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Calcium in PDB 5elb: Cholera Toxin Classical B-Pentamer in Complex with Lewis-Y

Protein crystallography data

The structure of Cholera Toxin Classical B-Pentamer in Complex with Lewis-Y, PDB code: 5elb 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) 49.49 / 1.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.333, 98.984, 152.019, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 15.5

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 5elb

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Calcium binding site 1 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:11.8
occ:1.00
 O6 A:BCN204 2.3 21.5 1.0
O22 A:BCN204 2.3 11.9 1.0
OE2 H:GLU79 2.4 14.2 1.0
O4 A:BCN204 2.4 22.7 1.0
O A:HOH406 2.4 24.6 1.0
OE1 A:GLU79 2.4 14.6 1.0
OE2 A:GLU79 2.6 16.7 1.0
N1 A:BCN204 2.7 19.0 1.0
CD A:GLU79 2.9 11.9 1.0
C2 A:BCN204 3.2 11.2 1.0
C6 A:BCN204 3.3 25.8 1.0
C3 A:BCN204 3.3 22.2 1.0
C4 A:BCN204 3.3 19.3 1.0
C5 A:BCN204 3.4 22.1 1.0
C1 A:BCN204 3.4 16.5 1.0
CD H:GLU79 3.5 11.6 1.0
CA A:CA205 3.9 12.2 1.0
O A:HOH411 4.0 24.8 1.0
O A:HOH334 4.0 38.6 1.0
CG H:GLU79 4.2 11.8 1.0
CG A:GLU79 4.4 12.7 1.0
O A:HOH322 4.4 36.4 1.0
O21 A:BCN204 4.4 13.1 1.0
OE1 H:GLU79 4.4 14.1 1.0
O A:HOH309 4.5 36.8 1.0
ND2 G:ASN103 4.6 35.2 1.0
O4 A:BCN206 4.6 22.4 1.0
O A:HOH374 4.8 18.6 0.5

Calcium binding site 2 out of 10 in 5elb

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Calcium binding site 2 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:12.2
occ:1.00
 O4 A:BCN206 2.3 22.4 1.0
O21 A:BCN206 2.3 13.5 1.0
OE2 A:GLU79 2.4 16.7 1.0
O A:HOH411 2.4 24.8 1.0
O6 A:BCN206 2.4 19.8 1.0
OE1 H:GLU79 2.5 14.1 1.0
OE2 H:GLU79 2.6 14.2 1.0
N1 A:BCN206 2.7 17.8 1.0
CD H:GLU79 2.9 11.6 1.0
C2 A:BCN206 3.3 12.5 1.0
C4 A:BCN206 3.3 26.6 1.0
C6 A:BCN206 3.4 20.6 1.0
C3 A:BCN206 3.4 20.8 1.0
C5 A:BCN206 3.4 23.6 1.0
C1 A:BCN206 3.5 15.9 1.0
CD A:GLU79 3.5 11.9 1.0
CA A:CA201 3.9 11.8 1.0
O A:HOH406 4.1 24.6 1.0
NZ H:LYS23 4.2 16.4 0.4
CG A:GLU79 4.3 12.7 1.0
O A:HOH322 4.4 36.4 1.0
ND2 E:ASN103 4.4 35.7 1.0
CG H:GLU79 4.4 11.8 1.0
OE1 A:GLU79 4.4 14.6 1.0
O A:HOH374 4.4 18.6 0.5
O22 A:BCN206 4.5 14.2 1.0
O A:HOH374 4.6 16.6 0.5
O6 A:BCN204 4.7 21.5 1.0

Calcium binding site 3 out of 10 in 5elb

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Calcium binding site 3 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:11.1
occ:1.00
 O22 B:BCN202 2.3 12.5 1.0
OE2 G:GLU79 2.3 14.0 1.0
O F:HOH1363 2.4 27.5 1.0
O4 B:BCN202 2.4 19.0 1.0
O6 B:BCN202 2.4 23.8 1.0
OE1 B:GLU79 2.4 13.1 1.0
OE2 B:GLU79 2.6 14.9 1.0
N1 B:BCN202 2.6 21.1 1.0
CD B:GLU79 2.9 11.9 1.0
C2 B:BCN202 3.3 12.8 1.0
C6 B:BCN202 3.3 27.4 1.0
C4 B:BCN202 3.4 27.2 1.0
C1 B:BCN202 3.4 18.9 1.0
C3 B:BCN202 3.4 29.1 1.0
C5 B:BCN202 3.4 27.0 1.0
CD G:GLU79 3.5 10.8 1.0
CA B:CA205 3.9 12.3 1.0
O B:HOH410 4.1 24.6 1.0
NZ B:LYS23 4.1 26.9 0.6
O B:HOH387 4.2 72.4 1.0
O B:HOH307 4.2 41.3 1.0
CG G:GLU79 4.3 10.3 1.0
CG B:GLU79 4.4 11.4 1.0
OE1 G:GLU79 4.4 13.3 1.0
NZ B:LYS23 4.4 12.1 0.4
O21 B:BCN202 4.4 14.1 1.0
O B:HOH388 4.5 15.2 0.5
O B:HOH388 4.5 15.1 0.5
O4 B:BCN206 4.6 22.1 1.0
O F:ASN103 4.7 39.1 1.0
CB F:ASN103 5.0 33.5 1.0

Calcium binding site 4 out of 10 in 5elb

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Calcium binding site 4 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:12.3
occ:1.00
 O4 B:BCN206 2.2 22.1 1.0
O21 B:BCN206 2.3 12.6 1.0
O6 B:BCN206 2.3 21.4 1.0
OE2 B:GLU79 2.4 14.9 1.0
O B:HOH410 2.4 24.6 1.0
OE1 G:GLU79 2.4 13.3 1.0
OE2 G:GLU79 2.5 14.0 1.0
N1 B:BCN206 2.7 17.9 1.0
CD G:GLU79 2.9 10.8 1.0
C4 B:BCN206 3.2 26.9 1.0
C2 B:BCN206 3.2 12.1 1.0
C6 B:BCN206 3.3 18.8 1.0
C5 B:BCN206 3.4 23.0 1.0
C3 B:BCN206 3.5 20.3 1.0
C1 B:BCN206 3.5 17.5 1.0
CD B:GLU79 3.5 11.9 1.0
CA B:CA201 3.9 11.1 1.0
O G:HOH313 3.9 37.0 1.0
O F:HOH1363 4.0 27.5 1.0
NZ G:LYS23 4.2 17.7 0.6
CG B:GLU79 4.3 11.4 1.0
O B:HOH307 4.3 41.3 1.0
CG G:GLU79 4.4 10.3 1.0
O22 B:BCN206 4.4 13.8 1.0
OE1 B:GLU79 4.4 13.1 1.0
O B:HOH320 4.5 38.5 1.0
OD1 A:ASN103 4.5 39.4 1.0
O4 B:BCN202 4.7 19.0 1.0
O B:HOH388 4.9 15.2 0.5

Calcium binding site 5 out of 10 in 5elb

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Calcium binding site 5 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:11.4
occ:1.00
 O4 C:BCN206 2.3 19.8 1.0
O6 C:BCN206 2.3 23.5 1.0
O22 C:BCN206 2.3 12.2 1.0
OE1 F:GLU79 2.4 15.4 1.0
O J:HOH1325 2.4 25.8 1.0
OE2 C:GLU79 2.5 13.0 1.0
OE1 C:GLU79 2.5 14.9 1.0
N1 C:BCN206 2.7 21.6 1.0
CD C:GLU79 2.9 11.6 1.0
C2 C:BCN206 3.2 11.5 1.0
C6 C:BCN206 3.3 24.8 1.0
C4 C:BCN206 3.4 25.6 1.0
C5 C:BCN206 3.4 25.9 1.0
C3 C:BCN206 3.4 27.3 1.0
C1 C:BCN206 3.4 18.2 1.0
CD F:GLU79 3.6 10.8 1.0
CA C:CA204 3.9 11.4 1.0
O C:HOH418 4.0 26.1 1.0
CG F:GLU79 4.3 9.8 1.0
O C:HOH318 4.4 53.8 1.0
CG C:GLU79 4.4 10.5 1.0
O21 C:BCN206 4.4 13.8 1.0
OE2 F:GLU79 4.4 13.0 1.0
O C:HOH413 4.5 15.9 0.5
O6 C:BCN205 4.5 23.2 1.0
O C:HOH413 4.6 16.8 0.5
ND2 J:ASN103 4.6 36.4 1.0
O C:HOH306 4.8 16.3 0.4
OXT J:ASN103 4.8 36.4 1.0
CB J:ASN103 5.0 31.3 1.0

Calcium binding site 6 out of 10 in 5elb

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Calcium binding site 6 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:11.4
occ:1.00
 O6 C:BCN205 2.2 23.2 1.0
O21 C:BCN205 2.3 11.9 1.0
OE1 C:GLU79 2.4 14.9 1.0
O4 C:BCN205 2.4 17.7 1.0
OE2 F:GLU79 2.4 13.0 1.0
O C:HOH418 2.5 26.1 1.0
OE1 F:GLU79 2.6 15.4 1.0
N1 C:BCN205 2.7 16.2 1.0
CD F:GLU79 2.9 10.8 1.0
C6 C:BCN205 3.2 23.7 1.0
C2 C:BCN205 3.3 11.9 1.0
C3 C:BCN205 3.3 17.8 1.0
C4 C:BCN205 3.4 16.4 1.0
C5 C:BCN205 3.4 21.2 1.0
C1 C:BCN205 3.4 14.3 1.0
CD C:GLU79 3.5 11.6 1.0
CA C:CA201 3.9 11.4 1.0
O F:HOH1373 4.1 82.0 1.0
O J:HOH1325 4.1 25.8 1.0
NZ F:LYS23 4.2 17.0 0.7
CG C:GLU79 4.2 10.5 1.0
O C:HOH318 4.4 53.8 1.0
CG F:GLU79 4.4 9.8 1.0
ND2 B:ASN103 4.4 37.2 1.0
O22 C:BCN205 4.4 12.9 1.0
OE2 C:GLU79 4.4 13.0 1.0
O C:HOH306 4.6 15.1 0.6
O C:HOH306 4.6 16.3 0.4
O4 C:BCN206 4.7 19.8 1.0
O C:HOH413 4.9 16.8 0.5

Calcium binding site 7 out of 10 in 5elb

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Calcium binding site 7 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:11.4
occ:1.00
 O22 D:BCN203 2.3 11.9 1.0
OE2 J:GLU79 2.3 13.1 1.0
O4 D:BCN203 2.4 20.0 1.0
O6 D:BCN203 2.4 20.6 1.0
O D:HOH397 2.4 19.9 1.0
OE1 D:GLU79 2.5 12.7 1.0
OE2 D:GLU79 2.6 12.3 1.0
N1 D:BCN203 2.7 20.6 1.0
CD D:GLU79 2.9 11.3 1.0
C2 D:BCN203 3.3 11.6 1.0
C4 D:BCN203 3.4 26.7 1.0
C3 D:BCN203 3.4 26.9 1.0
C5 D:BCN203 3.4 26.6 1.0
C6 D:BCN203 3.4 20.8 1.0
C1 D:BCN203 3.5 17.1 1.0
CD J:GLU79 3.6 11.0 1.0
CA D:CA206 4.0 11.3 1.0
O C:HOH355 4.0 19.4 1.0
O D:HOH330 4.0 27.5 0.5
NZ D:LYS23 4.0 23.9 0.6
CG J:GLU79 4.3 10.3 1.0
O D:HOH307 4.3 33.2 1.0
CG D:GLU79 4.4 9.9 1.0
O D:HOH330 4.4 23.3 0.5
O21 D:BCN203 4.5 14.0 1.0
O D:HOH331 4.5 32.6 1.0
OE1 J:GLU79 4.5 13.6 1.0
O4 D:BCN201 4.7 21.2 1.0
CB I:ASN103 4.9 49.5 1.0

Calcium binding site 8 out of 10 in 5elb

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Calcium binding site 8 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca206

b:11.3
occ:1.00
 O4 D:BCN201 2.3 21.2 1.0
O21 D:BCN201 2.4 11.5 1.0
OE2 D:GLU79 2.4 12.3 1.0
O6 D:BCN201 2.4 19.0 1.0
O C:HOH355 2.4 19.4 1.0
OE1 J:GLU79 2.4 13.6 1.0
OE2 J:GLU79 2.6 13.1 1.0
N1 D:BCN201 2.7 17.1 1.0
CD J:GLU79 2.9 11.0 1.0
C2 D:BCN201 3.3 10.9 1.0
C4 D:BCN201 3.3 28.0 1.0
C6 D:BCN201 3.4 18.6 1.0
C5 D:BCN201 3.4 22.0 1.0
C3 D:BCN201 3.4 21.4 1.0
C1 D:BCN201 3.5 15.4 1.0
CD D:GLU79 3.5 11.3 1.0
CA D:CA202 4.0 11.4 1.0
O D:HOH397 4.1 19.9 1.0
O J:HOH1302 4.1 29.6 0.5
CG D:GLU79 4.2 9.9 1.0
O J:HOH1302 4.3 32.3 0.5
O D:HOH307 4.4 33.2 1.0
CG J:GLU79 4.4 10.3 1.0
O22 D:BCN201 4.4 12.5 1.0
OE1 D:GLU79 4.5 12.7 1.0
O D:HOH312 4.5 35.9 1.0
O4 D:BCN203 4.7 20.0 1.0
OXT C:ASN103 4.7 48.0 1.0

Calcium binding site 9 out of 10 in 5elb

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Calcium binding site 9 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:12.0
occ:1.00
 O4 E:BCN203 2.3 24.2 1.0
O22 E:BCN203 2.4 12.4 1.0
OE2 I:GLU79 2.4 14.1 1.0
O E:HOH306 2.4 19.7 1.0
O6 E:BCN203 2.4 16.6 1.0
OE1 E:GLU79 2.5 15.0 1.0
OE2 E:GLU79 2.6 13.4 1.0
N1 E:BCN203 2.7 15.7 1.0
CD E:GLU79 2.9 14.1 1.0
C4 E:BCN203 3.2 25.0 1.0
C2 E:BCN203 3.3 12.3 1.0
C6 E:BCN203 3.4 16.3 1.0
C5 E:BCN203 3.4 17.8 1.0
C3 E:BCN203 3.4 18.7 1.0
C1 E:BCN203 3.4 15.8 1.0
CD I:GLU79 3.6 12.0 1.0
CA E:CA206 4.0 12.0 1.0
O D:HOH357 4.0 19.4 1.0
O E:HOH330 4.1 33.8 0.5
CG I:GLU79 4.2 11.2 1.0
NZ E:LYS23 4.3 23.2 0.5
O E:HOH330 4.3 25.2 0.5
CG E:GLU79 4.4 12.3 1.0
O21 E:BCN203 4.4 13.7 1.0
O E:HOH309 4.4 42.0 1.0
OE1 I:GLU79 4.5 15.8 1.0
O E:HOH312 4.7 27.6 1.0
O4 E:BCN201 4.7 23.4 1.0
ND2 H:ASN103 4.9 38.2 1.0

Calcium binding site 10 out of 10 in 5elb

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Calcium binding site 10 out of 10 in the Cholera Toxin Classical 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 Classical B-Pentamer in Complex with Lewis-Y within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca206

b:12.0
occ:1.00
 O4 E:BCN201 2.3 23.4 1.0
O21 E:BCN201 2.4 12.2 1.0
O D:HOH357 2.4 19.4 1.0
OE2 E:GLU79 2.4 13.4 1.0
O6 E:BCN201 2.4 18.0 1.0
OE1 I:GLU79 2.5 15.8 1.0
OE2 I:GLU79 2.6 14.1 1.0
N1 E:BCN201 2.7 19.4 1.0
CD I:GLU79 2.9 12.0 1.0
C2 E:BCN201 3.3 12.2 1.0
C4 E:BCN201 3.3 27.0 1.0
C3 E:BCN201 3.4 23.9 1.0
C6 E:BCN201 3.4 20.1 1.0
C5 E:BCN201 3.4 23.6 1.0
C1 E:BCN201 3.5 16.9 1.0
CD E:GLU79 3.6 14.1 1.0
CA E:CA202 4.0 12.0 1.0
O E:HOH306 4.0 19.7 1.0
NZ I:LYS23 4.1 15.6 0.3
O I:HOH1389 4.1 27.4 0.4
CG E:GLU79 4.3 12.3 1.0
O E:HOH309 4.3 42.0 1.0
O I:HOH1389 4.4 26.5 0.6
OXT D:ASN103 4.4 37.7 1.0
CG I:GLU79 4.4 11.2 1.0
O22 E:BCN201 4.5 13.4 1.0
OE1 E:GLU79 4.5 15.0 1.0
O4 E:BCN203 4.6 24.2 1.0
O D:ASN103 4.7 37.0 1.0
C D:ASN103 4.8 34.3 1.0
NZ E:LYS23 5.0 23.2 0.5

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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