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Sodium in PDB 8wci: Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae

Sodium Binding Sites:

The binding sites of Sodium atom in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae (pdb code 8wci). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae, PDB code: 8wci:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 8wci

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Sodium binding site 1 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:21.4
occ:1.00
 OE1 A:GLU139 2.3 23.3 1.0
OE1 A:GLN65 2.3 18.9 1.0
OG1 A:THR64 2.4 19.5 1.0
OE1 A:GLN110 2.5 18.4 1.0
O A:LEU61 2.5 21.1 1.0
CD A:GLN65 3.2 18.9 1.0
CD A:GLN110 3.3 18.4 1.0
CD A:GLU139 3.4 23.3 1.0
NE2 A:GLN65 3.5 18.9 1.0
NE2 A:GLN110 3.5 18.4 1.0
CB A:THR64 3.6 19.5 1.0
N A:THR64 3.6 19.5 1.0
C A:LEU61 3.6 21.1 1.0
OE2 A:GLU139 3.7 23.3 1.0
CA A:PRO62 3.7 19.5 1.0
C A:PRO62 3.8 19.5 1.0
CG2 A:THR64 4.0 19.5 1.0
CA A:THR64 4.0 19.5 1.0
N A:GLN65 4.1 18.9 1.0
O A:PRO62 4.1 19.5 1.0
N A:PRO62 4.2 19.5 1.0
N A:GLY63 4.2 20.0 1.0
C A:THR64 4.4 19.5 1.0
CG A:GLN65 4.5 18.9 1.0
CG A:GLN110 4.7 18.4 1.0
CG A:GLU139 4.7 23.3 1.0
C A:GLY63 4.7 20.0 1.0
CA A:LEU61 4.8 21.1 1.0
CB A:GLU139 4.9 23.3 1.0

Sodium binding site 2 out of 9 in 8wci

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Sodium binding site 2 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:18.7
occ:1.00
 O B:LEU61 2.3 20.1 1.0
OE1 B:GLN110 2.4 17.6 1.0
OG1 B:THR64 2.4 17.5 1.0
OE1 B:GLU139 2.4 19.4 1.0
OE1 B:GLN65 2.5 16.6 1.0
CD B:GLN110 3.2 17.6 1.0
CD B:GLU139 3.3 19.4 1.0
CD B:GLN65 3.3 16.6 1.0
C B:LEU61 3.4 20.1 1.0
OE2 B:GLU139 3.5 19.4 1.0
CA B:PRO62 3.5 18.0 1.0
N B:THR64 3.5 17.5 1.0
NE2 B:GLN110 3.6 17.6 1.0
C B:PRO62 3.6 18.0 1.0
NE2 B:GLN65 3.6 16.6 1.0
CB B:THR64 3.6 17.5 1.0
N B:GLY63 3.9 18.2 1.0
N B:PRO62 3.9 18.0 1.0
O B:PRO62 4.0 18.0 1.0
CA B:THR64 4.1 17.5 1.0
CG2 B:THR64 4.1 17.5 1.0
N B:GLN65 4.2 16.6 1.0
CG B:GLN110 4.4 17.6 1.0
C B:THR64 4.6 17.5 1.0
C B:GLY63 4.6 18.2 1.0
CA B:LEU61 4.6 20.1 1.0
CG B:GLN65 4.7 16.6 1.0
CG B:GLU139 4.7 19.4 1.0
CA B:GLY63 4.8 18.2 1.0
CB B:PRO62 4.9 18.0 1.0

Sodium binding site 3 out of 9 in 8wci

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Sodium binding site 3 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:21.0
occ:1.00
 OE1 D:GLN110 2.2 17.4 1.0
OE1 D:GLU139 2.4 21.6 1.0
O D:LEU61 2.4 19.9 1.0
OG1 D:THR64 2.5 18.4 1.0
OE1 D:GLN65 2.6 17.6 1.0
CD D:GLN65 3.2 17.6 1.0
CD D:GLN110 3.2 17.4 1.0
CD D:GLU139 3.4 21.6 1.0
NE2 D:GLN65 3.4 17.6 1.0
C D:LEU61 3.5 19.9 1.0
CA D:PRO62 3.6 17.9 1.0
NE2 D:GLN110 3.6 17.4 1.0
N D:THR64 3.6 18.4 1.0
CB D:THR64 3.7 18.4 1.0
OE2 D:GLU139 3.7 21.6 1.0
C D:PRO62 3.7 17.9 1.0
CG2 D:THR64 4.0 18.4 1.0
O D:PRO62 4.0 17.9 1.0
N D:PRO62 4.0 17.9 1.0
N D:GLN65 4.1 17.6 1.0
CA D:THR64 4.1 18.4 1.0
N D:GLY63 4.1 19.6 1.0
CG D:GLN65 4.4 17.6 1.0
CG D:GLN110 4.5 17.4 1.0
C D:THR64 4.5 18.4 1.0
C D:GLY63 4.7 19.6 1.0
CG D:GLU139 4.7 21.6 1.0
CA D:LEU61 4.7 19.9 1.0
CB D:GLN110 4.9 17.4 1.0
CB D:GLU139 4.9 21.6 1.0
CA D:GLY63 4.9 19.6 1.0
CB D:PRO62 4.9 17.9 1.0

Sodium binding site 4 out of 9 in 8wci

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Sodium binding site 4 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:20.9
occ:1.00
 OE1 E:GLU139 2.3 22.8 1.0
O E:LEU61 2.3 20.6 1.0
OG1 E:THR64 2.3 19.2 1.0
OE1 E:GLN110 2.4 18.4 1.0
OE1 E:GLN65 2.4 18.6 1.0
CD E:GLU139 3.2 22.8 1.0
CD E:GLN110 3.3 18.4 1.0
CD E:GLN65 3.3 18.6 1.0
OE2 E:GLU139 3.4 22.8 1.0
C E:LEU61 3.5 20.6 1.0
NE2 E:GLN110 3.5 18.4 1.0
CA E:PRO62 3.6 18.7 1.0
N E:THR64 3.6 19.2 1.0
CB E:THR64 3.6 19.2 1.0
NE2 E:GLN65 3.7 18.6 1.0
C E:PRO62 3.8 18.7 1.0
N E:PRO62 4.0 18.7 1.0
N E:GLY63 4.0 19.3 1.0
N E:GLN65 4.1 18.6 1.0
CA E:THR64 4.1 19.2 1.0
CG2 E:THR64 4.1 19.2 1.0
O E:PRO62 4.3 18.7 1.0
C E:THR64 4.5 19.2 1.0
CG E:GLU139 4.6 22.8 1.0
CG E:GLN65 4.6 18.6 1.0
CA E:LEU61 4.6 20.6 1.0
C E:GLY63 4.7 19.3 1.0
CG E:GLN110 4.7 18.4 1.0
CB E:GLU139 4.9 22.8 1.0
CA E:GLY63 4.9 19.3 1.0
CB E:PRO62 5.0 18.7 1.0

Sodium binding site 5 out of 9 in 8wci

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Sodium binding site 5 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:22.6
occ:1.00
 OE1 F:GLU139 2.3 22.7 1.0
OE1 F:GLN65 2.3 18.6 1.0
OE1 F:GLN110 2.3 19.0 1.0
OG1 F:THR64 2.4 19.7 1.0
O F:LEU61 2.4 20.7 1.0
CD F:GLU139 3.1 22.7 1.0
CD F:GLN110 3.2 19.0 1.0
CD F:GLN65 3.2 18.6 1.0
OE2 F:GLU139 3.2 22.7 1.0
NE2 F:GLN110 3.5 19.0 1.0
NE2 F:GLN65 3.5 18.6 1.0
C F:LEU61 3.5 20.7 1.0
CB F:THR64 3.6 19.7 1.0
N F:THR64 3.6 19.7 1.0
CA F:PRO62 3.7 19.2 1.0
C F:PRO62 3.8 19.2 1.0
CG2 F:THR64 4.1 19.7 1.0
CA F:THR64 4.1 19.7 1.0
O F:PRO62 4.1 19.2 1.0
N F:PRO62 4.1 19.2 1.0
N F:GLY63 4.1 19.7 1.0
N F:GLN65 4.1 18.6 1.0
C F:THR64 4.5 19.7 1.0
CG F:GLU139 4.5 22.7 1.0
CG F:GLN65 4.5 18.6 1.0
CG F:GLN110 4.5 19.0 1.0
CA F:LEU61 4.7 20.7 1.0
C F:GLY63 4.7 19.7 1.0
CB F:GLU139 4.9 22.7 1.0
CA F:GLY63 5.0 19.7 1.0

Sodium binding site 6 out of 9 in 8wci

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Sodium binding site 6 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:22.8
occ:1.00
 OG1 G:THR64 2.3 21.0 1.0
OE1 G:GLN110 2.3 18.6 1.0
O G:LEU61 2.3 21.3 1.0
OE1 G:GLU139 2.4 22.7 1.0
OE1 G:GLN65 2.5 20.1 1.0
CD G:GLN110 3.2 18.6 1.0
CD G:GLU139 3.2 22.7 1.0
CD G:GLN65 3.2 20.1 1.0
OE2 G:GLU139 3.3 22.7 1.0
NE2 G:GLN65 3.4 20.1 1.0
C G:LEU61 3.5 21.3 1.0
N G:THR64 3.5 21.0 1.0
CB G:THR64 3.5 21.0 1.0
NE2 G:GLN110 3.6 18.6 1.0
CA G:PRO62 3.7 19.8 1.0
C G:PRO62 3.8 19.8 1.0
CA G:THR64 4.0 21.0 1.0
CG2 G:THR64 4.0 21.0 1.0
N G:GLY63 4.0 20.8 1.0
N G:PRO62 4.1 19.8 1.0
N G:GLN65 4.2 20.1 1.0
O G:PRO62 4.2 19.8 1.0
C G:THR64 4.5 21.0 1.0
CG G:GLN110 4.5 18.6 1.0
C G:GLY63 4.6 20.8 1.0
CG G:GLN65 4.6 20.1 1.0
CG G:GLU139 4.7 22.7 1.0
CA G:LEU61 4.7 21.3 1.0
CA G:GLY63 4.9 20.8 1.0

Sodium binding site 7 out of 9 in 8wci

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Sodium binding site 7 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na202

b:22.7
occ:1.00
 O H:LEU61 2.3 23.0 1.0
OE1 H:GLN65 2.3 19.3 1.0
OG1 H:THR64 2.5 20.3 1.0
OE1 H:GLN110 2.5 18.9 1.0
OE1 H:GLU139 2.5 22.8 1.0
CD H:GLN65 3.2 19.3 1.0
N H:THR64 3.4 20.3 1.0
CD H:GLU139 3.4 22.8 1.0
CD H:GLN110 3.5 18.9 1.0
C H:LEU61 3.5 23.0 1.0
CB H:THR64 3.5 20.3 1.0
NE2 H:GLN65 3.6 19.3 1.0
CA H:PRO62 3.6 20.2 1.0
C H:PRO62 3.6 20.2 1.0
OE2 H:GLU139 3.7 22.8 1.0
CG2 H:THR64 3.8 20.3 1.0
N H:GLY63 3.8 21.1 1.0
NE2 H:GLN110 3.9 18.9 1.0
CA H:THR64 3.9 20.3 1.0
N H:GLN65 4.0 19.3 1.0
N H:PRO62 4.0 20.2 1.0
O H:PRO62 4.2 20.2 1.0
C H:THR64 4.3 20.3 1.0
C H:GLY63 4.5 21.1 1.0
CG H:GLN65 4.5 19.3 1.0
CA H:GLY63 4.7 21.1 1.0
CA H:LEU61 4.7 23.0 1.0
CG H:GLN110 4.8 18.9 1.0
CG H:GLU139 4.8 22.8 1.0
CA H:GLN65 5.0 19.3 1.0
CB H:PRO62 5.0 20.2 1.0

Sodium binding site 8 out of 9 in 8wci

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Sodium binding site 8 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na202

b:21.3
occ:1.00
 OG1 I:THR64 2.3 19.4 1.0
OE1 I:GLU139 2.3 23.5 1.0
OE1 I:GLN110 2.3 19.0 1.0
OE1 I:GLN65 2.5 18.3 1.0
O I:LEU61 2.6 20.5 1.0
CD I:GLN65 3.1 18.3 1.0
NE2 I:GLN65 3.2 18.3 1.0
CD I:GLN110 3.3 19.0 1.0
CD I:GLU139 3.3 23.5 1.0
CB I:THR64 3.6 19.4 1.0
NE2 I:GLN110 3.6 19.0 1.0
C I:LEU61 3.7 20.5 1.0
OE2 I:GLU139 3.7 23.5 1.0
N I:THR64 3.7 19.4 1.0
CA I:PRO62 3.7 18.9 1.0
C I:PRO62 3.8 18.9 1.0
CG2 I:THR64 4.1 19.4 1.0
CA I:THR64 4.1 19.4 1.0
N I:GLN65 4.1 18.3 1.0
N I:PRO62 4.2 18.9 1.0
O I:PRO62 4.2 18.9 1.0
N I:GLY63 4.2 20.6 1.0
CG I:GLN65 4.4 18.3 1.0
C I:THR64 4.5 19.4 1.0
CG I:GLN110 4.6 19.0 1.0
CG I:GLU139 4.6 23.5 1.0
C I:GLY63 4.8 20.6 1.0
CB I:GLU139 4.8 23.5 1.0
CA I:LEU61 4.8 20.5 1.0
CB I:GLN65 5.0 18.3 1.0

Sodium binding site 9 out of 9 in 8wci

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Sodium binding site 9 out of 9 in the Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Cryo-Em Structure of the Inhibitor-Bound Vo Complex From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na201

b:21.2
occ:1.00
 O J:LEU61 2.3 22.2 1.0
OE1 J:GLN110 2.3 19.1 1.0
OE1 J:GLN65 2.4 19.3 1.0
OG1 J:THR64 2.4 19.9 1.0
OE1 J:GLU139 2.5 24.3 1.0
CD J:GLN65 3.2 19.3 1.0
CD J:GLU139 3.3 24.3 1.0
CD J:GLN110 3.3 19.1 1.0
OE2 J:GLU139 3.4 24.3 1.0
C J:LEU61 3.4 22.2 1.0
NE2 J:GLN65 3.5 19.3 1.0
N J:THR64 3.6 19.9 1.0
CA J:PRO62 3.6 19.6 1.0
CB J:THR64 3.6 19.9 1.0
C J:PRO62 3.6 19.6 1.0
NE2 J:GLN110 3.7 19.1 1.0
N J:GLY63 4.0 20.4 1.0
N J:PRO62 4.0 19.6 1.0
O J:PRO62 4.0 19.6 1.0
CG2 J:THR64 4.1 19.9 1.0
CA J:THR64 4.1 19.9 1.0
N J:GLN65 4.1 19.3 1.0
C J:THR64 4.5 19.9 1.0
C J:GLY63 4.6 20.4 1.0
CG J:GLN110 4.6 19.1 1.0
CG J:GLN65 4.6 19.3 1.0
CA J:LEU61 4.6 22.2 1.0
CG J:GLU139 4.7 24.3 1.0
CA J:GLY63 4.8 20.4 1.0

Reference:

K.Suzuki, Y.Goto, A.Otomo, K.Shimizu, S.Abe, K.Moriyama, S.Yasuda, Y.Hashimoto, J.Kurushima, S.Mikuriya, F.L.Imai, N.Adachi, M.Kawasaki, Y.Sato, S.Ogasawara, I.Iwata, T.Senda, M.Ikeguchi, H.Tomita, R.Iino, T.Moriya, T.Murata. Novel Inhibitor of Na+-Transporting V-Atpase Suppresses Vre Colonization in Mice and Reveals the High-Resolution Structure of the Na+ Transport Pathway To Be Published.
Page generated: Mon Aug 18 16:17:47 2025

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