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Calcium in PDB 6hmy: Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1

Protein crystallography data

The structure of Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1, PDB code: 6hmy 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) 44.32 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.626, 74.137, 111.245, 90.00, 105.59, 90.00
R / Rfree (%) 18.4 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1 (pdb code 6hmy). 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 Fucosyl-GM1, PDB code: 6hmy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 6hmy

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Calcium binding site 1 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:10.2
occ:1.00
 O4 A:BCN209 2.2 21.2 1.0
O21 A:BCN209 2.4 13.6 1.0
O F:HOH549 2.4 17.4 1.0
O6 A:BCN209 2.4 20.7 1.0
OE2 G:GLU79 2.4 11.5 1.0
OE1 A:GLU79 2.4 13.2 1.0
OE2 A:GLU79 2.6 12.5 1.0
N1 A:BCN209 2.7 17.7 1.0
CD A:GLU79 2.9 12.3 1.0
C4 A:BCN209 3.2 20.3 1.0
C2 A:BCN209 3.3 15.4 1.0
C6 A:BCN209 3.4 19.3 1.0
C5 A:BCN209 3.4 19.7 1.0
C3 A:BCN209 3.5 19.1 1.0
C1 A:BCN209 3.6 16.6 1.0
CD G:GLU79 3.6 11.3 1.0
O E:HOH367 4.0 19.2 1.0
CA A:CA210 4.1 10.6 1.0
CG G:GLU79 4.2 10.5 1.0
CG A:GLU79 4.4 11.2 1.0
O A:HOH335 4.5 31.4 1.0
O22 A:BCN209 4.5 13.3 1.0
O A:HOH303 4.6 29.0 1.0
OE1 G:GLU79 4.6 12.0 1.0
O4 A:BCN208 4.7 22.4 1.0
OXT F:ASN103 4.9 38.4 1.0

Calcium binding site 2 out of 10 in 6hmy

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Calcium binding site 2 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca210

b:10.6
occ:1.00
 O4 A:BCN208 2.3 22.4 1.0
O E:HOH367 2.3 19.2 1.0
O22 A:BCN208 2.4 13.7 1.0
OE2 A:GLU79 2.4 12.5 1.0
O6 A:BCN208 2.4 18.0 1.0
OE1 G:GLU79 2.5 12.0 1.0
OE2 G:GLU79 2.5 11.5 1.0
N1 A:BCN208 2.7 19.6 1.0
CD G:GLU79 2.9 11.3 1.0
C2 A:BCN208 3.2 15.9 1.0
C4 A:BCN208 3.3 22.8 1.0
C1 A:BCN208 3.5 17.6 1.0
C6 A:BCN208 3.5 18.1 1.0
C3 A:BCN208 3.5 21.1 1.0
CD A:GLU79 3.5 12.3 1.0
C5 A:BCN208 3.5 19.6 1.0
CA A:CA201 4.1 10.2 1.0
O F:HOH549 4.1 17.4 1.0
CG A:GLU79 4.2 11.2 1.0
CG G:GLU79 4.4 10.5 1.0
O21 A:BCN208 4.4 15.1 1.0
OE1 A:GLU79 4.5 13.2 1.0
O4 A:BCN209 4.6 21.2 1.0

Calcium binding site 3 out of 10 in 6hmy

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Calcium binding site 3 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:11.1
occ:1.00
 O4 J:BCN201 2.1 23.6 1.0
OE2 F:GLU79 2.3 11.3 1.0
O22 J:BCN201 2.4 13.0 1.0
O6 J:BCN201 2.4 17.0 1.0
OE1 B:GLU79 2.4 11.9 1.0
O J:HOH530 2.5 20.0 1.0
OE2 B:GLU79 2.7 11.4 1.0
N1 J:BCN201 2.7 18.2 1.0
CD B:GLU79 2.9 11.1 1.0
C4 J:BCN201 3.2 22.9 1.0
C2 J:BCN201 3.3 16.1 1.0
C5 J:BCN201 3.3 18.1 1.0
C6 J:BCN201 3.3 17.3 1.0
C3 J:BCN201 3.4 20.4 1.0
CD F:GLU79 3.5 11.0 1.0
C1 J:BCN201 3.5 17.1 1.0
CA F:CA201 4.0 10.5 1.0
O A:HOH333 4.1 23.7 1.0
CG F:GLU79 4.2 10.2 1.0
OD1 J:ASN103 4.4 33.3 1.0
CG B:GLU79 4.4 10.3 1.0
OE1 F:GLU79 4.5 11.8 1.0
O21 J:BCN201 4.5 15.0 1.0
O J:HOH506 4.6 27.5 1.0
O4 A:BCN211 4.6 23.2 1.0
OXT J:ASN103 4.9 33.4 1.0
CB J:ASN103 5.0 29.6 1.0

Calcium binding site 4 out of 10 in 6hmy

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Calcium binding site 4 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:11.5
occ:1.00
 O4 I:BCN201 2.3 20.2 1.0
O22 I:BCN201 2.4 14.7 1.0
OE2 C:GLU79 2.4 13.7 1.0
OE2 J:GLU79 2.4 12.2 1.0
O I:HOH356 2.5 15.7 1.0
O6 I:BCN201 2.5 20.6 1.0
OE1 C:GLU79 2.5 12.9 1.0
N1 I:BCN201 2.7 19.1 1.0
CD C:GLU79 2.8 12.8 1.0
C4 I:BCN201 3.2 20.8 1.0
C2 I:BCN201 3.3 16.3 1.0
C6 I:BCN201 3.3 18.3 1.0
C5 I:BCN201 3.4 18.9 1.0
C1 I:BCN201 3.5 18.5 1.0
C3 I:BCN201 3.5 20.0 1.0
CD J:GLU79 3.6 11.9 1.0
CA J:CA202 4.1 10.7 1.0
CG J:GLU79 4.2 11.1 1.0
O C:HOH306 4.2 25.4 1.0
O I:HOH302 4.3 21.1 1.0
O B:HOH330 4.3 18.9 1.0
O4 B:BCN209 4.3 22.9 1.0
CG C:GLU79 4.3 11.8 1.0
O21 I:BCN201 4.5 14.7 1.0
OE1 J:GLU79 4.6 12.7 1.0
OD1 I:ASN103 4.6 26.0 1.0
O I:ASN103 5.0 26.1 1.0

Calcium binding site 5 out of 10 in 6hmy

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Calcium binding site 5 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:11.2
occ:1.00
 O4 D:BCN210 2.4 20.9 1.0
O6 D:BCN210 2.4 20.1 1.0
OE2 I:GLU79 2.4 13.2 1.0
O22 D:BCN210 2.4 15.1 1.0
ND2 H:ASN103 2.4 25.8 1.0
OE1 D:GLU79 2.4 12.0 1.0
OE2 D:GLU79 2.6 11.5 1.0
N1 D:BCN210 2.7 20.2 1.0
CD D:GLU79 2.9 11.3 1.0
C6 D:BCN210 3.3 20.8 1.0
C4 D:BCN210 3.3 22.8 1.0
C2 D:BCN210 3.3 18.3 1.0
C3 D:BCN210 3.4 22.2 1.0
C5 D:BCN210 3.5 19.3 1.0
C1 D:BCN210 3.6 20.6 1.0
CD I:GLU79 3.6 12.3 1.0
CG H:ASN103 3.7 28.1 1.0
O D:HOH305 3.9 23.2 1.0
CA D:CA209 4.1 10.9 1.0
O C:HOH312 4.1 23.1 1.0
CG I:GLU79 4.2 11.5 1.0
NZ D:LYS23 4.3 19.5 1.0
CG D:GLU79 4.4 10.5 1.0
O21 D:BCN210 4.5 15.8 1.0
OE1 I:GLU79 4.5 13.0 1.0
O I:HOH301 4.6 31.0 1.0
CB H:ASN103 4.6 26.2 1.0
OD1 H:ASN103 4.6 32.6 1.0
O4 D:BCN201 4.6 21.4 1.0
CA H:ASN103 4.8 25.0 1.0

Calcium binding site 6 out of 10 in 6hmy

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Calcium binding site 6 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca209

b:10.9
occ:1.00
 O4 D:BCN201 2.2 21.4 1.0
O21 D:BCN201 2.3 13.4 1.0
OE2 D:GLU79 2.3 11.5 1.0
O6 D:BCN201 2.4 18.2 1.0
OE1 I:GLU79 2.5 13.0 1.0
O C:HOH312 2.5 23.1 1.0
OE2 I:GLU79 2.6 13.2 1.0
N1 D:BCN201 2.7 18.3 1.0
CD I:GLU79 2.9 12.3 1.0
C2 D:BCN201 3.2 15.9 1.0
C4 D:BCN201 3.3 20.9 1.0
C6 D:BCN201 3.4 18.0 1.0
C1 D:BCN201 3.4 18.1 1.0
C5 D:BCN201 3.5 18.1 1.0
C3 D:BCN201 3.5 19.7 1.0
CD D:GLU79 3.5 11.3 1.0
CA D:CA202 4.1 11.2 1.0
CG D:GLU79 4.2 10.5 1.0
O I:HOH316 4.2 32.4 1.0
CG I:GLU79 4.4 11.5 1.0
O22 D:BCN201 4.4 16.0 1.0
ND2 C:ASN103 4.5 40.1 1.0
O D:HOH318 4.5 22.0 1.0
ND2 H:ASN103 4.5 25.8 1.0
OE1 D:GLU79 4.6 12.0 1.0
OXT C:ASN103 4.6 44.3 1.0
O4 D:BCN210 4.8 20.9 1.0
CB C:ASN103 4.8 36.7 1.0

Calcium binding site 7 out of 10 in 6hmy

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Calcium binding site 7 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:11.1
occ:1.00
 O4 E:BCN209 2.3 25.3 1.0
OE1 H:GLU79 2.3 13.5 1.0
O22 E:BCN209 2.3 12.4 1.0
OE1 E:GLU79 2.4 13.9 1.0
O G:HOH367 2.4 19.4 1.0
O6 E:BCN209 2.5 17.9 1.0
OE2 E:GLU79 2.5 12.9 1.0
N1 E:BCN209 2.7 17.1 1.0
CD E:GLU79 2.9 12.5 1.0
C4 E:BCN209 3.2 23.7 1.0
C2 E:BCN209 3.3 14.0 1.0
C6 E:BCN209 3.4 15.6 1.0
C5 E:BCN209 3.5 16.5 1.0
C3 E:BCN209 3.5 20.6 1.0
CD H:GLU79 3.5 13.4 1.0
C1 E:BCN209 3.6 15.5 1.0
CA E:CA210 4.1 11.5 1.0
CG H:GLU79 4.2 12.4 1.0
O E:HOH305 4.2 26.0 1.0
O E:HOH342 4.2 25.0 1.0
O4 E:BCN201 4.4 25.8 1.0
CG E:GLU79 4.4 11.5 1.0
OE2 H:GLU79 4.4 15.1 1.0
O21 E:BCN209 4.4 13.2 1.0
ND2 G:ASN103 4.5 20.3 1.0
O E:HOH324 4.7 19.9 1.0
NZ H:LYS23 4.9 12.9 0.5

Calcium binding site 8 out of 10 in 6hmy

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Calcium binding site 8 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca210

b:11.5
occ:1.00
 O4 E:BCN201 2.3 25.8 1.0
O6 E:BCN201 2.3 15.1 1.0
OE2 H:GLU79 2.4 15.1 1.0
O21 E:BCN201 2.4 13.6 1.0
OE2 E:GLU79 2.4 12.9 1.0
O E:HOH342 2.5 25.0 1.0
OE1 H:GLU79 2.6 13.5 1.0
N1 E:BCN201 2.7 17.6 1.0
CD H:GLU79 2.8 13.4 1.0
C4 E:BCN201 3.2 22.7 1.0
C6 E:BCN201 3.2 16.0 1.0
C2 E:BCN201 3.3 15.3 1.0
C5 E:BCN201 3.3 16.4 1.0
C1 E:BCN201 3.5 16.2 1.0
C3 E:BCN201 3.5 20.0 1.0
CD E:GLU79 3.5 12.5 1.0
CA E:CA202 4.1 11.1 1.0
CG E:GLU79 4.1 11.5 1.0
O G:HOH367 4.2 19.4 1.0
O H:HOH347 4.3 26.3 1.0
CG H:GLU79 4.4 12.4 1.0
O22 E:BCN201 4.4 14.1 1.0
O4 E:BCN209 4.4 25.3 1.0
OD1 D:ASN103 4.5 21.3 1.0
O E:HOH313 4.5 18.1 1.0
OE1 E:GLU79 4.5 13.9 1.0
NZ H:LYS23 4.6 12.9 0.5

Calcium binding site 9 out of 10 in 6hmy

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Calcium binding site 9 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:10.5
occ:1.00
 O4 A:BCN211 2.3 23.2 1.0
OE2 B:GLU79 2.3 11.4 1.0
O21 A:BCN211 2.3 13.3 1.0
O A:HOH333 2.4 23.7 1.0
OE1 F:GLU79 2.4 11.8 1.0
O6 A:BCN211 2.4 17.8 1.0
OE2 F:GLU79 2.6 11.3 1.0
N1 A:BCN211 2.7 18.5 1.0
CD F:GLU79 2.9 11.0 1.0
C4 A:BCN211 3.1 21.5 1.0
C2 A:BCN211 3.2 16.8 1.0
C3 A:BCN211 3.4 19.3 1.0
C6 A:BCN211 3.4 16.6 1.0
C5 A:BCN211 3.4 17.4 1.0
C1 A:BCN211 3.5 17.6 1.0
CD B:GLU79 3.5 11.1 1.0
CA B:CA201 4.0 11.1 1.0
CG B:GLU79 4.2 10.3 1.0
O F:HOH507 4.2 25.4 1.0
O J:HOH530 4.3 20.0 1.0
O4 J:BCN201 4.3 23.6 1.0
CG F:GLU79 4.4 10.2 1.0
O22 A:BCN211 4.4 14.8 1.0
OE1 B:GLU79 4.4 11.9 1.0
ND2 A:ASN103 4.8 35.0 1.0
OXT A:ASN103 4.8 38.6 1.0

Calcium binding site 10 out of 10 in 6hmy

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Calcium binding site 10 out of 10 in the Cholera Toxin Classical B-Pentamer in Complex with Fucosyl-GM1


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 Fucosyl-GM1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca202

b:10.7
occ:1.00
 O4 B:BCN209 2.1 22.9 1.0
O6 B:BCN209 2.4 21.3 1.0
O B:HOH330 2.4 18.9 1.0
O21 B:BCN209 2.4 13.7 1.0
OE1 J:GLU79 2.4 12.7 1.0
OE1 C:GLU79 2.4 12.9 1.0
OE2 J:GLU79 2.6 12.2 1.0
N1 B:BCN209 2.7 18.3 1.0
CD J:GLU79 2.8 11.9 1.0
C4 B:BCN209 3.2 21.3 1.0
C2 B:BCN209 3.3 15.7 1.0
C6 B:BCN209 3.3 21.2 1.0
C5 B:BCN209 3.4 20.4 1.0
C1 B:BCN209 3.5 17.8 1.0
C3 B:BCN209 3.5 19.5 1.0
CD C:GLU79 3.6 12.8 1.0
CA C:CA201 4.1 11.5 1.0
O I:HOH356 4.2 15.7 1.0
CG C:GLU79 4.2 11.8 1.0
O J:HOH522 4.3 21.3 1.0
O4 I:BCN201 4.4 20.2 1.0
CG J:GLU79 4.4 11.1 1.0
O B:HOH315 4.4 20.0 1.0
O22 B:BCN209 4.5 14.0 1.0
OE2 C:GLU79 4.6 13.7 1.0
ND2 B:ASN103 4.6 23.8 1.0
OXT B:ASN103 4.9 26.9 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 08:28:33 2024

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