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Sodium in PDB 6ial: Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose

Protein crystallography data

The structure of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose, PDB code: 6ial was solved by J.B.Heim, J.E.Heggelund, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.73 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.079, 65.587, 96.266, 90.00, 108.64, 90.00
R / Rfree (%) 17.5 / 20.1

Other elements in 6ial:

The structure of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose (pdb code 6ial). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose, PDB code: 6ial:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 6ial

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Sodium binding site 1 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:18.0
occ:1.00
 O D:HOH314 2.2 22.2 1.0
OE2 C:GLU79 2.4 16.8 0.5
OE1 D:GLU79 2.6 21.5 1.0
OE2 D:GLU79 2.6 24.2 1.0
OE1 C:GLU79 2.7 21.8 0.5
O C:HOH367 2.8 32.5 1.0
CD D:GLU79 2.9 24.6 1.0
CD C:GLU79 3.5 26.2 0.5
CD C:GLU79 3.6 22.3 0.5
NZ D:LYS23 4.0 16.9 0.5
NA D:NA205 4.1 18.0 1.0
O D:HOH344 4.1 22.2 1.0
OXT B:ASN103 4.1 38.3 1.0
OE2 C:GLU79 4.2 22.8 0.5
CG C:GLU79 4.3 12.2 0.5
CG C:GLU79 4.3 11.6 0.5
O B:ASN103 4.3 37.6 1.0
O2 D:GOL201 4.3 29.5 1.0
CG D:GLU79 4.4 14.0 1.0
OE1 C:GLU79 4.5 15.9 0.5
C B:ASN103 4.7 23.6 1.0
O B:HOH342 4.8 31.8 1.0
O3 D:GOL201 4.9 30.7 1.0
O D:HOH341 4.9 24.6 1.0

Sodium binding site 2 out of 14 in 6ial

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Sodium binding site 2 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na204

b:8.6
occ:1.00
 O D:HOH302 0.3 6.0 1.0
O1 D:GOL202 2.2 28.5 1.0
O3 D:GOL202 2.3 13.3 1.0
O D:HOH322 2.4 14.4 1.0
O D:ILE20 2.4 7.6 1.0
O D:HOH317 2.5 12.2 1.0
C1 D:GOL202 2.6 15.6 1.0
O D:HOH318 2.6 11.9 1.0
C3 D:GOL202 3.3 21.4 1.0
C2 D:GOL202 3.5 18.3 1.0
C D:ILE20 3.6 6.4 1.0
O2 D:GOL202 4.1 34.7 1.0
CA D:ILE20 4.2 7.7 1.0
OG D:SER44 4.3 11.6 1.0
O D:ASN21 4.4 7.8 0.5
O D:ASN21 4.4 7.6 0.5
O D:THR19 4.5 9.7 1.0
O D:HOH351 4.6 19.6 1.0
CB D:ASP22 4.6 7.3 1.0
N D:ASN21 4.6 7.5 0.5
N D:ASN21 4.6 8.3 0.5
CB D:SER44 4.6 11.3 1.0
C D:ASN21 4.7 6.8 0.5
C D:ASN21 4.7 6.4 0.5
CB D:ASN21 4.8 7.9 0.5
OE2 D:GLU46 4.8 18.8 1.0
CB D:ASN21 4.9 12.3 0.5
OD2 D:ASP22 4.9 17.3 1.0
CA D:ASN21 4.9 7.3 0.5
CA D:ASN21 4.9 9.3 0.5

Sodium binding site 3 out of 14 in 6ial

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Sodium binding site 3 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na205

b:18.0
occ:1.00
 O1 D:GOL201 2.2 22.7 1.0
O D:HOH336 2.4 35.1 1.0
OE1 C:GLU79 2.4 15.9 0.5
OE2 D:GLU79 2.4 24.2 1.0
O2 D:GOL201 2.4 29.5 1.0
OE1 C:GLU79 2.5 21.8 0.5
OE2 C:GLU79 2.7 16.8 0.5
OE2 C:GLU79 2.7 22.8 0.5
CD C:GLU79 2.9 22.3 0.5
CD C:GLU79 2.9 26.2 0.5
C1 D:GOL201 3.1 26.3 1.0
C2 D:GOL201 3.2 27.4 1.0
CD D:GLU79 3.5 24.6 1.0
C3 D:GOL201 4.0 30.4 1.0
CG D:GLU79 4.0 14.0 1.0
NA D:NA203 4.1 18.0 1.0
O D:HOH314 4.2 22.2 1.0
O C:HOH350 4.3 26.3 1.0
CG C:GLU79 4.4 11.6 0.5
CG C:GLU79 4.4 12.2 0.5
OE1 D:GLU79 4.5 21.5 1.0
O D:LEU77 4.6 12.9 1.0
O H:HOH304 4.6 18.9 1.0
O3 D:GOL201 4.8 30.7 1.0

Sodium binding site 4 out of 14 in 6ial

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Sodium binding site 4 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:29.1
occ:1.00
 OE2 B:GLU79 2.1 21.4 0.5
OE2 E:GLU79 2.4 19.5 0.5
OE1 E:GLU79 2.4 14.0 0.5
OE2 B:GLU79 2.8 13.0 0.5
OE2 E:GLU79 2.9 18.8 0.5
CD E:GLU79 3.0 27.9 0.5
CD E:GLU79 3.0 28.8 0.5
OE1 E:GLU79 3.0 15.2 0.5
CD B:GLU79 3.2 27.4 0.5
CD B:GLU79 3.3 32.9 0.5
OE1 B:GLU79 3.5 17.6 0.5
O B:HOH332 3.7 26.2 1.0
O A:HOH336 3.9 21.0 1.0
NZ E:LYS23 4.0 38.1 1.0
CG B:GLU79 4.0 16.7 1.0
NA E:NA204 4.2 13.5 1.0
OE1 B:GLU79 4.2 17.4 0.5
CG E:GLU79 4.4 15.4 1.0
OXT A:ASN103 4.5 34.6 1.0
NZ B:LYS23 4.8 25.5 0.5
C A:ASN103 5.0 34.7 1.0

Sodium binding site 5 out of 14 in 6ial

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Sodium binding site 5 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:20.7
occ:1.00
 O E:HOH346 2.1 26.7 1.0
O E:TYR12 2.3 20.0 1.0
O E:CYS9 2.5 16.6 0.5
O E:CYS9 2.5 16.6 0.5
OG1 E:THR15 2.5 19.0 1.0
O E:THR15 2.5 16.1 1.0
O E:HOH347 2.6 22.6 1.0
C E:THR15 3.3 12.4 1.0
C E:CYS9 3.4 16.1 0.5
C E:CYS9 3.4 16.5 0.5
C E:TYR12 3.6 22.3 1.0
CB E:THR15 3.6 15.8 1.0
SG E:CYS9 3.6 17.1 0.5
CA E:THR15 3.7 15.2 1.0
N E:THR15 3.8 16.4 1.0
CA E:SER10 4.0 15.8 1.0
N E:SER10 4.1 14.9 1.0
N E:GLN16 4.2 10.9 1.0
N E:TYR12 4.2 15.9 1.0
SG E:CYS9 4.3 10.2 0.5
CA E:TYR12 4.3 16.7 1.0
C E:SER10 4.4 17.6 1.0
O E:ARG13 4.4 21.9 1.0
CA E:CYS9 4.4 13.1 0.5
CA E:CYS9 4.4 12.3 0.5
C E:ARG13 4.6 18.6 1.0
N E:ARG13 4.6 20.7 1.0
CB E:TYR12 4.6 17.4 1.0
O E:SER10 4.6 20.1 1.0
CB E:CYS9 4.6 12.6 0.5
CB E:CYS9 4.6 11.3 0.5
CA E:GLN16 4.6 10.6 1.0
CA E:ARG13 4.7 18.6 1.0
CG2 E:THR15 4.8 18.6 1.0
N E:GLU11 4.9 16.0 1.0

Sodium binding site 6 out of 14 in 6ial

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Sodium binding site 6 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na203

b:21.5
occ:1.00
 OE1 E:GLN61 1.9 60.0 1.0
O E:HOH317 2.3 30.4 1.0
OE1 F:GLU36 2.3 80.9 1.0
O F:GLY33 2.4 25.7 0.5
O F:MET31 2.8 25.4 1.0
OE2 F:GLU36 2.8 35.6 1.0
CD F:GLU36 2.9 48.8 1.0
CD E:GLN61 3.0 51.5 1.0
O F:GLY33 3.0 22.5 0.5
C F:MET31 3.6 21.5 1.0
NE2 E:GLN61 3.6 71.4 1.0
C F:GLY33 3.7 30.4 0.5
C F:GLY33 3.9 31.3 0.5
CA F:MET31 3.9 15.9 1.0
CB F:MET31 4.0 19.3 1.0
CG E:GLN61 4.3 53.3 1.0
CG F:GLU36 4.3 27.7 1.0
C F:ALA32 4.4 20.8 0.5
N F:GLY33 4.4 23.8 0.5
CB E:ALA64 4.5 16.4 1.0
O F:ALA32 4.5 18.2 0.5
CA E:GLN61 4.5 32.6 1.0
CA F:GLY33 4.6 23.9 0.5
N F:ALA32 4.6 19.5 0.5
N F:GLY33 4.6 24.8 0.5
N F:LYS34 4.6 29.8 1.0
N F:ALA32 4.6 19.4 0.5
CB E:GLN61 4.7 49.6 1.0
CA F:LYS34 4.7 26.4 1.0
C F:ALA32 4.7 22.4 0.5
CA F:GLY33 4.8 27.4 0.5
CA F:ALA32 5.0 21.5 0.5

Sodium binding site 7 out of 14 in 6ial

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Sodium binding site 7 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na204

b:13.5
occ:1.00
 O D:HOH352 2.3 27.8 1.0
OE1 B:GLU79 2.4 17.4 0.5
O E:HOH307 2.5 25.5 1.0
OE2 E:GLU79 2.5 18.8 0.5
OE2 B:GLU79 2.6 13.0 0.5
OE2 E:GLU79 2.8 19.5 0.5
O E:HOH338 2.9 30.1 1.0
OE2 B:GLU79 3.0 21.4 0.5
OE1 B:GLU79 3.0 17.6 0.5
CD B:GLU79 3.1 32.9 0.5
CD B:GLU79 3.1 27.4 0.5
CD E:GLU79 3.5 27.9 0.5
CD E:GLU79 3.6 28.8 0.5
O B:HOH330 4.0 25.1 1.0
CG E:GLU79 4.2 15.4 1.0
NA E:NA201 4.2 29.1 1.0
O E:LEU77 4.3 13.2 1.0
OE1 E:GLU79 4.3 15.2 0.5
OE1 E:GLU79 4.4 14.0 0.5
CG B:GLU79 4.6 16.7 1.0
OG1 D:THR80 4.8 10.6 1.0
O D:THR78 5.0 10.4 1.0
O B:HOH346 5.0 19.5 1.0

Sodium binding site 8 out of 14 in 6ial

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Sodium binding site 8 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:29.8
occ:1.00
 OE2 A:GLU79 2.3 27.3 1.0
OE2 F:GLU79 2.7 27.6 1.0
OE1 F:GLU79 3.0 29.7 1.0
CD F:GLU79 3.2 27.9 1.0
CD A:GLU79 3.4 25.1 1.0
NA F:NA202 4.0 21.1 1.0
CG A:GLU79 4.0 13.0 1.0
OE1 A:GLU79 4.4 29.8 1.0
O A:LEU77 4.4 13.1 1.0
O J:HOH367 4.5 27.2 1.0
O J:HOH309 4.5 24.2 1.0
CG F:GLU79 4.6 14.4 1.0

Sodium binding site 9 out of 14 in 6ial

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Sodium binding site 9 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:21.1
occ:1.00
 OE2 F:GLU79 2.3 27.6 1.0
OE2 A:GLU79 2.5 27.3 1.0
OE1 A:GLU79 2.5 29.8 1.0
CD A:GLU79 2.9 25.1 1.0
CD F:GLU79 3.4 27.9 1.0
NA F:NA201 4.0 29.8 1.0
CG F:GLU79 4.0 14.4 1.0
O E:HOH309 4.3 18.2 1.0
OE1 F:GLU79 4.4 29.7 1.0
CG A:GLU79 4.4 13.0 1.0
NZ A:LYS23 4.6 39.8 1.0
O F:LEU77 4.8 17.0 1.0

Sodium binding site 10 out of 14 in 6ial

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Sodium binding site 10 out of 14 in the Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Porcine E.Coli Heat-Labile Enterotoxin B-Pentamer in Complex with Lacto-N-Neohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:29.3
occ:1.00
 OE2 J:GLU79 2.4 37.4 1.0
OE1 G:GLU79 2.5 32.4 1.0
OE2 G:GLU79 2.8 33.5 1.0
CD G:GLU79 3.0 26.3 1.0
CD J:GLU79 3.4 33.3 1.0
CG J:GLU79 4.0 16.6 1.0
NA G:NA202 4.2 19.9 1.0
O I:HOH236 4.3 29.6 1.0
OE1 J:GLU79 4.3 24.5 1.0
O I:HOH206 4.3 24.1 1.0
O J:LEU77 4.4 15.5 1.0
O J:HOH379 4.4 33.3 1.0
CG G:GLU79 4.5 18.2 1.0

Reference:

J.E.Heggelund, J.B.Heim, G.Bajc, V.Hodnik, G.Anderluh, U.Krengel. Specificity Ofescherichia Coliheat-Labile Enterotoxin Investigated By Single-Site Mutagenesis and Crystallography. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 30736336
DOI: 10.3390/IJMS20030703
Page generated: Tue Oct 8 09:35:58 2024

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