Calcium in PDB 5t5l: Lectin From Bauhinia Forficata in Complex with Tn-Peptide

The structure of Lectin From Bauhinia Forficata in Complex with Tn-Peptide, PDB code: 5t5l 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)	30.30 / 1.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.865, 88.502, 110.783, 90.00, 90.00, 90.00
R / Rfree (%)	10.7 / 13

The structure of Lectin From Bauhinia Forficata in Complex with Tn-Peptide 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 Tn-Peptide (pdb code 5t5l). 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 Tn-Peptide, PDB code: 5t5l:
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 Tn-Peptide


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 Tn-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:12.3 occ:1.00 OD2 A:ASP120 2.1 13.7 1.0 O A:HOH448 2.2 16.9 1.0 OE2 A:GLU129 2.2 14.8 0.5 OE2 A:GLU118 2.2 13.6 1.0 O A:HOH427 2.2 14.9 1.0 OE1 A:GLU129 2.2 16.9 0.5 NE2 A:HIS134 2.3 14.8 1.0 CD A:GLU129 3.2 13.4 0.5 CD A:GLU129 3.2 13.3 0.5 CD2 A:HIS134 3.2 13.5 1.0 CG A:ASP120 3.2 12.6 1.0 CD A:GLU118 3.2 12.8 1.0 CE1 A:HIS134 3.3 14.7 1.0 OE1 A:GLU118 3.6 14.3 1.0 CB A:ASP120 3.7 12.1 1.0 OE1 A:GLU129 3.7 15.3 0.5 OE2 A:GLU129 3.7 13.3 0.5 O A:HOH486 3.7 14.1 1.0 CA A:CA302 4.1 12.8 1.0 CB A:GLU129 4.1 17.6 0.5 CG A:GLU129 4.3 17.8 0.5 OG A:SER144 4.3 14.3 1.0 OD1 A:ASP120 4.3 13.6 1.0 O A:ILE142 4.3 14.6 1.0 CG A:GLU129 4.3 18.2 0.5 ND1 A:HIS134 4.4 14.4 1.0 CG A:HIS134 4.4 14.2 1.0 O A:HOH507 4.5 18.7 1.0 CG A:GLU118 4.6 12.8 1.0 CB A:GLU129 4.9 17.2 0.5

Calcium binding site 2 out of 4 in the Lectin From Bauhinia Forficata in Complex with Tn-Peptide


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 Tn-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:12.8 occ:1.00 O A:TRP122 2.3 13.9 1.0 OD1 A:ASN124 2.3 13.9 1.0 O A:HOH453 2.4 13.3 1.0 OE2 A:GLU129 2.4 13.3 0.5 O A:HOH486 2.4 14.1 1.0 OE1 A:GLU129 2.4 15.3 0.5 OD1 A:ASP120 2.5 13.6 1.0 OD2 A:ASP120 2.5 13.7 1.0 CG A:ASP120 2.9 12.6 1.0 CD A:GLU129 3.3 13.4 0.5 CD A:GLU129 3.3 13.3 0.5 CG A:ASN124 3.5 13.8 1.0 OE1 A:GLU129 3.5 16.9 0.5 OE2 A:GLU129 3.5 14.8 0.5 C A:TRP122 3.5 13.5 1.0 N A:ASN124 4.0 15.0 1.0 CA A:CA301 4.1 12.3 1.0 CB A:ASN124 4.1 14.5 1.0 CB A:ASP120 4.3 12.1 1.0 CA A:TRP122 4.4 13.6 1.0 N A:TRP122 4.4 13.4 1.0 N A:VAL123 4.5 14.8 1.0 O A:HOH427 4.5 14.9 1.0 ND2 A:ASN124 4.6 13.9 1.0 CB A:TRP122 4.6 13.9 1.0 CA A:VAL123 4.6 16.4 1.0 CG A:GLU129 4.6 18.2 0.5 OD1 A:ASP78 4.7 12.8 1.0 CD1 A:TRP122 4.7 14.9 1.0 O A:GLY96 4.7 12.8 1.0 CE1 A:HIS134 4.7 14.7 1.0 C A:VAL123 4.7 15.5 1.0 CA A:ASN124 4.7 15.0 1.0 CG A:GLU129 4.7 17.8 0.5 CA A:GLY96 4.7 13.1 1.0 O A:ASP78 4.8 13.2 1.0 NE2 A:HIS134 4.8 14.8 1.0 CZ2 A:TRP127 4.9 15.5 1.0 NE1 A:TRP127 5.0 15.6 1.0

Calcium binding site 3 out of 4 in the Lectin From Bauhinia Forficata in Complex with Tn-Peptide


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 Tn-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:12.4 occ:1.00 OD2 B:ASP120 2.1 12.9 1.0 O B:HOH447 2.2 17.2 1.0 OE1 B:GLU129 2.2 16.4 0.5 OE1 B:GLU129 2.2 16.3 0.5 OE2 B:GLU118 2.2 13.7 1.0 O B:HOH427 2.2 14.4 1.0 NE2 B:HIS134 2.3 15.7 1.0 CG B:ASP120 3.2 12.7 1.0 CD B:GLU129 3.2 13.9 0.5 CD B:GLU129 3.2 13.9 0.5 CD2 B:HIS134 3.2 15.2 1.0 CD B:GLU118 3.2 13.5 1.0 CE1 B:HIS134 3.3 16.2 1.0 OE1 B:GLU118 3.6 14.0 1.0 CB B:ASP120 3.7 12.6 1.0 OE2 B:GLU129 3.7 13.9 0.5 OE2 B:GLU129 3.7 13.9 0.5 O B:HOH482 3.8 13.9 1.0 CA B:CA302 4.1 12.7 1.0 CB B:GLU129 4.1 18.5 0.5 O B:ILE142 4.3 14.0 1.0 CG B:GLU129 4.3 17.2 0.5 OD1 B:ASP120 4.3 13.9 1.0 OG B:SER144 4.3 14.3 1.0 CG B:GLU129 4.4 17.3 0.5 ND1 B:HIS134 4.4 16.7 1.0 CG B:HIS134 4.4 15.4 1.0 O B:HOH495 4.5 19.5 1.0 CG B:GLU118 4.6 12.7 1.0 CB B:GLU129 4.9 15.7 0.5

Calcium binding site 4 out of 4 in the Lectin From Bauhinia Forficata in Complex with Tn-Peptide


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 Tn-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:12.7 occ:1.00 OD1 B:ASN124 2.3 13.2 1.0 O B:TRP122 2.3 13.8 1.0 O B:HOH457 2.4 13.0 1.0 OE2 B:GLU129 2.4 13.9 0.5 O B:HOH482 2.4 13.9 1.0 OE2 B:GLU129 2.4 13.9 0.5 OD1 B:ASP120 2.4 13.9 1.0 OD2 B:ASP120 2.5 12.9 1.0 CG B:ASP120 2.8 12.7 1.0 CD B:GLU129 3.3 13.9 0.5 CD B:GLU129 3.3 13.9 0.5 CG B:ASN124 3.5 13.3 1.0 OE1 B:GLU129 3.5 16.4 0.5 C B:TRP122 3.5 13.9 1.0 OE1 B:GLU129 3.6 16.3 0.5 N B:ASN124 4.0 14.9 1.0 CA B:CA301 4.1 12.4 1.0 CB B:ASN124 4.2 14.3 1.0 CB B:ASP120 4.3 12.6 1.0 CA B:TRP122 4.4 14.4 1.0 N B:TRP122 4.4 13.8 1.0 O B:HOH427 4.5 14.4 1.0 N B:VAL123 4.5 15.4 1.0 CA B:VAL123 4.5 16.5 1.0 CB B:TRP122 4.6 13.9 1.0 ND2 B:ASN124 4.6 13.8 1.0 C B:VAL123 4.6 15.5 1.0 CG B:GLU129 4.6 17.3 0.5 CD1 B:TRP122 4.7 14.3 1.0 OD1 B:ASP78 4.7 12.8 1.0 CE1 B:HIS134 4.7 16.2 1.0 O B:GLY96 4.7 12.4 1.0 CA B:ASN124 4.7 15.1 1.0 CG B:GLU129 4.7 17.2 0.5 O B:ASP78 4.8 13.3 1.0 CA B:GLY96 4.8 12.1 1.0 NE2 B:HIS134 4.8 15.7 1.0 CZ2 B:TRP127 4.9 15.2 1.0 NE1 B:TRP127 4.9 15.6 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