 CA A:GLY96 4.8 9.9 1.0 NE2 A:HIS134 4.8 13.8 1.0 O A:ASP78 4.8 11.7 1.0 CZ2 A:TRP127 4.9 13.4 1.0 NE1 A:TRP127 5.0 12.6 1.0

Calcium binding site 3 out of 4 in the Lectin From Bauhinia Forficata in Complex with Globotetraose


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 Globotetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:12.4 occ:1.00 OD2 B:ASP120 2.1 11.4 1.0 OE1 B:GLU129 2.2 18.0 1.0 O B:HOH435 2.2 16.8 1.0 OE2 B:GLU118 2.2 12.8 1.0 O B:HOH425 2.2 13.6 1.0 NE2 B:HIS134 2.3 14.9 1.0 CG B:ASP120 3.2 11.1 1.0 CD B:GLU129 3.2 13.8 1.0 CD2 B:HIS134 3.2 14.8 1.0 CD B:GLU118 3.2 13.1 1.0 CE1 B:HIS134 3.3 15.2 1.0 OE1 B:GLU118 3.6 13.2 1.0 CB B:ASP120 3.6 10.2 1.0 O B:HOH451 3.8 11.7 1.0 OE2 B:GLU129 3.8 13.6 1.0 CA B:CA302 4.0 11.5 1.0 OD1 B:ASP120 4.2 12.3 1.0 OG B:SER144 4.3 13.0 1.0 O B:ILE142 4.3 13.5 1.0 CG B:GLU129 4.3 17.3 1.0 ND1 B:HIS134 4.4 17.1 1.0 CG B:HIS134 4.4 13.9 1.0 O B:HOH464 4.5 18.9 1.0 CG B:GLU118 4.6 10.8 1.0 CB B:GLU129 4.8 22.1 1.0 O B:HOH406 4.9 49.1 1.0

Calcium binding site 4 out of 4 in the Lectin From Bauhinia Forficata in Complex with Globotetraose


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 Globotetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:11.5 occ:1.00 O B:TRP122 2.3 13.3 1.0 OD1 B:ASN124 2.3 12.3 1.0 O B:HOH483 2.4 11.4 1.0 O B:HOH451 2.4 11.7 1.0 OD1 B:ASP120 2.5 12.3 1.0 OD2 B:ASP120 2.5 11.4 1.0 OE2 B:GLU129 2.5 13.6 1.0 CG B:ASP120 2.8 11.1 1.0 CD B:GLU129 3.3 13.8 1.0 OE1 B:GLU129 3.4 18.0 1.0 CG B:ASN124 3.5 11.7 1.0 C B:TRP122 3.5 12.9 1.0 N B:ASN124 4.0 13.5 1.0 CA B:CA301 4.0 12.4 1.0 CB B:ASN124 4.1 12.5 1.0 CB B:ASP120 4.3 10.2 1.0 CA B:TRP122 4.4 12.3 1.0 N B:TRP122 4.4 11.8 1.0 N B:VAL123 4.5 15.0 1.0 O B:HOH425 4.5 13.6 1.0 ND2 B:ASN124 4.6 12.9 1.0 CA B:VAL123 4.6 15.2 1.0 C B:VAL123 4.6 13.4 1.0 CB B:TRP122 4.6 12.2 1.0 CE1 B:HIS134 4.6 15.2 1.0 CG B:GLU129 4.6 17.3 1.0 O B:HOH470 4.7 42.0 1.0 OD1 B:ASP78 4.7 11.4 1.0 O B:GLY96 4.7 11.0 1.0 CA B:ASN124 4.7 14.0 1.0 CD1 B:TRP122 4.7 12.9 1.0 O B:ASP78 4.7 12.4 1.0 CA B:GLY96 4.8 11.0 1.0 NE2 B:HIS134 4.8 14.9 1.0 CZ2 B:TRP127 4.8 13.9 1.0 O B:HOH406 4.9 49.1 1.0 NE1 B:TRP127 4.9 15.1 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