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Sodium in PDB 5g3l: Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar

Protein crystallography data

The structure of Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar, PDB code: 5g3l was solved by D.Zalem, J.Benktander, J.P.Ribeiro, A.Varrot, M.Lebens, A.Imberty, S.Teneberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.33 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.564, 68.015, 154.513, 90.00, 90.00, 90.00
R / Rfree (%) 17.106 / 19.659

Sodium Binding Sites:

The binding sites of Sodium atom in the Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar (pdb code 5g3l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar, PDB code: 5g3l:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5g3l

Go back to Sodium Binding Sites List in 5g3l
Sodium binding site 1 out of 4 in the Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na100

b:28.6
occ:1.00
O D:ALA15 2.7 22.2 1.0
O D:THR13 2.7 17.5 1.0
O D:HOH2024 3.2 35.2 1.0
C D:ALA15 3.8 20.5 1.0
C D:THR13 3.8 17.4 1.0
C D:THR14 4.0 22.2 1.0
N D:ALA15 4.1 20.6 1.0
CA D:THR14 4.2 20.4 1.0
O D:CYS10 4.3 15.3 1.0
O D:THR14 4.3 21.7 1.0
O D:HOH2031 4.4 37.7 1.0
N D:THR14 4.5 19.4 1.0
CA D:ALA15 4.6 19.1 1.0
O D:ASN11 4.6 23.1 1.0
O D:HOH2038 4.6 36.1 1.0
N D:SER16 4.8 17.1 1.0
CA D:ASN11 4.8 20.5 1.0
OG1 D:THR13 4.9 16.1 1.0
CA D:SER16 4.9 19.0 1.0
C D:ASN11 5.0 19.5 1.0
CA D:THR13 5.0 17.9 1.0
N D:THR13 5.0 18.7 1.0

Sodium binding site 2 out of 4 in 5g3l

Go back to Sodium Binding Sites List in 5g3l
Sodium binding site 2 out of 4 in the Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na100

b:20.2
occ:1.00
O E:ALA15 2.5 19.6 1.0
O E:THR13 2.6 20.6 1.0
O E:HOH2026 2.7 26.7 1.0
O E:HOH2027 2.7 39.9 1.0
O E:CYS10 3.1 19.1 1.0
C E:THR13 3.6 19.2 1.0
C E:ALA15 3.7 18.2 1.0
C E:CYS10 3.9 18.8 1.0
CA E:ASN11 3.9 26.1 1.0
OG1 E:THR13 4.1 18.1 1.0
N E:ALA15 4.1 20.0 1.0
O E:ASN11 4.2 26.2 1.0
C E:ASN11 4.2 24.1 1.0
O E:HOH2034 4.2 18.4 1.0
C E:THR14 4.3 21.0 1.0
N E:THR13 4.3 19.8 1.0
N E:ASN11 4.3 20.6 1.0
CA E:ALA15 4.5 18.8 1.0
N E:THR14 4.5 20.8 1.0
CA E:THR13 4.5 21.2 1.0
CA E:THR14 4.6 20.8 1.0
SG E:CYS10 4.6 21.4 1.0
N E:SER16 4.7 17.0 1.0
O E:THR14 4.8 20.2 1.0
O E:HOH2031 4.9 32.1 1.0
CA E:SER16 4.9 17.2 1.0
CB E:THR13 5.0 19.2 1.0

Sodium binding site 3 out of 4 in 5g3l

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Sodium binding site 3 out of 4 in the Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na100

b:16.2
occ:1.00
O G:ALA15 2.5 18.1 1.0
O G:HOH2023 2.7 18.2 1.0
O G:THR13 2.7 15.9 1.0
O G:HOH2024 2.8 20.8 1.0
O G:CYS10 3.0 12.9 1.0
C G:ALA15 3.7 18.1 1.0
C G:THR13 3.7 15.3 1.0
C G:CYS10 3.8 16.2 1.0
CA G:ASN11 4.0 16.6 1.0
OG1 G:THR13 4.0 15.2 1.0
N G:ALA15 4.2 17.6 1.0
O G:HOH2030 4.2 29.7 1.0
O G:ASN11 4.3 16.9 1.0
N G:ASN11 4.3 14.9 1.0
C G:ASN11 4.3 17.2 1.0
N G:THR13 4.4 17.4 1.0
SG G:CYS10 4.4 17.9 1.0
C G:THR14 4.4 18.6 1.0
CA G:ALA15 4.5 17.6 1.0
CA G:THR13 4.5 15.7 1.0
N G:THR14 4.6 15.9 1.0
N G:SER16 4.6 18.7 1.0
CA G:THR14 4.7 17.4 1.0
CA G:SER16 4.7 19.7 1.0
OD1 G:ASN11 4.8 24.2 1.0
CB G:THR13 4.9 15.7 1.0
CA G:CYS10 5.0 14.3 1.0
O G:THR14 5.0 21.9 1.0

Sodium binding site 4 out of 4 in 5g3l

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Sodium binding site 4 out of 4 in the Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Escherichia Coli Heat Labile Enterotoxin Type Iib B- Pentamer Complexed with Sialylated Sugar within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na100

b:11.5
occ:1.00
O H:ALA15 2.5 15.4 1.0
O H:HOH2024 2.7 19.4 1.0
O H:THR13 2.7 14.6 1.0
O H:HOH2033 2.9 24.2 1.0
O H:HOH2029 2.9 35.1 1.0
O H:CYS10 3.0 15.4 1.0
C H:ALA15 3.7 14.9 1.0
C H:THR13 3.7 12.2 1.0
C H:CYS10 3.9 16.0 1.0
CA H:ASN11 3.9 19.1 1.0
O H:HOH2037 4.0 20.7 1.0
OG1 H:THR13 4.1 12.9 1.0
N H:ALA15 4.2 13.7 1.0
O H:ASN11 4.2 20.9 1.0
C H:ASN11 4.3 19.1 1.0
N H:ASN11 4.3 16.1 1.0
N H:THR13 4.4 15.6 1.0
C H:THR14 4.4 12.9 1.0
SG H:CYS10 4.5 16.9 1.0
CA H:ALA15 4.5 13.5 1.0
CA H:THR13 4.6 14.7 1.0
N H:THR14 4.6 12.6 1.0
OD1 H:ASN11 4.6 29.2 1.0
N H:SER16 4.7 14.6 1.0
CA H:THR14 4.7 13.1 1.0
O H:HOH2031 4.8 19.9 1.0
CA H:SER16 4.8 17.1 1.0
O H:THR14 4.9 13.9 1.0

Reference:

D.Zalem, J.P.Ribeiro, A.Varrot, M.Lebens, A.Imberty, S.Teneberg. Biochemical and Structural Characterization of the Novel Sialic Acid-Binding Site of Escherichia Coli Heat-Labile Enterotoxin Lt-Iib. Biochem.J. V. 473 3923 2016.
ISSN: ISSN 0264-6021
PubMed: 27562297
DOI: 10.1042/BCJ20160575
Page generated: Tue Dec 15 11:01:11 2020

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