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Calcium in PDB 5lzh: Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262

Protein crystallography data

The structure of Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262, PDB code: 5lzh was solved by J.E.Heggelund, T.Martinsen, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.55 / 1.13
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.736, 66.063, 76.389, 90.00, 105.67, 90.00
R / Rfree (%) 19.7 / 22.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262 (pdb code 5lzh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262, PDB code: 5lzh:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5lzh

Go back to Calcium Binding Sites List in 5lzh
Calcium binding site 1 out of 3 in the Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:49.7
occ:1.00
OE2 C:GLU79 2.6 22.2 0.5
OE1 C:GLU79 2.6 23.1 0.5
OE1 C:GLU79 2.9 22.7 0.5
CD C:GLU79 3.1 21.6 0.5
OE2 C:GLU79 3.2 24.0 0.5
CD C:GLU79 3.3 22.2 0.5
CA C:CA203 3.9 60.9 1.0
NZ C:LYS23 4.0 25.0 1.0
CG C:GLU79 4.6 20.3 0.5
CG C:GLU79 4.7 20.9 0.5

Calcium binding site 2 out of 3 in 5lzh

Go back to Calcium Binding Sites List in 5lzh
Calcium binding site 2 out of 3 in the Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:60.9
occ:1.00
OE2 C:GLU79 2.5 24.0 0.5
O C:HOH347 2.7 44.2 1.0
OE1 C:GLU79 3.4 22.7 0.5
CD C:GLU79 3.7 22.2 0.5
CD C:GLU79 3.8 21.6 0.5
CA C:CA202 3.9 49.7 1.0
OE2 C:GLU79 4.0 22.2 0.5
OE1 C:GLU79 4.3 23.1 0.5
O C:HOH389 4.4 30.8 1.0
O B:HOH387 4.6 21.5 1.0
CG C:GLU79 4.6 20.3 0.5
ND2 B:ASN103 4.7 26.1 1.0
O C:HOH366 4.7 33.8 1.0
O C:HOH395 4.7 40.6 1.0
CG C:GLU79 4.7 20.9 0.5

Calcium binding site 3 out of 3 in 5lzh

Go back to Calcium Binding Sites List in 5lzh
Calcium binding site 3 out of 3 in the Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cholera Toxin Classical B-Pentamer in Complex with Inhibitor PC262 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:98.8
occ:1.00
O D:HOH321 2.4 38.2 1.0
OE2 E:GLU79 3.3 29.2 1.0
O D:HOH384 3.9 61.1 1.0
OE1 E:GLU79 3.9 30.4 1.0
CD E:GLU79 4.0 25.5 1.0
CB D:ASN103 4.3 37.0 1.0
ND2 D:ASN103 4.4 35.3 1.0
CG D:ASN103 4.5 35.9 1.0
N D:TRS202 4.8 42.0 1.0
O D:HOH319 4.9 36.7 1.0

Reference:

J.E.Heggelund, A.Mackenzie, T.Martinsen, J.Benjamin Heim, P.Cheshev, A.Bernardi, U.Krengel. Towards New Cholera Prophylactics and Treatment: Crystal Structures of Bacterial Enterotoxins in Complex with GM1 Mimics. Sci Rep V. 7 2326 2017.
ISSN: ESSN 2045-2322
PubMed: 28539625
DOI: 10.1038/S41598-017-02179-0
Page generated: Wed Jul 9 08:02:30 2025

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