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Sodium in PDB 4fo2: Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant

Protein crystallography data

The structure of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant, PDB code: 4fo2 was solved by V.Cody, J.Pace, H.Nawar, S.Liang, T.Connell, G.Hajishengallis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.74 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.310, 119.976, 142.446, 90.00, 90.05, 90.00
R / Rfree (%) 22.3 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant (pdb code 4fo2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant, PDB code: 4fo2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4fo2

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Sodium binding site 1 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:25.1
occ:1.00
 O E:HOH216 2.3 32.1 1.0
O E:HOH217 2.3 23.6 1.0
O E:ALA15 2.4 19.8 1.0
O E:ARG12 2.4 17.9 1.0
C E:ALA15 3.2 19.3 1.0
C E:ARG12 3.3 15.7 1.0
CA E:ARG12 3.7 18.5 1.0
CB E:ARG12 3.9 21.9 1.0
N E:ALA15 3.9 14.4 1.0
N E:SER16 3.9 19.1 1.0
CA E:SER16 4.0 22.2 1.0
O E:HOH201 4.0 20.3 1.0
CA E:ALA15 4.1 17.3 1.0
CB E:SER16 4.2 24.2 1.0
N E:ILE13 4.5 15.8 1.0
OG E:SER16 4.7 36.0 1.0
C E:ILE13 4.7 15.4 1.0
O E:ASN11 4.8 17.5 1.0
C E:THR14 4.9 15.6 1.0
N E:THR14 4.9 15.6 1.0
O E:ILE13 4.9 16.2 1.0
CA E:ILE13 5.0 13.7 1.0
N E:ARG12 5.0 17.0 1.0

Sodium binding site 2 out of 8 in 4fo2

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Sodium binding site 2 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na101

b:23.7
occ:1.00
 O F:HOH232 2.1 22.5 1.0
O F:ALA15 2.3 20.2 1.0
O F:ARG12 2.4 18.6 1.0
O F:HOH233 2.4 27.8 1.0
O F:HOH234 2.5 37.0 1.0
O F:HOH214 2.5 22.4 1.0
C F:ARG12 3.5 17.1 1.0
C F:ALA15 3.6 16.9 1.0
N F:ARG12 4.0 19.8 1.0
CA F:SER16 4.0 19.1 1.0
CA F:ILE13 4.2 15.2 1.0
O F:ILE13 4.3 17.5 1.0
N F:SER16 4.3 15.4 1.0
N F:ILE13 4.3 17.3 1.0
C F:ILE13 4.3 16.5 1.0
CA F:ARG12 4.4 20.1 1.0
N F:ALA15 4.4 14.3 1.0
N F:LEU17 4.5 18.4 1.0
OG F:SER16 4.7 23.6 1.0
CA F:ALA15 4.7 15.7 1.0
C F:SER16 4.8 18.8 1.0
O F:CYS10 4.8 20.8 1.0

Sodium binding site 3 out of 8 in 4fo2

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Sodium binding site 3 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:30.2
occ:1.00
 O B:HOH220 2.3 17.8 1.0
O B:HOH224 2.4 30.0 1.0
O B:HOH201 2.8 18.1 1.0
C B:ALA15 3.0 19.1 1.0
O B:ALA15 3.1 20.1 1.0
CA B:ALA15 3.4 17.5 1.0
CD B:PRO84 3.5 17.7 1.0
N B:ALA15 3.5 14.2 1.0
N B:SER16 3.6 19.9 1.0
CG B:PRO84 3.6 15.9 1.0
CB B:SER16 3.9 23.7 1.0
O B:ARG12 4.0 16.5 1.0
C B:THR14 4.0 15.4 1.0
CA B:SER16 4.1 21.1 1.0
O B:THR14 4.4 16.2 1.0
CB B:PRO84 4.5 18.6 1.0
O B:ILE13 4.8 15.9 1.0
N B:PRO84 4.8 18.1 1.0
O B:ALA82 4.8 19.5 1.0
CA B:THR14 4.9 14.9 1.0
C B:ARG12 4.9 15.4 1.0
CB B:ALA15 4.9 19.2 1.0
OG B:SER16 4.9 31.6 1.0
N B:THR14 5.0 13.8 1.0

Sodium binding site 4 out of 8 in 4fo2

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Sodium binding site 4 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:23.2
occ:1.00
 O C:HOH228 2.1 24.1 1.0
O C:ARG12 2.4 18.7 1.0
O M:HOH229 2.4 31.7 1.0
O C:HOH216 2.4 22.2 1.0
O C:ALA15 2.4 19.2 1.0
O C:HOH229 2.6 26.7 1.0
C C:ARG12 3.5 16.9 1.0
C C:ALA15 3.6 15.9 1.0
N C:ARG12 4.0 19.5 1.0
CA C:SER16 4.1 17.7 1.0
CA C:ILE13 4.2 16.1 1.0
N C:ILE13 4.3 17.5 1.0
O C:ILE13 4.3 17.5 1.0
N C:SER16 4.3 15.0 1.0
C C:ILE13 4.3 14.8 1.0
CA C:ARG12 4.4 19.5 1.0
N C:ALA15 4.5 15.0 1.0
N C:LEU17 4.5 18.3 1.0
OG C:SER16 4.7 25.6 1.0
CA C:ALA15 4.7 14.5 1.0
C C:SER16 4.8 19.0 1.0
O C:CYS10 4.9 21.4 1.0
OD1 M:ASN32 4.9 54.7 1.0

Sodium binding site 5 out of 8 in 4fo2

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Sodium binding site 5 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na101

b:23.3
occ:1.00
 O L:ARG12 2.3 18.2 1.0
O L:ALA15 2.3 18.1 1.0
O L:HOH215 2.4 30.0 1.0
O L:HOH212 2.4 21.0 1.0
OG L:SER16 2.6 25.0 1.0
C L:ALA15 3.1 16.9 1.0
C L:ARG12 3.2 19.0 1.0
CA L:ARG12 3.6 19.1 1.0
N L:SER16 3.8 19.7 1.0
CB L:SER16 3.8 22.4 1.0
N L:ALA15 3.8 15.0 1.0
CB L:ARG12 3.9 22.0 1.0
CA L:SER16 3.9 19.4 1.0
CA L:ALA15 4.0 15.2 1.0
N L:ILE13 4.5 18.0 1.0
O L:HOH211 4.5 19.1 1.0
O L:ASN11 4.7 18.4 1.0
C L:ILE13 4.8 15.7 1.0
C L:THR14 4.8 17.1 1.0
N L:THR14 4.9 15.7 1.0
CG L:ARG12 4.9 25.4 1.0
N L:ARG12 4.9 17.9 1.0
O L:ILE13 4.9 16.6 1.0
CA L:ILE13 5.0 16.5 1.0

Sodium binding site 6 out of 8 in 4fo2

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Sodium binding site 6 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na101

b:18.3
occ:1.00
 O M:HOH224 2.3 22.7 1.0
O M:ALA15 2.3 17.6 1.0
O M:ARG12 2.4 16.8 1.0
O M:HOH232 2.4 26.3 1.0
O M:HOH209 2.5 20.9 1.0
O M:HOH205 2.5 18.6 1.0
C M:ARG12 3.5 18.1 1.0
C M:ALA15 3.5 15.7 1.0
CA M:SER16 4.0 16.5 1.0
N M:ARG12 4.1 18.4 1.0
CA M:ILE13 4.1 13.9 1.0
N M:SER16 4.2 14.3 1.0
O M:ILE13 4.2 15.2 1.0
C M:ILE13 4.3 15.3 1.0
N M:ILE13 4.3 16.2 1.0
N M:LEU17 4.3 16.3 1.0
CA M:ARG12 4.4 16.7 1.0
N M:ALA15 4.5 16.4 1.0
C M:SER16 4.6 16.3 1.0
CA M:ALA15 4.7 14.4 1.0
N M:THR14 5.0 14.7 1.0

Sodium binding site 7 out of 8 in 4fo2

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Sodium binding site 7 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Na101

b:23.1
occ:1.00
 O Q:ARG12 2.3 19.7 1.0
O Q:ALA15 2.4 19.3 1.0
O Q:HOH212 2.5 21.3 1.0
OG Q:SER16 2.6 27.2 1.0
O Q:HOH213 2.6 30.0 1.0
C Q:ALA15 3.2 18.2 1.0
C Q:ARG12 3.3 17.8 1.0
CA Q:ARG12 3.6 19.1 1.0
CB Q:SER16 3.8 24.1 1.0
N Q:SER16 3.8 19.2 1.0
CA Q:SER16 3.9 21.9 1.0
CB Q:ARG12 3.9 20.6 1.0
N Q:ALA15 3.9 14.9 1.0
CA Q:ALA15 4.1 15.8 1.0
N Q:ILE13 4.5 17.2 1.0
O Q:ASN11 4.8 17.8 1.0
C Q:ILE13 4.8 16.6 1.0
N Q:ARG12 4.9 19.1 1.0
N Q:THR14 4.9 15.4 1.0
C Q:THR14 4.9 16.1 1.0
O Q:ILE13 5.0 17.1 1.0

Sodium binding site 8 out of 8 in 4fo2

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Sodium binding site 8 out of 8 in the Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Heat-Labile Enterotoxin Lt-Iib-B5(T13I) Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na101

b:18.0
occ:1.00
 O R:ARG12 2.3 21.8 1.0
O R:ALA15 2.4 17.4 1.0
O R:HOH217 2.4 24.4 1.0
O R:HOH232 2.4 30.6 1.0
O R:HOH213 2.5 20.6 1.0
O R:HOH204 2.5 19.1 1.0
C R:ARG12 3.4 19.8 1.0
C R:ALA15 3.6 17.0 1.0
CA R:ILE13 4.1 14.4 1.0
CA R:SER16 4.1 17.0 1.0
N R:ARG12 4.1 16.7 1.0
O R:ILE13 4.2 15.2 1.0
N R:ILE13 4.2 15.5 1.0
C R:ILE13 4.3 16.8 1.0
N R:SER16 4.3 15.1 1.0
N R:LEU17 4.3 16.4 1.0
CA R:ARG12 4.4 18.1 1.0
N R:ALA15 4.5 15.1 1.0
C R:SER16 4.6 16.2 1.0
CA R:ALA15 4.7 15.6 1.0
N R:THR14 5.0 15.0 1.0

Reference:

V.Cody, J.Pace, H.F.Nawar, N.King-Lyons, S.Liang, T.D.Connell, G.Hajishengallis. Structure-Activity Correlations of Variant Forms of the B Pentamer of Escherichia Coli Type II Heat-Labile Enterotoxin Lt-Iib with Toll-Like Receptor 2 Binding. Acta Crystallogr.,Sect.D V. 68 1604 2012.
ISSN: ISSN 0907-4449
PubMed: 23151625
DOI: 10.1107/S0907444912038917
Page generated: Mon Oct 7 15:25:15 2024

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