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Calcium in PDB 6hmw: Cholera Toxin Classical B-Pentamer in Complex with Fucose

Protein crystallography data

The structure of Cholera Toxin Classical B-Pentamer in Complex with Fucose, PDB code: 6hmw 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) 47.42 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.785, 100.543, 93.012, 90.00, 117.00, 90.00
R / Rfree (%) 18.7 / 23.7

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 6hmw

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


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

b:25.4
occ:1.00
 O22 A:BCN205 2.2 23.1 1.0
OE2 J:GLU79 2.2 26.7 1.0
O4 A:BCN205 2.4 24.4 1.0
OE1 A:GLU79 2.5 25.7 1.0
O6 A:BCN205 2.5 29.0 1.0
OD1 I:ASN103 2.6 51.2 1.0
OE2 A:GLU79 2.7 26.6 1.0
N1 A:BCN205 2.7 26.9 1.0
CD A:GLU79 2.9 25.2 1.0
C2 A:BCN205 3.2 25.3 1.0
C4 A:BCN205 3.2 26.6 1.0
C5 A:BCN205 3.3 28.1 1.0
C6 A:BCN205 3.3 27.9 1.0
C3 A:BCN205 3.4 26.4 1.0
C1 A:BCN205 3.5 26.0 1.0
CD J:GLU79 3.5 26.6 1.0
CG I:ASN103 3.7 55.9 1.0
O E:HOH301 3.8 38.9 1.0
CA A:CA204 4.0 23.9 1.0
CG J:GLU79 4.3 27.0 1.0
O21 A:BCN205 4.3 24.9 1.0
CB I:ASN103 4.4 55.3 1.0
OE1 J:GLU79 4.4 27.5 1.0
CG A:GLU79 4.5 23.8 1.0
O4 A:BCN202 4.6 35.5 1.0
ND2 I:ASN103 4.7 57.1 1.0
NZ A:LYS23 4.8 41.1 1.0
CA I:ASN103 4.9 53.7 1.0
NZ J:LYS23 4.9 28.7 0.5

Calcium binding site 2 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:23.9
occ:1.00
 OE2 A:GLU79 2.3 26.6 1.0
OE1 J:GLU79 2.3 27.5 1.0
O E:HOH301 2.3 38.9 1.0
O22 A:BCN202 2.4 31.8 1.0
O4 A:BCN202 2.5 35.5 1.0
O6 A:BCN202 2.6 28.8 1.0
N1 A:BCN202 2.7 29.6 1.0
OE2 J:GLU79 2.7 26.7 1.0
CD J:GLU79 2.8 26.6 1.0
C4 A:BCN202 3.2 33.4 1.0
C5 A:BCN202 3.2 29.7 1.0
C6 A:BCN202 3.3 28.3 1.0
C2 A:BCN202 3.3 28.6 1.0
C3 A:BCN202 3.4 31.6 1.0
CD A:GLU79 3.5 25.2 1.0
C1 A:BCN202 3.5 29.2 1.0
CA A:CA201 4.0 25.4 1.0
O E:ASN103 4.0 52.5 1.0
NZ J:LYS23 4.1 32.8 0.5
OD1 I:ASN103 4.2 51.2 1.0
CG A:GLU79 4.2 23.8 1.0
OXT E:ASN103 4.3 50.4 1.0
CG J:GLU79 4.3 27.0 1.0
O21 A:BCN202 4.4 25.4 1.0
OE1 A:GLU79 4.4 25.7 1.0
O4 A:BCN205 4.5 24.4 1.0
C E:ASN103 4.6 47.6 1.0
CE J:LYS23 4.9 32.1 0.5

Calcium binding site 3 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:23.9
occ:1.00
 O B:HOH323 2.2 22.0 1.0
O4 B:BCN205 2.2 26.7 1.0
OE2 I:GLU79 2.3 23.3 1.0
O21 B:BCN205 2.4 25.0 1.0
O6 B:BCN205 2.5 31.2 1.0
OE1 B:GLU79 2.5 25.1 1.0
OE2 B:GLU79 2.6 24.6 1.0
N1 B:BCN205 2.6 28.2 1.0
CD B:GLU79 2.9 24.4 1.0
C4 B:BCN205 3.2 27.5 1.0
C2 B:BCN205 3.3 26.7 1.0
C5 B:BCN205 3.3 28.1 1.0
C6 B:BCN205 3.3 28.3 1.0
C3 B:BCN205 3.4 27.4 1.0
C1 B:BCN205 3.5 28.1 1.0
CD I:GLU79 3.6 23.5 1.0
O B:HOH327 3.9 25.8 1.0
NZ B:LYS23 4.0 27.9 0.5
CA B:CA206 4.0 22.8 1.0
O H:ASN103 4.0 49.9 1.0
CG I:GLU79 4.3 22.7 1.0
CG B:GLU79 4.4 22.2 1.0
O4 B:BCN201 4.4 29.8 1.0
O22 B:BCN205 4.5 27.0 1.0
OE1 I:GLU79 4.5 24.4 1.0
NZ B:LYS23 4.7 29.1 0.5
C H:ASN103 4.7 49.5 1.0
OXT H:ASN103 4.8 52.1 1.0

Calcium binding site 4 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca206

b:22.8
occ:1.00
 O B:HOH327 2.0 25.8 1.0
O4 B:BCN201 2.1 29.8 1.0
OE2 B:GLU79 2.3 24.6 1.0
O22 B:BCN201 2.4 27.9 1.0
OE1 I:GLU79 2.5 24.4 1.0
O6 B:BCN201 2.6 31.5 1.0
OE2 I:GLU79 2.7 23.3 1.0
N1 B:BCN201 2.7 31.4 1.0
CD I:GLU79 2.9 23.5 1.0
C4 B:BCN201 3.2 31.0 1.0
C2 B:BCN201 3.3 27.0 1.0
C5 B:BCN201 3.3 29.9 1.0
C6 B:BCN201 3.4 29.4 1.0
C1 B:BCN201 3.5 30.4 1.0
C3 B:BCN201 3.5 30.6 1.0
CD B:GLU79 3.6 24.4 1.0
O B:HOH323 3.9 22.0 1.0
CA B:CA203 4.0 23.9 1.0
NZ I:LYS23 4.0 40.4 1.0
CG B:GLU79 4.2 22.2 1.0
OXT A:ASN103 4.3 51.0 1.0
CG I:GLU79 4.4 22.7 1.0
O21 B:BCN201 4.4 24.3 1.0
OE1 B:GLU79 4.5 25.1 1.0
O4 B:BCN205 4.6 26.7 1.0
C A:ASN103 4.9 52.4 1.0

Calcium binding site 5 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:25.4
occ:1.00
 O4 C:BCN206 2.3 29.1 1.0
O C:HOH327 2.3 34.4 1.0
OE2 H:GLU79 2.4 26.5 1.0
O22 C:BCN206 2.5 28.1 1.0
OE1 C:GLU79 2.5 23.0 1.0
N1 C:BCN206 2.6 27.7 1.0
O6 C:BCN206 2.7 37.9 1.0
OE2 C:GLU79 2.7 21.5 1.0
CD C:GLU79 2.9 22.1 1.0
C4 C:BCN206 3.3 27.4 1.0
C2 C:BCN206 3.3 27.1 1.0
C5 C:BCN206 3.4 28.9 1.0
C3 C:BCN206 3.4 26.8 1.0
C1 C:BCN206 3.5 29.1 1.0
C6 C:BCN206 3.5 33.9 1.0
CD H:GLU79 3.5 27.2 1.0
CA C:CA204 4.1 22.5 1.0
CG H:GLU79 4.2 25.9 1.0
O B:HOH314 4.3 32.7 1.0
CG C:GLU79 4.4 21.1 1.0
OE1 H:GLU79 4.5 29.6 1.0
O21 C:BCN206 4.5 30.5 1.0
O4 C:BCN205 4.8 23.1 1.0
NZ C:LYS23 5.0 43.0 1.0

Calcium binding site 6 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:22.5
occ:1.00
 OE2 C:GLU79 2.3 21.5 1.0
O4 C:BCN205 2.3 23.1 1.0
O6 C:BCN205 2.3 29.4 1.0
O21 C:BCN205 2.4 26.9 1.0
O B:HOH314 2.4 32.7 1.0
OE1 H:GLU79 2.5 29.6 1.0
OE2 H:GLU79 2.7 26.5 1.0
N1 C:BCN205 2.7 25.2 1.0
CD H:GLU79 3.0 27.2 1.0
C6 C:BCN205 3.3 25.9 1.0
C5 C:BCN205 3.3 25.6 1.0
C4 C:BCN205 3.3 23.0 1.0
C2 C:BCN205 3.3 27.4 1.0
CD C:GLU79 3.4 22.1 1.0
C3 C:BCN205 3.5 23.9 1.0
C1 C:BCN205 3.6 26.4 1.0
O C:HOH327 4.1 34.4 1.0
CA C:CA202 4.1 25.4 1.0
CG C:GLU79 4.1 21.1 1.0
OE1 C:GLU79 4.4 23.0 1.0
O22 C:BCN205 4.5 27.5 1.0
CG H:GLU79 4.5 25.9 1.0
NZ H:LYS23 4.6 43.9 1.0
O B:ASN103 4.7 50.8 1.0
O4 C:BCN206 4.9 29.1 1.0

Calcium binding site 7 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:27.2
occ:1.00
 O4 D:BCN205 2.3 32.8 1.0
OE2 G:GLU79 2.4 27.0 1.0
O22 D:BCN205 2.4 34.5 1.0
OE1 D:GLU79 2.5 26.9 1.0
OE2 D:GLU79 2.6 25.0 1.0
N1 D:BCN205 2.6 32.5 1.0
CD D:GLU79 2.9 25.2 1.0
O6 D:BCN205 2.9 31.8 1.0
C6 D:BCN205 3.0 30.9 1.0
OD1 F:ASN103 3.2 48.9 1.0
C5 D:BCN205 3.3 29.8 1.0
C2 D:BCN205 3.3 33.1 1.0
C4 D:BCN205 3.3 30.3 1.0
C3 D:BCN205 3.4 31.8 1.0
C1 D:BCN205 3.5 34.4 1.0
CD G:GLU79 3.5 27.7 1.0
CB F:ASN103 3.7 47.5 1.0
CG F:ASN103 3.9 49.5 1.0
O G:HOH322 4.1 38.0 1.0
CA D:CA206 4.1 26.6 1.0
CG G:GLU79 4.2 26.7 1.0
CG D:GLU79 4.4 24.0 1.0
O21 D:BCN205 4.4 30.5 1.0
O4 D:BCN201 4.5 31.6 1.0
OE1 G:GLU79 4.6 27.6 1.0
NZ D:LYS23 4.6 28.5 0.5
NZ G:LYS23 4.9 40.1 1.0
CE D:LYS23 4.9 29.7 0.5
NZ D:LYS23 4.9 29.0 0.5

Calcium binding site 8 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca206

b:26.6
occ:1.00
 OE2 D:GLU79 2.3 25.0 1.0
O4 D:BCN201 2.3 31.6 1.0
O G:HOH322 2.4 38.0 1.0
O6 D:BCN201 2.4 37.9 1.0
O21 D:BCN201 2.4 25.8 1.0
OE2 G:GLU79 2.6 27.0 1.0
OE1 G:GLU79 2.6 27.6 1.0
N1 D:BCN201 2.7 30.1 1.0
CD G:GLU79 2.9 27.7 1.0
C4 D:BCN201 3.2 32.6 1.0
C2 D:BCN201 3.3 26.5 1.0
C6 D:BCN201 3.3 34.0 1.0
C5 D:BCN201 3.4 32.3 1.0
C3 D:BCN201 3.4 30.9 1.0
C1 D:BCN201 3.4 31.5 1.0
CD D:GLU79 3.5 25.2 1.0
CA D:CA203 4.1 27.2 1.0
CG D:GLU79 4.1 24.0 1.0
O22 D:BCN201 4.4 26.5 1.0
CG G:GLU79 4.5 26.7 1.0
OE1 D:GLU79 4.5 26.9 1.0
ND2 C:ASN103 4.5 54.6 1.0
OD1 F:ASN103 4.6 48.9 1.0
O4 D:BCN205 4.7 32.8 1.0
NZ D:LYS23 4.8 29.0 0.5

Calcium binding site 9 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca203

b:30.4
occ:1.00
 OE2 F:GLU79 2.1 28.9 1.0
O22 E:BCN206 2.2 30.7 1.0
O6 E:BCN206 2.4 43.2 1.0
O4 E:BCN206 2.4 34.6 1.0
OD1 J:ASN103 2.5 44.0 0.5
OE1 E:GLU79 2.6 27.5 1.0
OE2 E:GLU79 2.6 26.8 1.0
N1 E:BCN206 2.7 35.3 1.0
CD E:GLU79 2.9 26.3 1.0
C6 E:BCN206 3.2 39.2 1.0
C2 E:BCN206 3.2 34.0 1.0
C5 E:BCN206 3.3 35.9 1.0
CD F:GLU79 3.3 28.7 1.0
C4 E:BCN206 3.4 36.1 1.0
C1 E:BCN206 3.5 33.4 1.0
C3 E:BCN206 3.6 35.5 1.0
CG J:ASN103 3.7 45.4 0.5
CA E:CA205 3.9 28.1 1.0
NZ E:LYS23 3.9 38.4 1.0
OXT J:ASN103 4.1 51.6 0.5
CG F:GLU79 4.1 28.0 1.0
O D:HOH301 4.3 44.0 1.0
OE1 F:GLU79 4.3 29.6 1.0
O21 E:BCN206 4.3 32.5 1.0
CB J:ASN103 4.4 44.6 0.5
CG E:GLU79 4.4 24.6 1.0
O4 E:BCN201 4.5 33.4 1.0
CE E:LYS23 4.7 37.0 1.0
ND2 J:ASN103 4.8 46.8 0.5
CB J:ASN103 4.8 48.2 0.5
NZ F:LYS23 4.8 42.9 1.0

Calcium binding site 10 out of 10 in 6hmw

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


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 Fucose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca205

b:28.1
occ:1.00
 O21 E:BCN201 2.2 28.3 1.0
O4 E:BCN201 2.2 33.4 1.0
O D:HOH301 2.4 44.0 1.0
OE1 F:GLU79 2.4 29.6 1.0
OE2 E:GLU79 2.4 26.8 1.0
O6 E:BCN201 2.5 35.0 1.0
OE2 F:GLU79 2.6 28.9 1.0
N1 E:BCN201 2.8 31.6 1.0
CD F:GLU79 2.8 28.7 1.0
C6 E:BCN201 3.2 32.1 1.0
C2 E:BCN201 3.2 29.2 1.0
C5 E:BCN201 3.3 32.6 1.0
C4 E:BCN201 3.4 32.8 1.0
C1 E:BCN201 3.6 30.3 1.0
CD E:GLU79 3.6 26.3 1.0
C3 E:BCN201 3.6 31.2 1.0
CA E:CA203 3.9 30.4 1.0
OD1 J:ASN103 4.2 44.0 0.5
CG E:GLU79 4.3 24.6 1.0
ND2 D:ASN103 4.3 36.3 0.5
CG F:GLU79 4.4 28.0 1.0
O D:ASN103 4.4 34.5 0.5
O22 E:BCN201 4.4 25.5 1.0
OE1 E:GLU79 4.5 27.5 1.0
O4 E:BCN206 4.5 34.6 1.0
CG D:ASN103 4.7 37.4 0.5
CB D:ASN103 4.8 35.5 0.5
O6 E:BCN206 5.0 43.2 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 08:28:19 2024

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