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Sodium in PDB 8zyv: Bacterial Flagellar Sodium-Driven Stator POMA5POMB2 with 100 Mm Nacl

Sodium Binding Sites:

The binding sites of Sodium atom in the Bacterial Flagellar Sodium-Driven Stator POMA5POMB2 with 100 Mm Nacl (pdb code 8zyv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bacterial Flagellar Sodium-Driven Stator POMA5POMB2 with 100 Mm Nacl, PDB code: 8zyv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8zyv

Go back to Sodium Binding Sites List in 8zyv
Sodium binding site 1 out of 2 in the Bacterial Flagellar Sodium-Driven Stator POMA5POMB2 with 100 Mm Nacl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacterial Flagellar Sodium-Driven Stator POMA5POMB2 with 100 Mm Nacl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:35.0
occ:1.00
CB A:PHE32 3.1 42.7 1.0
CA A:PHE32 3.8 39.3 1.0
CD1 C:LEU162 3.9 22.3 1.0
CD1 A:PHE32 4.0 49.0 1.0
CG A:PHE32 4.0 51.7 1.0
N A:PHE32 4.1 42.7 1.0
CD2 C:LEU162 4.3 18.8 1.0
CD1 C:LEU166 4.4 32.5 1.0
CE G:MET179 4.4 30.4 1.0
O A:LEU28 4.5 32.1 1.0
CG C:LEU162 4.5 20.4 1.0
CD1 G:LEU183 4.6 22.8 1.0
CD2 A:LEU28 4.7 46.5 1.0
SD G:MET179 4.8 55.9 1.0
CB C:LEU162 4.8 17.1 1.0
CG C:LEU166 4.8 34.1 1.0
CD2 C:LEU166 4.9 34.1 1.0
C A:CYS31 5.0 34.3 1.0

Sodium binding site 2 out of 2 in 8zyv

Go back to Sodium Binding Sites List in 8zyv
Sodium binding site 2 out of 2 in the Bacterial Flagellar Sodium-Driven Stator POMA5POMB2 with 100 Mm Nacl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacterial Flagellar Sodium-Driven Stator POMA5POMB2 with 100 Mm Nacl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:30.1
occ:0.97
CD2 G:LEU183 3.1 23.1 1.0
CD2 A:LEU28 3.3 46.5 1.0
OG1 G:THR186 3.5 22.8 1.0
CG2 G:THR158 3.8 13.6 1.0
CG A:LEU28 3.9 47.2 1.0
O A:HOH601 3.9 40.8 0.7
CB G:THR186 4.1 16.4 1.0
CA G:LEU183 4.2 11.6 1.0
CA A:LEU28 4.3 35.5 1.0
O G:ALA182 4.3 23.0 1.0
SG A:CYS31 4.4 48.6 1.0
CG G:LEU183 4.4 18.8 1.0
CG2 G:THR186 4.5 15.6 1.0
CD2 C:LEU159 4.5 10.7 1.0
C G:ALA182 4.5 21.4 1.0
OG1 G:THR158 4.5 27.1 1.0
N G:LEU183 4.5 25.0 1.0
CB A:LEU28 4.6 33.0 1.0
N A:LEU28 4.7 42.4 1.0
CB G:THR158 4.8 22.1 1.0
CB A:CYS31 4.8 36.1 1.0
CB G:LEU183 4.9 15.7 1.0
CB G:ALA182 5.0 4.9 1.0
O A:SER27 5.0 37.8 1.0

Reference:

T.Nishikino, N.Takekawa, J.Kishikawa, M.Hirose, S.Kojima, M.Homma, T.Kato, K.Imada. Structural Insight Into Sodium Ion Pathway in the Bacterial Flagellar Stator From Marine Vibrio Proc.Natl.Acad.Sci.Usa.
ISSN: ESSN 1091-6490
DOI: DOI.ORG/10.1073/PNAS.2415713122
Page generated: Mon Aug 18 16:32:57 2025

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