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Calcium in PDB 5elf: Cholera Toxin El Tor B-Pentamer in Complex with A-Pentasaccharide

Protein crystallography data

The structure of Cholera Toxin El Tor B-Pentamer in Complex with A-Pentasaccharide, PDB code: 5elf 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) 48.92 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.626, 84.720, 195.680, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 5elf

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


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

b:13.7
occ:1.00
O4 A:BCN202 2.1 26.8 1.0
O6 A:BCN202 2.2 21.7 1.0
OE1 A:GLU79 2.3 15.5 1.0
OE2 F:GLU79 2.3 17.6 1.0
O22 A:BCN202 2.4 18.1 1.0
OE2 A:GLU79 2.6 18.1 1.0
N1 A:BCN202 2.7 21.4 1.0
ND2 J:ASN103 2.8 40.7 1.0
CD A:GLU79 2.8 16.1 1.0
C4 A:BCN202 3.3 25.3 1.0
C6 A:BCN202 3.3 20.1 1.0
C2 A:BCN202 3.3 19.2 1.0
C3 A:BCN202 3.4 22.4 1.0
C5 A:BCN202 3.5 21.8 1.0
C1 A:BCN202 3.5 21.6 1.0
CD F:GLU79 3.5 17.1 1.0
CG J:ASN103 3.9 49.2 1.0
CA A:CA203 4.0 15.6 1.0
CG F:GLU79 4.3 15.2 1.0
CG A:GLU79 4.3 14.5 1.0
O A:HOH321 4.4 46.1 1.0
ND2 E:ASN103 4.4 27.8 1.0
OE1 F:GLU79 4.5 15.1 1.0
O21 A:BCN202 4.5 18.1 1.0
O A:HOH367 4.5 50.2 1.0
CB J:ASN103 4.6 42.7 1.0
O6 A:BCN204 4.6 24.2 1.0
O A:HOH342 4.7 28.8 1.0
OD1 J:ASN103 4.8 57.3 1.0

Calcium binding site 2 out of 10 in 5elf

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


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 A-Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:15.6
occ:1.00
O6 A:BCN204 2.2 24.2 1.0
OE2 A:GLU79 2.3 18.1 1.0
O21 A:BCN204 2.4 19.7 1.0
OE1 F:GLU79 2.4 15.1 1.0
ND2 E:ASN103 2.5 27.8 1.0
O4 A:BCN204 2.5 23.4 1.0
OE2 F:GLU79 2.6 17.6 1.0
CD F:GLU79 2.9 17.1 1.0
C3 A:BCN204 3.1 26.0 1.0
N1 A:BCN204 3.2 25.7 1.0
C4 A:BCN204 3.3 22.5 1.0
C2 A:BCN204 3.3 19.6 1.0
C6 A:BCN204 3.3 28.6 1.0
CD A:GLU79 3.5 16.1 1.0
C1 A:BCN204 3.6 24.0 1.0
C5 A:BCN204 3.7 26.4 1.0
CG E:ASN103 3.8 32.8 1.0
CA A:CA201 4.0 13.7 1.0
O F:HOH340 4.0 14.7 0.5
NZ F:LYS23 4.2 26.9 1.0
CG A:GLU79 4.2 14.5 1.0
ND2 J:ASN103 4.3 40.7 1.0
O A:HOH367 4.4 50.2 1.0
CG F:GLU79 4.4 15.2 1.0
OE1 A:GLU79 4.4 15.5 1.0
O A:HOH311 4.5 32.5 1.0
CB E:ASN103 4.5 29.0 1.0
O F:HOH340 4.5 16.0 0.5
O22 A:BCN204 4.5 18.3 1.0
O4 A:BCN202 4.5 26.8 1.0
O A:HOH321 4.7 46.1 1.0
OD1 E:ASN103 4.8 35.4 1.0
CA E:ASN103 4.9 32.1 1.0
O6 A:BCN202 5.0 21.7 1.0

Calcium binding site 3 out of 10 in 5elf

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


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 A-Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:15.6
occ:1.00
OE2 J:GLU79 2.3 17.0 1.0
O4 B:BCN204 2.3 28.0 1.0
O6 B:BCN204 2.3 25.0 1.0
O22 B:BCN204 2.3 21.0 1.0
O I:HOH327 2.4 25.7 1.0
OE1 B:GLU79 2.4 20.0 1.0
OE2 B:GLU79 2.6 19.4 1.0
N1 B:BCN204 2.8 25.9 1.0
CD B:GLU79 2.8 18.6 1.0
C4 B:BCN204 3.1 29.8 1.0
C2 B:BCN204 3.3 23.1 1.0
C6 B:BCN204 3.4 24.7 1.0
C5 B:BCN204 3.5 25.7 1.0
CD J:GLU79 3.5 15.6 1.0
C3 B:BCN204 3.5 25.1 1.0
C1 B:BCN204 3.5 23.7 1.0
CA B:CA205 4.0 16.0 1.0
CG J:GLU79 4.2 14.4 1.0
O J:HOH367 4.2 20.7 1.0
O B:HOH347 4.2 32.1 1.0
CG B:GLU79 4.4 16.0 1.0
OE1 J:GLU79 4.4 15.7 1.0
ND2 I:ASN103 4.4 30.3 1.0
O21 B:BCN204 4.4 20.1 1.0
O6 B:BCN201 4.5 32.2 1.0
O B:HOH322 4.6 26.6 1.0
NZ B:LYS23 4.6 35.9 1.0
CB I:ASN103 4.8 25.7 1.0
O B:HOH365 4.8 44.6 1.0
OXT I:ASN103 4.9 29.7 1.0

Calcium binding site 4 out of 10 in 5elf

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


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 A-Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:16.0
occ:1.00
O6 B:BCN201 2.2 32.2 1.0
OE2 B:GLU79 2.3 19.4 1.0
OE1 J:GLU79 2.3 15.7 1.0
O4 B:BCN201 2.4 20.6 1.0
O21 B:BCN201 2.4 19.2 1.0
OE2 J:GLU79 2.5 17.0 1.0
O J:HOH367 2.6 20.7 1.0
CD J:GLU79 2.8 15.6 1.0
C6 B:BCN201 3.1 30.9 1.0
N1 B:BCN201 3.2 26.6 1.0
C2 B:BCN201 3.3 24.2 1.0
C4 B:BCN201 3.3 23.2 1.0
C3 B:BCN201 3.4 25.4 1.0
C1 B:BCN201 3.5 24.5 1.0
CD B:GLU79 3.5 18.6 1.0
C5 B:BCN201 3.6 26.9 1.0
CA B:CA202 4.0 15.6 1.0
O I:HOH327 4.1 25.7 1.0
CG B:GLU79 4.2 16.0 1.0
CG J:GLU79 4.3 14.4 1.0
OE1 B:GLU79 4.4 20.0 1.0
O22 B:BCN201 4.5 21.5 1.0
NZ J:LYS23 4.5 32.6 1.0
ND2 A:ASN103 4.5 35.1 1.0
O B:HOH303 4.5 31.0 1.0
O4 B:BCN204 4.5 28.0 1.0
O B:HOH372 4.8 50.1 1.0
NZ B:LYS23 5.0 35.9 1.0
CB A:ASN103 5.0 31.6 1.0

Calcium binding site 5 out of 10 in 5elf

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


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

b:15.5
occ:1.00
O4 C:BCN203 2.0 26.4 1.0
O6 C:BCN203 2.3 24.4 1.0
O22 C:BCN203 2.3 16.6 1.0
O C:HOH345 2.4 23.1 1.0
OE1 C:GLU79 2.4 17.0 1.0
OE2 I:GLU79 2.5 17.3 1.0
OE2 C:GLU79 2.6 17.8 1.0
N1 C:BCN203 2.7 22.8 1.0
CD C:GLU79 2.9 17.6 1.0
C4 C:BCN203 3.2 25.4 1.0
C2 C:BCN203 3.3 20.2 1.0
C6 C:BCN203 3.3 23.2 1.0
C5 C:BCN203 3.4 24.1 1.0
C3 C:BCN203 3.5 23.8 1.0
C1 C:BCN203 3.5 22.7 1.0
CD I:GLU79 3.7 17.4 1.0
CA C:CA204 4.0 16.4 1.0
O B:HOH341 4.1 25.6 1.0
O C:HOH372 4.1 42.6 1.0
O C:HOH304 4.3 46.3 1.0
ND2 H:ASN103 4.3 45.0 1.0
CG I:GLU79 4.3 16.1 1.0
NZ C:LYS23 4.4 21.4 0.4
CG C:GLU79 4.4 14.8 1.0
O21 C:BCN203 4.4 17.7 1.0
O4 C:BCN202 4.6 22.7 1.0
O C:HOH313 4.6 31.2 1.0
OE1 I:GLU79 4.6 17.1 1.0
CB H:ASN103 4.8 46.0 1.0
O H:HOH304 4.8 44.2 1.0
O H:ASN103 5.0 44.1 1.0

Calcium binding site 6 out of 10 in 5elf

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


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 A-Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:16.4
occ:1.00
O4 C:BCN202 2.1 22.7 1.0
OE2 C:GLU79 2.3 17.8 1.0
O B:HOH341 2.4 25.6 1.0
O6 C:BCN202 2.4 25.7 1.0
O21 C:BCN202 2.4 17.9 1.0
OE1 I:GLU79 2.5 17.1 1.0
OE2 I:GLU79 2.5 17.3 1.0
N1 C:BCN202 2.7 22.7 1.0
CD I:GLU79 2.9 17.4 1.0
C4 C:BCN202 3.3 26.4 1.0
C2 C:BCN202 3.3 20.4 1.0
C6 C:BCN202 3.4 22.6 1.0
C3 C:BCN202 3.4 22.8 1.0
CD C:GLU79 3.5 17.6 1.0
C5 C:BCN202 3.5 23.8 1.0
C1 C:BCN202 3.5 22.1 1.0
CA C:CA201 4.0 15.5 1.0
O C:HOH345 4.1 23.1 1.0
O C:HOH304 4.1 46.3 1.0
O B:HOH373 4.1 26.4 0.5
OXT B:ASN103 4.2 55.1 1.0
CG C:GLU79 4.2 14.8 1.0
CG I:GLU79 4.4 16.1 1.0
OE1 C:GLU79 4.4 17.0 1.0
O22 C:BCN202 4.4 19.4 1.0
NZ C:LYS23 4.5 21.4 0.4
O4 C:BCN203 4.5 26.4 1.0
O C:HOH301 4.6 32.1 1.0
C B:ASN103 5.0 50.5 1.0

Calcium binding site 7 out of 10 in 5elf

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


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

b:14.6
occ:1.00
O4 D:BCN203 2.2 27.4 1.0
OE2 H:GLU79 2.3 16.7 1.0
O C:HOH370 2.4 26.2 1.0
O22 D:BCN203 2.4 17.8 1.0
O6 D:BCN203 2.5 21.8 1.0
OE1 D:GLU79 2.5 16.1 1.0
OE2 D:GLU79 2.5 15.4 1.0
N1 D:BCN203 2.7 24.0 1.0
CD D:GLU79 2.9 17.4 1.0
C4 D:BCN203 3.2 27.1 1.0
C5 D:BCN203 3.3 24.8 1.0
C2 D:BCN203 3.4 20.1 1.0
C6 D:BCN203 3.4 23.0 1.0
C3 D:BCN203 3.5 25.7 1.0
CD H:GLU79 3.5 17.7 1.0
C1 D:BCN203 3.6 22.1 1.0
NZ D:LYS23 4.0 37.5 1.0
CA D:CA204 4.0 15.0 1.0
CG H:GLU79 4.2 15.8 1.0
ND2 C:ASN103 4.3 38.8 1.0
O D:HOH336 4.4 39.8 1.0
CG D:GLU79 4.4 15.8 1.0
OE1 H:GLU79 4.4 17.7 1.0
O21 D:BCN203 4.5 17.4 1.0
O4 D:BCN202 4.6 25.6 1.0

Calcium binding site 8 out of 10 in 5elf

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


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 A-Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:15.0
occ:1.00
O4 D:BCN202 2.3 25.6 1.0
OE2 D:GLU79 2.3 15.4 1.0
O21 D:BCN202 2.3 16.6 1.0
O6 D:BCN202 2.4 23.1 1.0
OE1 H:GLU79 2.5 17.7 1.0
OE2 H:GLU79 2.6 16.7 1.0
ND2 C:ASN103 2.6 38.8 1.0
N1 D:BCN202 2.7 23.8 1.0
CD H:GLU79 2.9 17.7 1.0
C2 D:BCN202 3.3 21.1 1.0
C4 D:BCN202 3.3 27.2 1.0
C3 D:BCN202 3.3 24.9 1.0
C6 D:BCN202 3.4 24.1 1.0
C1 D:BCN202 3.5 23.2 1.0
C5 D:BCN202 3.5 24.3 1.0
CD D:GLU79 3.5 17.4 1.0
CG C:ASN103 3.8 48.4 1.0
O C:HOH370 3.9 26.2 1.0
CA D:CA201 4.0 14.6 1.0
CG D:GLU79 4.2 15.8 1.0
NZ H:LYS23 4.2 33.9 1.0
CG H:GLU79 4.4 15.8 1.0
O22 D:BCN202 4.4 18.7 1.0
O H:HOH374 4.4 44.1 1.0
O D:HOH317 4.5 34.9 1.0
OE1 D:GLU79 4.5 16.1 1.0
CB C:ASN103 4.5 42.5 1.0
O4 D:BCN203 4.6 27.4 1.0
OD1 C:ASN103 4.8 60.5 1.0

Calcium binding site 9 out of 10 in 5elf

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


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

b:14.5
occ:1.00
O21 E:BCN203 2.3 17.2 1.0
O E:HOH303 2.3 24.1 1.0
OE2 G:GLU79 2.3 15.2 1.0
O4 E:BCN203 2.3 23.3 1.0
O6 E:BCN203 2.4 25.6 1.0
OE1 E:GLU79 2.4 15.7 1.0
OE2 E:GLU79 2.5 15.0 1.0
CD E:GLU79 2.8 15.8 1.0
N1 E:BCN203 3.2 25.8 1.0
C2 E:BCN203 3.2 19.9 1.0
C5 E:BCN203 3.3 27.9 1.0
C1 E:BCN203 3.3 22.8 1.0
C4 E:BCN203 3.3 25.3 1.0
C6 E:BCN203 3.4 25.4 1.0
CD G:GLU79 3.5 15.7 1.0
C3 E:BCN203 3.5 26.9 1.0
CA E:CA204 3.9 14.8 1.0
O G:HOH304 4.2 26.9 1.0
O6 E:BCN201 4.2 24.3 1.0
CG G:GLU79 4.2 13.6 1.0
CG E:GLU79 4.4 13.4 1.0
OE1 G:GLU79 4.4 16.0 1.0
O22 E:BCN203 4.5 17.1 1.0
ND2 F:ASN103 4.5 41.6 1.0
NZ E:LYS23 4.5 38.8 1.0
O G:HOH340 4.6 30.5 1.0
O F:ASN103 4.8 35.9 1.0
CB F:ASN103 4.8 37.2 1.0

Calcium binding site 10 out of 10 in 5elf

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


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 A-Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca204

b:14.8
occ:1.00
O6 E:BCN201 1.9 24.3 1.0
O21 E:BCN201 2.3 17.1 1.0
O G:HOH304 2.4 26.9 1.0
OE2 E:GLU79 2.4 15.0 1.0
OE1 G:GLU79 2.4 16.0 1.0
O4 E:BCN201 2.5 19.1 1.0
OE2 G:GLU79 2.6 15.2 1.0
CD G:GLU79 2.9 15.7 1.0
N1 E:BCN201 3.0 21.0 1.0
C6 E:BCN201 3.1 22.2 1.0
C2 E:BCN201 3.2 18.2 1.0
C3 E:BCN201 3.3 23.7 1.0
C5 E:BCN201 3.4 22.0 1.0
C4 E:BCN201 3.4 20.9 1.0
C1 E:BCN201 3.5 19.6 1.0
CD E:GLU79 3.5 15.8 1.0
CA E:CA202 3.9 14.5 1.0
O G:HOH316 4.0 41.9 1.0
NZ G:LYS23 4.1 16.5 0.5
NZ G:LYS23 4.2 23.5 0.5
O E:HOH303 4.2 24.1 1.0
CG E:GLU79 4.3 13.4 1.0
O22 E:BCN201 4.4 18.9 1.0
CG G:GLU79 4.4 13.6 1.0
OD1 D:ASN103 4.4 41.3 1.0
OE1 E:GLU79 4.5 15.7 1.0
O E:HOH304 4.6 30.7 1.0
O6 E:BCN203 4.8 25.6 1.0
ND2 D:ASN103 4.8 43.5 1.0
CG D:ASN103 4.9 43.3 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: Sat Dec 12 05:23:29 2020

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