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Calcium in PDB 5elc: Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y

Protein crystallography data

The structure of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y, PDB code: 5elc was solved by J.E.Heggelund, D.Burschowsky, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.62 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.667, 80.916, 95.770, 90.00, 96.07, 90.00
R / Rfree (%) 22.1 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y (pdb code 5elc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y, PDB code: 5elc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5elc

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Calcium binding site 1 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:16.2
occ:1.00
 O4 A:BCN204 2.3 27.1 1.0
O6 A:BCN204 2.3 24.2 1.0
O22 A:BCN204 2.3 22.2 1.0
OE2 F:GLU79 2.4 16.4 1.0
OE1 A:GLU79 2.5 19.3 1.0
OE2 A:GLU79 2.6 17.4 1.0
OD1 J:ASN103 2.6 34.6 1.0
CD A:GLU79 2.9 16.6 1.0
C5 A:BCN204 3.1 27.4 1.0
C6 A:BCN204 3.2 25.4 1.0
N1 A:BCN204 3.3 27.5 1.0
C2 A:BCN204 3.3 24.1 1.0
C4 A:BCN204 3.3 27.3 1.0
CD F:GLU79 3.6 16.0 1.0
C1 A:BCN204 3.6 25.6 1.0
C3 A:BCN204 3.7 28.0 1.0
O F:HOH332 3.8 22.0 1.0
CG J:ASN103 3.8 40.0 1.0
CA A:CA203 3.9 15.5 1.0
CG F:GLU79 4.3 14.6 1.0
CG A:GLU79 4.4 15.3 1.0
O4 A:BCN202 4.4 26.4 1.0
O21 A:BCN204 4.5 21.4 1.0
OE1 F:GLU79 4.5 18.1 1.0
CB J:ASN103 4.5 36.4 1.0
NZ A:LYS23 4.7 30.2 1.0
ND2 J:ASN103 4.9 37.7 1.0
CE A:LYS23 4.9 28.4 1.0

Calcium binding site 2 out of 10 in 5elc

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Calcium binding site 2 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

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

b:15.5
occ:1.00
 O F:HOH332 2.2 22.0 1.0
O21 A:BCN202 2.3 17.6 1.0
OE1 A:GLU79 2.3 19.3 1.0
O4 A:BCN202 2.5 26.4 1.0
O6 A:BCN202 2.5 20.9 1.0
OE1 F:GLU79 2.5 18.1 1.0
OE2 F:GLU79 2.6 16.4 1.0
N1 A:BCN202 2.7 23.5 1.0
CD F:GLU79 2.9 16.0 1.0
C2 A:BCN202 3.2 18.6 1.0
C4 A:BCN202 3.3 28.9 1.0
C6 A:BCN202 3.4 20.7 1.0
C5 A:BCN202 3.5 21.0 1.0
C1 A:BCN202 3.5 20.0 1.0
C3 A:BCN202 3.5 24.1 1.0
CD A:GLU79 3.5 16.6 1.0
CA A:CA201 3.9 16.2 1.0
CG A:GLU79 4.2 15.3 1.0
O22 A:BCN202 4.4 16.6 1.0
CG F:GLU79 4.4 14.6 1.0
OD1 J:ASN103 4.4 34.6 1.0
OE2 A:GLU79 4.5 17.4 1.0
O6 A:BCN204 4.7 24.2 1.0
CE F:LYS23 4.9 28.1 1.0
O4 A:BCN204 4.9 27.1 1.0
O E:ASN103 4.9 43.0 1.0

Calcium binding site 3 out of 10 in 5elc

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Calcium binding site 3 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:14.6
occ:1.00
 OE1 B:GLU79 2.1 10.4 1.0
O4 B:BCN203 2.2 23.1 1.0
OE2 J:GLU79 2.3 15.5 1.0
O21 B:BCN203 2.4 15.4 1.0
O B:HOH312 2.4 26.8 1.0
OE2 B:GLU79 2.5 15.3 1.0
O6 B:BCN203 2.6 25.7 1.0
CD B:GLU79 2.7 12.6 1.0
C4 B:BCN203 3.2 22.7 1.0
N1 B:BCN203 3.3 23.3 1.0
C2 B:BCN203 3.3 18.0 1.0
C5 B:BCN203 3.4 23.5 1.0
C3 B:BCN203 3.4 22.5 1.0
C6 B:BCN203 3.4 25.8 1.0
CD J:GLU79 3.5 15.8 1.0
C1 B:BCN203 3.7 20.7 1.0
CA B:CA204 3.9 14.2 1.0
O J:HOH301 4.0 22.7 1.0
O B:HOH307 4.1 34.8 1.0
NZ B:LYS23 4.1 22.2 1.0
CG J:GLU79 4.2 13.7 1.0
CG B:GLU79 4.3 12.5 1.0
ND2 I:ASN103 4.4 29.2 1.0
OE1 J:GLU79 4.4 15.4 1.0
O B:HOH319 4.4 26.9 1.0
O22 B:BCN203 4.5 16.5 1.0
O4 B:BCN201 4.5 23.7 1.0
NZ J:LYS23 4.7 23.9 1.0
OXT I:ASN103 4.9 27.6 1.0
CB I:ASN103 4.9 27.4 1.0

Calcium binding site 4 out of 10 in 5elc

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Calcium binding site 4 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:14.2
occ:1.00
 OE1 J:GLU79 2.3 15.4 1.0
OE2 B:GLU79 2.3 15.3 1.0
O22 B:BCN201 2.3 17.5 1.0
O6 B:BCN201 2.4 17.8 1.0
O J:HOH301 2.5 22.7 1.0
OE2 J:GLU79 2.5 15.5 1.0
O4 B:BCN201 2.6 23.7 1.0
N1 B:BCN201 2.7 18.5 1.0
CD J:GLU79 2.8 15.8 1.0
C4 B:BCN201 3.2 21.2 1.0
C2 B:BCN201 3.3 16.9 1.0
C6 B:BCN201 3.3 18.0 1.0
C5 B:BCN201 3.4 17.9 1.0
C3 B:BCN201 3.4 20.0 1.0
C1 B:BCN201 3.6 17.9 1.0
CD B:GLU79 3.6 12.6 1.0
NZ J:LYS23 3.8 23.9 1.0
CA B:CA202 3.9 14.6 1.0
O A:ASN103 4.2 31.6 1.0
CG B:GLU79 4.2 12.5 1.0
OD1 A:ASN103 4.2 25.7 1.0
O B:HOH312 4.2 26.8 1.0
O6 B:BCN203 4.3 25.7 1.0
CG J:GLU79 4.3 13.7 1.0
O21 B:BCN201 4.4 15.1 1.0
OE1 B:GLU79 4.5 10.4 1.0
O B:HOH314 4.6 20.0 1.0
C A:ASN103 4.7 29.1 1.0
NZ B:LYS23 4.8 22.2 1.0
OXT A:ASN103 5.0 30.9 1.0
CB A:ASN103 5.0 25.3 1.0
CG A:ASN103 5.0 26.2 1.0

Calcium binding site 5 out of 10 in 5elc

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Calcium binding site 5 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:14.3
occ:1.00
 O C:HOH355 2.3 21.2 1.0
O4 C:BCN202 2.3 25.4 1.0
O22 C:BCN202 2.4 18.8 1.0
OE2 I:GLU79 2.4 16.6 1.0
O6 C:BCN202 2.4 24.2 1.0
OE1 C:GLU79 2.6 13.3 1.0
OE2 C:GLU79 2.6 15.6 1.0
CD C:GLU79 3.0 12.7 1.0
N1 C:BCN202 3.1 24.2 1.0
C4 C:BCN202 3.2 25.9 1.0
C2 C:BCN202 3.3 19.3 1.0
C6 C:BCN202 3.4 24.4 1.0
C1 C:BCN202 3.4 23.4 1.0
C5 C:BCN202 3.4 25.8 1.0
C3 C:BCN202 3.4 23.5 1.0
CD I:GLU79 3.5 14.5 1.0
O C:HOH310 3.9 22.5 1.0
CA C:CA203 4.0 14.2 1.0
NZ C:LYS23 4.0 17.8 1.0
OXT H:ASN103 4.1 36.9 1.0
CG I:GLU79 4.2 14.6 1.0
O C:HOH339 4.4 22.1 1.0
O H:HOH350 4.4 23.9 1.0
O21 C:BCN202 4.4 17.5 1.0
O6 C:BCN204 4.5 23.8 1.0
OE1 I:GLU79 4.5 13.7 1.0
CG C:GLU79 4.5 11.8 1.0
O C:HOH331 4.9 24.7 1.0
O4 C:BCN204 4.9 17.9 1.0

Calcium binding site 6 out of 10 in 5elc

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Calcium binding site 6 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:14.2
occ:1.00
 O6 C:BCN204 2.3 23.8 1.0
O4 C:BCN204 2.3 17.9 1.0
OE1 I:GLU79 2.3 13.7 1.0
O21 C:BCN204 2.4 14.9 1.0
O C:HOH339 2.4 22.1 1.0
OE2 C:GLU79 2.4 15.6 1.0
OE2 I:GLU79 2.5 16.6 1.0
CD I:GLU79 2.8 14.5 1.0
C6 C:BCN204 3.1 24.7 1.0
C4 C:BCN204 3.1 18.7 1.0
N1 C:BCN204 3.1 20.7 1.0
C3 C:BCN204 3.2 18.9 1.0
C2 C:BCN204 3.3 15.4 1.0
C5 C:BCN204 3.5 22.8 1.0
CD C:GLU79 3.6 12.7 1.0
C1 C:BCN204 3.6 18.6 1.0
CA C:CA201 4.0 14.3 1.0
O C:HOH355 4.2 21.2 1.0
NZ I:LYS23 4.2 16.8 1.0
CG C:GLU79 4.3 11.8 1.0
CG I:GLU79 4.3 14.6 1.0
O22 C:BCN204 4.4 13.8 1.0
O I:HOH353 4.4 43.3 1.0
OE1 C:GLU79 4.5 13.3 1.0
O6 C:BCN202 4.6 24.2 1.0
O C:HOH301 4.6 19.1 1.0
O C:HOH372 4.8 32.7 1.0
CB B:ASN103 4.9 24.9 1.0
CA B:ASN103 4.9 24.1 1.0

Calcium binding site 7 out of 10 in 5elc

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Calcium binding site 7 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:14.2
occ:1.00
 O22 D:BCN203 2.3 15.0 1.0
OE2 H:GLU79 2.3 14.0 1.0
O6 D:BCN203 2.5 28.4 1.0
O4 D:BCN203 2.5 18.0 1.0
OE2 D:GLU79 2.5 13.8 1.0
OE1 D:GLU79 2.5 15.0 1.0
O D:HOH355 2.5 24.3 1.0
CD D:GLU79 2.8 13.7 1.0
N1 D:BCN203 3.2 22.0 1.0
C6 D:BCN203 3.3 26.0 1.0
C2 D:BCN203 3.3 17.1 1.0
C3 D:BCN203 3.3 19.6 1.0
C4 D:BCN203 3.4 18.1 1.0
C5 D:BCN203 3.5 23.5 1.0
CD H:GLU79 3.5 13.9 1.0
C1 D:BCN203 3.6 19.2 1.0
CA D:CA204 3.9 13.7 1.0
O H:HOH303 4.0 30.8 1.0
O D:HOH335 4.1 38.7 1.0
CG H:GLU79 4.2 12.8 1.0
CG D:GLU79 4.3 13.1 1.0
O21 D:BCN203 4.4 18.0 1.0
OE1 H:GLU79 4.5 15.0 1.0
O4 D:BCN201 4.6 26.4 1.0
NZ H:LYS23 4.8 31.3 1.0
O G:ASN103 4.9 35.1 1.0
CE D:LYS23 4.9 16.7 0.7
NZ D:LYS23 5.0 17.3 0.7
O G:HOH352 5.0 38.6 1.0

Calcium binding site 8 out of 10 in 5elc

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Calcium binding site 8 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:13.7
occ:1.00
 O21 D:BCN201 2.3 20.8 1.0
O H:HOH303 2.3 30.8 1.0
OE2 D:GLU79 2.4 13.8 1.0
OE2 H:GLU79 2.5 14.0 1.0
O6 D:BCN201 2.5 22.3 1.0
O4 D:BCN201 2.5 26.4 1.0
OE1 H:GLU79 2.5 15.0 1.0
N1 D:BCN201 2.7 22.2 1.0
CD H:GLU79 2.9 13.9 1.0
C4 D:BCN201 3.2 24.6 1.0
C2 D:BCN201 3.2 21.5 1.0
C6 D:BCN201 3.4 22.0 1.0
C3 D:BCN201 3.4 24.0 1.0
C5 D:BCN201 3.4 21.8 1.0
C1 D:BCN201 3.5 21.1 1.0
CD D:GLU79 3.5 13.7 1.0
CA D:CA202 3.9 14.2 1.0
CG D:GLU79 4.2 13.1 1.0
ND2 C:ASN103 4.2 32.7 1.0
O D:HOH355 4.3 24.3 1.0
CG H:GLU79 4.4 12.8 1.0
O22 D:BCN201 4.4 18.1 1.0
OXT C:ASN103 4.4 36.2 1.0
O H:HOH333 4.4 31.5 1.0
O6 D:BCN203 4.5 28.4 1.0
NZ H:LYS23 4.5 31.3 1.0
OE1 D:GLU79 4.5 15.0 1.0
NZ D:LYS23 4.8 17.3 0.7
CB C:ASN103 4.9 30.9 1.0

Calcium binding site 9 out of 10 in 5elc

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Calcium binding site 9 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:15.3
occ:1.00
 O22 E:BCN204 2.3 18.8 1.0
OE2 G:GLU79 2.3 15.9 1.0
O4 E:BCN204 2.4 23.8 1.0
OE1 E:GLU79 2.5 15.0 1.0
O E:HOH359 2.5 27.8 1.0
O6 E:BCN204 2.6 22.5 1.0
OE2 E:GLU79 2.6 15.5 1.0
CD E:GLU79 3.0 15.2 1.0
C5 E:BCN204 3.1 24.6 1.0
C2 E:BCN204 3.2 22.5 1.0
N1 E:BCN204 3.2 26.0 1.0
C1 E:BCN204 3.3 23.4 1.0
C6 E:BCN204 3.4 24.2 1.0
C4 E:BCN204 3.5 25.0 1.0
CD G:GLU79 3.5 17.5 1.0
C3 E:BCN204 3.7 27.5 1.0
CA E:CA203 3.9 16.0 1.0
O E:HOH357 4.0 24.6 1.0
CG G:GLU79 4.2 15.5 1.0
O E:HOH346 4.3 49.6 1.0
O21 E:BCN204 4.4 23.5 1.0
OE1 G:GLU79 4.4 18.1 1.0
CG E:GLU79 4.5 15.4 1.0
O E:HOH302 4.7 32.6 1.0
O6 E:BCN202 4.7 29.9 1.0

Calcium binding site 10 out of 10 in 5elc

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Calcium binding site 10 out of 10 in the Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cholera Toxin El Tor B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:16.0
occ:1.00
 O6 E:BCN202 2.3 29.9 1.0
O21 E:BCN202 2.4 19.0 1.0
OE1 G:GLU79 2.4 18.1 1.0
O4 E:BCN202 2.4 25.4 1.0
OE2 E:GLU79 2.4 15.5 1.0
O E:HOH357 2.5 24.6 1.0
OE2 G:GLU79 2.6 15.9 1.0
CD G:GLU79 2.9 17.5 1.0
C3 E:BCN202 3.2 28.1 1.0
C4 E:BCN202 3.3 27.2 1.0
C2 E:BCN202 3.3 23.0 1.0
C1 E:BCN202 3.3 26.1 1.0
N1 E:BCN202 3.5 31.5 1.0
C6 E:BCN202 3.5 31.5 1.0
CD E:GLU79 3.6 15.2 1.0
O E:HOH359 3.8 27.8 1.0
CA E:CA201 3.9 15.3 1.0
C5 E:BCN202 4.0 31.6 1.0
CG E:GLU79 4.3 15.4 1.0
CG G:GLU79 4.4 15.5 1.0
O22 E:BCN202 4.4 17.1 1.0
O E:HOH327 4.4 23.3 1.0
OE1 E:GLU79 4.4 15.0 1.0
O6 E:BCN204 4.7 22.5 1.0
CB D:ASN103 4.9 33.9 1.0

Reference:

J.E.Heggelund, D.Burschowsky, V.A.Bjrnestad, V.Hodnik, G.Anderluh, U.Krengel. High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence. Plos Pathog. V. 12 05567 2016.
ISSN: ESSN 1553-7374
PubMed: 27082955
DOI: 10.1371/JOURNAL.PPAT.1005567
Page generated: Sun Jul 14 18:40:11 2024

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