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Calcium in PDB 6hjd: Cholera Toxin Classical B-Pentamer in Complex with Lewis-X

Protein crystallography data

The structure of Cholera Toxin Classical B-Pentamer in Complex with Lewis-X, PDB code: 6hjd was solved by U.Krengel, J.B.Heim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.16 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.965, 108.291, 115.621, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X (pdb code 6hjd). 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 Classical B-Pentamer in Complex with Lewis-X, PDB code: 6hjd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 6hjd

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Calcium binding site 1 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


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 Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:15.7
occ:1.00
 O4 G:BCN203 2.1 26.8 1.0
O21 G:BCN203 2.4 16.9 1.0
OE2 G:GLU79 2.4 16.1 1.0
O F:HOH304 2.4 24.1 1.0
OE1 A:GLU79 2.5 17.5 1.0
OE2 A:GLU79 2.5 17.4 1.0
O6 G:BCN203 2.5 27.2 1.0
N1 G:BCN203 2.8 23.8 1.0
CD A:GLU79 2.8 16.8 1.0
C4 G:BCN203 3.1 27.1 1.0
C2 G:BCN203 3.3 19.8 1.0
C6 G:BCN203 3.4 23.7 1.0
C5 G:BCN203 3.4 23.0 1.0
C3 G:BCN203 3.4 24.1 1.0
C1 G:BCN203 3.6 21.6 1.0
CD G:GLU79 3.6 16.1 1.0
NZ A:LYS23 3.9 31.9 1.0
CA G:CA201 4.0 15.2 1.0
O A:HOH324 4.0 23.9 1.0
CG G:GLU79 4.3 15.1 1.0
CG A:GLU79 4.4 15.3 1.0
O22 G:BCN203 4.5 19.5 1.0
OE1 G:GLU79 4.5 17.3 1.0
O F:ASN103 4.6 45.2 1.0
O4 A:BCN202 4.6 25.1 1.0
NZ G:LYS23 4.6 18.9 0.5
OXT F:ASN103 4.6 47.6 1.0
C F:ASN103 4.8 43.1 1.0

Calcium binding site 2 out of 10 in 6hjd

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Calcium binding site 2 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


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 Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:16.4
occ:1.00
 O J:HOH317 2.3 21.5 1.0
O4 J:BCN202 2.3 26.1 1.0
O6 J:BCN202 2.4 26.3 1.0
OE2 F:GLU79 2.4 16.9 1.0
O22 J:BCN202 2.4 16.6 1.0
OE1 B:GLU79 2.4 16.5 1.0
OE2 B:GLU79 2.6 16.8 1.0
N1 J:BCN202 2.8 23.8 1.0
CD B:GLU79 2.8 16.1 1.0
C4 J:BCN202 3.3 27.0 1.0
C2 J:BCN202 3.3 20.1 1.0
C6 J:BCN202 3.4 25.1 1.0
C5 J:BCN202 3.5 26.2 1.0
C1 J:BCN202 3.6 21.7 1.0
C3 J:BCN202 3.6 25.0 1.0
CD F:GLU79 3.6 17.0 1.0
O F:HOH349 4.0 22.0 1.0
CA F:CA201 4.0 15.9 1.0
NZ F:LYS23 4.1 17.2 0.3
CG F:GLU79 4.2 15.9 1.0
CG B:GLU79 4.4 15.0 1.0
O J:ASN103 4.4 38.1 1.0
O21 J:BCN202 4.5 18.7 1.0
OE1 F:GLU79 4.6 18.2 1.0
OXT J:ASN103 4.6 41.7 1.0
O4 F:BCN202 4.6 24.6 1.0
C J:ASN103 4.7 39.7 1.0

Calcium binding site 3 out of 10 in 6hjd

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Calcium binding site 3 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


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 Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:15.1
occ:1.00
 O4 I:BCN202 2.1 29.4 1.0
OE2 J:GLU79 2.3 15.1 1.0
O22 I:BCN202 2.4 19.4 1.0
OE1 C:GLU79 2.4 16.3 1.0
OE2 C:GLU79 2.5 15.6 1.0
O I:HOH341 2.5 19.9 1.0
O6 I:BCN202 2.5 20.1 1.0
N1 I:BCN202 2.8 24.1 1.0
CD C:GLU79 2.8 15.7 1.0
C4 I:BCN202 3.2 27.5 1.0
C2 I:BCN202 3.3 19.6 1.0
C6 I:BCN202 3.4 22.3 1.0
C5 I:BCN202 3.4 23.7 1.0
C3 I:BCN202 3.5 27.3 1.0
CD J:GLU79 3.5 15.4 1.0
C1 I:BCN202 3.6 21.3 1.0
CA J:CA201 4.0 14.1 1.0
CG J:GLU79 4.2 14.5 1.0
O B:HOH303 4.2 21.6 1.0
ND2 I:ASN103 4.3 41.6 1.0
CG C:GLU79 4.3 14.3 1.0
O21 I:BCN202 4.5 17.6 1.0
OE1 J:GLU79 4.5 16.2 1.0
O4 B:BCN202 4.5 26.1 1.0
O I:ASN103 5.0 43.1 1.0

Calcium binding site 4 out of 10 in 6hjd

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Calcium binding site 4 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cholera Toxin Classical B-Pentamer in Complex with Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:15.2
occ:1.00
 O4 I:BCN203 2.1 20.3 1.0
O6 I:BCN203 2.3 24.8 1.0
OE2 I:GLU79 2.3 16.6 1.0
OE1 D:GLU79 2.4 16.2 1.0
ND2 H:ASN103 2.4 30.4 1.0
O21 I:BCN203 2.4 18.1 1.0
OE2 D:GLU79 2.5 16.8 1.0
N1 I:BCN203 2.7 21.4 1.0
CD D:GLU79 2.8 16.4 1.0
C4 I:BCN203 3.2 22.4 1.0
C2 I:BCN203 3.3 19.6 1.0
C6 I:BCN203 3.3 23.7 1.0
C5 I:BCN203 3.4 22.2 1.0
C3 I:BCN203 3.4 22.6 1.0
C1 I:BCN203 3.5 19.9 1.0
CD I:GLU79 3.5 15.7 1.0
CG H:ASN103 3.7 34.4 1.0
CA I:CA201 3.9 15.0 1.0
NZ D:LYS23 4.2 27.1 1.0
CG I:GLU79 4.3 14.4 1.0
CG D:GLU79 4.3 14.8 1.0
OD1 C:ASN103 4.3 28.4 1.0
CB H:ASN103 4.4 32.6 1.0
O4 D:BCN203 4.4 21.6 1.0
OE1 I:GLU79 4.5 17.4 1.0
O22 I:BCN203 4.5 18.7 1.0
O I:HOH304 4.5 28.6 1.0
OD1 H:ASN103 4.6 33.4 1.0

Calcium binding site 5 out of 10 in 6hjd

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Calcium binding site 5 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


Mono view


Stereo pair view

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

b:14.1
occ:1.00
 O21 G:BCN202 2.3 15.6 1.0
O6 G:BCN202 2.3 20.2 1.0
O4 G:BCN202 2.3 26.9 1.0
OE2 H:GLU79 2.3 16.4 1.0
OE1 E:GLU79 2.4 17.1 1.0
O E:HOH301 2.5 29.2 1.0
OE2 E:GLU79 2.6 16.4 1.0
N1 G:BCN202 2.8 22.1 1.0
CD E:GLU79 2.8 16.3 1.0
C4 G:BCN202 3.3 24.7 1.0
C2 G:BCN202 3.3 19.6 1.0
C6 G:BCN202 3.3 21.8 1.0
C5 G:BCN202 3.4 21.3 1.0
CD H:GLU79 3.5 16.6 1.0
NZ E:LYS23 3.5 18.8 0.2
C3 G:BCN202 3.6 23.6 1.0
C1 G:BCN202 3.6 20.5 1.0
CA H:CA201 4.0 14.9 1.0
CG H:GLU79 4.2 15.1 1.0
O D:HOH336 4.2 32.3 1.0
O4 D:BCN202 4.2 28.8 1.0
CG E:GLU79 4.4 14.9 1.0
O22 G:BCN202 4.4 16.2 1.0
OE1 H:GLU79 4.5 16.9 1.0
CE E:LYS23 4.7 17.7 0.2
ND2 G:ASN103 4.8 31.3 1.0
NZ H:LYS23 4.9 19.0 0.5
CE E:LYS23 4.9 16.8 0.2
CB G:ASN103 5.0 29.9 1.0

Calcium binding site 6 out of 10 in 6hjd

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Calcium binding site 6 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cholera Toxin Classical B-Pentamer in Complex with Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:15.9
occ:1.00
 OE2 B:GLU79 2.3 16.8 1.0
O6 F:BCN202 2.3 21.6 1.0
O4 F:BCN202 2.4 24.6 1.0
O F:HOH349 2.4 22.0 1.0
O21 F:BCN202 2.4 15.0 1.0
OE1 F:GLU79 2.5 18.2 1.0
OE2 F:GLU79 2.5 16.9 1.0
N1 F:BCN202 2.7 21.4 1.0
CD F:GLU79 2.9 17.0 1.0
C6 F:BCN202 3.3 22.1 1.0
C2 F:BCN202 3.3 17.3 1.0
C4 F:BCN202 3.4 26.1 1.0
C5 F:BCN202 3.4 23.0 1.0
C1 F:BCN202 3.5 19.8 1.0
CD B:GLU79 3.5 16.1 1.0
C3 F:BCN202 3.5 23.8 1.0
CA B:CA201 4.0 16.4 1.0
O J:HOH317 4.0 21.5 1.0
NZ F:LYS23 4.1 18.3 0.3
O F:HOH325 4.2 36.4 1.0
CG B:GLU79 4.2 15.0 1.0
OXT A:ASN103 4.2 44.8 1.0
CG F:GLU79 4.4 15.9 1.0
O22 F:BCN202 4.5 16.7 1.0
OE1 B:GLU79 4.5 16.5 1.0
NZ F:LYS23 4.6 17.2 0.3
O4 J:BCN202 4.7 26.1 1.0

Calcium binding site 7 out of 10 in 6hjd

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Calcium binding site 7 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cholera Toxin Classical B-Pentamer in Complex with Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:15.2
occ:1.00
 O4 A:BCN202 2.0 25.1 1.0
O A:HOH324 2.3 23.9 1.0
O22 A:BCN202 2.4 18.6 1.0
OE2 A:GLU79 2.4 17.4 1.0
O6 A:BCN202 2.5 24.6 1.0
OE1 G:GLU79 2.5 17.3 1.0
OE2 G:GLU79 2.6 16.1 1.0
N1 A:BCN202 2.7 24.6 1.0
CD G:GLU79 2.9 16.1 1.0
C4 A:BCN202 3.2 26.9 1.0
C2 A:BCN202 3.3 20.8 1.0
C6 A:BCN202 3.4 24.9 1.0
C5 A:BCN202 3.4 24.4 1.0
C3 A:BCN202 3.5 25.4 1.0
CD A:GLU79 3.5 16.8 1.0
C1 A:BCN202 3.5 21.6 1.0
CA A:CA201 4.0 15.7 1.0
OD1 E:ASN103 4.0 46.6 1.0
O F:HOH304 4.0 24.1 1.0
CG A:GLU79 4.2 15.3 1.0
O A:HOH303 4.4 33.2 1.0
O4 G:BCN203 4.4 26.8 1.0
CG G:GLU79 4.4 15.1 1.0
O21 A:BCN202 4.5 17.8 1.0
OE1 A:GLU79 4.5 17.5 1.0
NZ G:LYS23 4.5 18.9 0.5
CB E:ASN103 4.5 44.6 1.0
CG E:ASN103 4.7 45.5 1.0

Calcium binding site 8 out of 10 in 6hjd

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Calcium binding site 8 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cholera Toxin Classical B-Pentamer in Complex with Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:14.9
occ:1.00
 O4 D:BCN202 1.9 28.8 1.0
OE2 E:GLU79 2.2 16.4 1.0
O22 D:BCN202 2.3 18.9 1.0
O6 D:BCN202 2.4 20.4 1.0
OE1 H:GLU79 2.4 16.9 1.0
OE2 H:GLU79 2.5 16.4 1.0
O D:HOH336 2.6 32.3 1.0
N1 D:BCN202 2.7 22.0 1.0
CD H:GLU79 2.8 16.6 1.0
C4 D:BCN202 3.1 27.7 1.0
C2 D:BCN202 3.2 20.4 1.0
C6 D:BCN202 3.3 20.8 1.0
C5 D:BCN202 3.4 22.1 1.0
CD E:GLU79 3.4 16.3 1.0
C3 D:BCN202 3.5 26.3 1.0
C1 D:BCN202 3.5 21.6 1.0
CA E:CA201 4.0 14.1 1.0
O E:HOH301 4.1 29.2 1.0
CG E:GLU79 4.1 14.9 1.0
CG H:GLU79 4.3 15.1 1.0
O21 D:BCN202 4.4 20.3 1.0
OE1 E:GLU79 4.4 17.1 1.0
ND2 D:ASN103 4.4 30.9 1.0
O4 G:BCN202 4.5 26.9 1.0
CE H:LYS23 4.9 19.4 0.5
CB D:ASN103 4.9 30.5 1.0
NZ E:LYS23 4.9 18.8 0.2

Calcium binding site 9 out of 10 in 6hjd

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Calcium binding site 9 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


Mono view


Stereo pair view

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

b:15.0
occ:1.00
 O4 D:BCN203 2.0 21.6 1.0
OE2 D:GLU79 2.3 16.8 1.0
OD1 C:ASN103 2.4 28.4 1.0
O22 D:BCN203 2.4 21.2 1.0
OE1 I:GLU79 2.4 17.4 1.0
O6 D:BCN203 2.5 22.1 1.0
OE2 I:GLU79 2.6 16.6 1.0
N1 D:BCN203 2.7 22.4 1.0
CD I:GLU79 2.8 15.7 1.0
C4 D:BCN203 3.2 23.3 1.0
C2 D:BCN203 3.3 20.1 1.0
C5 D:BCN203 3.4 22.9 1.0
C6 D:BCN203 3.4 24.4 1.0
C3 D:BCN203 3.5 22.9 1.0
C1 D:BCN203 3.5 21.6 1.0
CD D:GLU79 3.5 16.4 1.0
CG C:ASN103 3.6 31.1 1.0
O I:HOH303 3.7 29.3 1.0
CA D:CA201 3.9 15.2 1.0
NZ I:LYS23 4.1 20.3 0.5
ND2 H:ASN103 4.1 30.4 1.0
CG D:GLU79 4.3 14.8 1.0
CG I:GLU79 4.4 14.4 1.0
CB C:ASN103 4.4 29.9 1.0
OE1 D:GLU79 4.4 16.2 1.0
O21 D:BCN203 4.5 18.0 1.0
O4 I:BCN203 4.5 20.3 1.0
ND2 C:ASN103 4.5 32.2 1.0
O D:HOH306 4.6 26.1 1.0
CA C:ASN103 4.9 29.9 1.0
O6 I:BCN203 5.0 24.8 1.0

Calcium binding site 10 out of 10 in 6hjd

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Calcium binding site 10 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Lewis-X


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cholera Toxin Classical B-Pentamer in Complex with Lewis-X within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca201

b:14.1
occ:1.00
 O4 B:BCN202 2.1 26.1 1.0
OE2 C:GLU79 2.3 15.6 1.0
O6 B:BCN202 2.4 20.2 1.0
O21 B:BCN202 2.4 18.8 1.0
OE1 J:GLU79 2.5 16.2 1.0
OE2 J:GLU79 2.5 15.1 1.0
O B:HOH303 2.6 21.6 1.0
N1 B:BCN202 2.7 21.8 1.0
CD J:GLU79 2.9 15.4 1.0
C4 B:BCN202 3.1 25.6 1.0
C6 B:BCN202 3.3 20.7 1.0
C2 B:BCN202 3.4 19.1 1.0
C5 B:BCN202 3.4 21.5 1.0
C3 B:BCN202 3.4 23.8 1.0
CD C:GLU79 3.5 15.7 1.0
C1 B:BCN202 3.6 21.9 1.0
CA C:CA201 4.0 15.1 1.0
O I:HOH341 4.1 19.9 1.0
CG C:GLU79 4.2 14.3 1.0
CG J:GLU79 4.4 14.5 1.0
O4 I:BCN202 4.5 29.4 1.0
OE1 C:GLU79 4.5 16.3 1.0
O22 B:BCN202 4.5 16.9 1.0
ND2 B:ASN103 4.6 34.8 1.0
OXT B:ASN103 4.9 39.0 1.0
CB B:ASN103 5.0 34.7 1.0

Reference:

J.B.Heim, V.Hodnik, J.E.Heggelund, G.Anderluh, U.Krengel. Crystal Structures of Cholera Toxin in Complex with Fucosylated Receptors Point to Importance of Secondary Binding Site. Sci Rep V. 9 12243 2019.
ISSN: ESSN 2045-2322
PubMed: 31439922
DOI: 10.1038/S41598-019-48579-2
Page generated: Tue Jul 16 08:26:19 2024

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