Calcium in PDB 5t5j: Lectin From Bauhinia Forficata in Complex with Tn-Peptide

Protein crystallography data

The structure of Lectin From Bauhinia Forficata in Complex with Tn-Peptide, PDB code: 5t5j 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) 32.59 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.378, 46.159, 92.107, 90.00, 92.56, 90.00
R / Rfree (%) 10.5 / 14.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Lectin From Bauhinia Forficata in Complex with Tn-Peptide (pdb code 5t5j). 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: 5t5j:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5t5j

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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:9.8
occ:1.00
OE1 A:GLU129 2.2 13.4 1.0
OD2 A:ASP120 2.2 9.6 1.0
O A:HOH479 2.2 15.1 1.0
OE2 A:GLU118 2.2 11.7 1.0
O A:HOH447 2.3 12.1 1.0
NE2 A:HIS134 2.3 11.7 1.0
CD A:GLU129 3.2 10.7 1.0
CG A:ASP120 3.2 9.1 1.0
CD A:GLU118 3.2 11.9 1.0
CD2 A:HIS134 3.3 10.9 1.0
CE1 A:HIS134 3.3 12.5 1.0
OE1 A:GLU118 3.6 11.9 1.0
CB A:ASP120 3.7 9.1 1.0
OE2 A:GLU129 3.7 11.5 1.0
O A:HOH474 3.8 11.3 1.0
CA A:CA302 4.1 9.4 1.0
OG A:SER144 4.3 13.7 1.0
O A:ILE142 4.3 11.5 1.0
OD1 A:ASP120 4.3 10.0 1.0
CG A:GLU129 4.4 16.6 1.0
ND1 A:HIS134 4.4 11.3 1.0
CG A:HIS134 4.4 10.8 1.0
O A:HOH506 4.5 18.6 1.0
CG A:GLU118 4.6 10.3 1.0
CB A:GLU129 4.9 17.6 1.0
NE1 A:TRP127 5.0 11.8 1.0

Calcium binding site 2 out of 4 in 5t5j

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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:9.4
occ:1.00
O A:TRP122 2.3 10.8 1.0
OD1 A:ASN124 2.3 10.5 1.0
OE2 A:GLU129 2.4 11.5 1.0
O A:HOH474 2.4 11.3 1.0
O A:HOH473 2.4 10.5 1.0
OD2 A:ASP120 2.4 9.6 1.0
OD1 A:ASP120 2.5 10.0 1.0
CG A:ASP120 2.8 9.1 1.0
CD A:GLU129 3.3 10.7 1.0
CG A:ASN124 3.5 10.2 1.0
C A:TRP122 3.5 10.2 1.0
OE1 A:GLU129 3.6 13.4 1.0
N A:ASN124 4.0 10.7 1.0
CA A:CA301 4.1 9.8 1.0
CB A:ASN124 4.1 9.9 1.0
CB A:ASP120 4.3 9.1 1.0
CA A:TRP122 4.4 9.7 1.0
N A:TRP122 4.4 9.8 1.0
O A:HOH447 4.5 12.1 1.0
N A:VAL123 4.5 10.9 1.0
ND2 A:ASN124 4.6 9.6 1.0
CA A:VAL123 4.6 11.8 1.0
CB A:TRP122 4.6 10.3 1.0
CD1 A:TRP122 4.6 10.9 1.0
C A:VAL123 4.6 10.3 1.0
O A:GLY96 4.6 10.1 1.0
CA A:ASN124 4.6 10.8 1.0
CG A:GLU129 4.6 16.6 1.0
OD1 A:ASP78 4.7 9.6 1.0
CE1 A:HIS134 4.7 12.5 1.0
CA A:GLY96 4.8 8.9 1.0
O A:ASP78 4.8 10.5 1.0
NE2 A:HIS134 4.9 11.7 1.0
CZ2 A:TRP127 4.9 11.2 1.0
NE1 A:TRP127 5.0 11.8 1.0

Calcium binding site 3 out of 4 in 5t5j

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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:13.8
occ:1.00
OE1 B:GLU129 2.1 19.2 1.0
O B:HOH431 2.2 18.6 1.0
OD2 B:ASP120 2.2 15.1 1.0
OE2 B:GLU118 2.2 14.0 1.0
O B:HOH435 2.2 16.0 1.0
NE2 B:HIS134 2.3 16.5 1.0
CD B:GLU129 3.2 15.1 1.0
CD B:GLU118 3.2 13.1 1.0
CD2 B:HIS134 3.2 14.1 1.0
CG B:ASP120 3.2 13.3 1.0
CE1 B:HIS134 3.3 17.7 1.0
OE1 B:GLU118 3.6 16.1 1.0
OE2 B:GLU129 3.7 16.7 1.0
CB B:ASP120 3.7 13.6 1.0
O B:HOH443 3.7 15.3 1.0
CA B:CA302 4.1 14.6 1.0
OG B:SER144 4.2 14.9 1.0
OD1 B:ASP120 4.3 14.9 1.0
CG B:GLU129 4.3 21.2 1.0
O B:ILE142 4.4 15.4 1.0
CG B:HIS134 4.4 12.9 1.0
ND1 B:HIS134 4.4 16.2 1.0
O B:HOH506 4.5 20.3 1.0
CG B:GLU118 4.5 14.8 1.0
CB B:GLU129 4.8 21.8 1.0

Calcium binding site 4 out of 4 in 5t5j

Go back to Calcium Binding Sites List in 5t5j
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:14.6
occ:1.00
O B:TRP122 2.3 16.5 1.0
O B:HOH470 2.3 14.8 1.0
OD1 B:ASN124 2.4 15.8 1.0
O B:HOH443 2.4 15.3 1.0
OE2 B:GLU129 2.4 16.7 1.0
OD1 B:ASP120 2.5 14.9 1.0
OD2 B:ASP120 2.5 15.1 1.0
CG B:ASP120 2.8 13.3 1.0
CD B:GLU129 3.3 15.1 1.0
OE1 B:GLU129 3.5 19.2 1.0
CG B:ASN124 3.5 15.3 1.0
C B:TRP122 3.5 14.6 1.0
N B:ASN124 4.0 17.6 1.0
CA B:CA301 4.1 13.8 1.0
CB B:ASN124 4.2 17.6 1.0
CB B:ASP120 4.3 13.6 1.0
N B:TRP122 4.4 14.5 1.0
CA B:TRP122 4.4 14.8 1.0
O B:HOH435 4.5 16.0 1.0
N B:VAL123 4.5 16.9 1.0
CB B:TRP122 4.5 15.8 1.0
CD1 B:TRP122 4.6 16.4 1.0
CA B:VAL123 4.6 18.9 1.0
ND2 B:ASN124 4.6 17.1 1.0
O B:GLY96 4.6 15.6 1.0
OD1 B:ASP78 4.6 15.2 1.0
CA B:ASN124 4.7 18.5 1.0
CG B:GLU129 4.7 21.2 1.0
CE1 B:HIS134 4.7 17.7 1.0
C B:VAL123 4.7 17.4 1.0
CA B:GLY96 4.8 14.5 1.0
O B:ASP78 4.8 14.5 1.0
NE2 B:HIS134 4.8 16.5 1.0
CZ2 B:TRP127 4.9 18.8 1.0
NE1 B:TRP127 5.0 18.2 1.0

Reference:

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
Page generated: Sat Dec 12 05:43:34 2020

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