Sodium in PDB 8thi: Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Parallel Dimer)

The binding sites of Sodium atom in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Parallel Dimer) (pdb code 8thi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Parallel Dimer), PDB code: 8thi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Parallel Dimer)


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 Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Parallel Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:100.8 occ:1.00 O A:SER298 2.2 101.5 1.0 O A:GLY337 2.3 97.7 1.0 O A:SER295 2.5 97.0 1.0 O A:VAL340 2.8 96.0 1.0 O A:PRO342 2.9 95.4 1.0 C A:GLY337 3.3 94.6 1.0 C A:SER298 3.4 99.5 1.0 C A:SER295 3.5 94.2 1.0 CA A:GLY337 3.8 92.6 1.0 CA A:GLY299 3.8 99.5 1.0 CA A:SER295 3.8 92.6 1.0 C A:VAL340 3.9 94.6 1.0 N A:GLY299 4.0 100.1 1.0 CB A:SER295 4.0 94.8 1.0 C A:PRO342 4.1 91.0 1.0 N A:PRO342 4.3 87.2 1.0 C A:PRO341 4.3 89.1 1.0 N A:PRO338 4.4 93.0 1.0 CD A:PRO342 4.5 92.0 1.0 O A:PRO341 4.5 92.9 1.0 C A:GLY299 4.5 105.6 1.0 CA A:SER298 4.6 98.0 1.0 N A:SER298 4.6 96.8 1.0 OG A:SER298 4.6 107.0 1.0 CB A:VAL340 4.7 94.5 1.0 CA A:VAL340 4.7 94.0 1.0 CA A:PRO338 4.7 92.6 1.0 N A:GLY296 4.7 95.1 1.0 N A:VAL340 4.8 94.4 1.0 CA A:PRO342 4.8 87.6 1.0 N A:PRO341 4.8 92.2 1.0 CA A:PRO341 4.8 90.2 1.0 N A:SER300 4.9 106.6 1.0 CG A:PRO342 4.9 89.4 1.0 O A:ILE336 4.9 96.4 1.0 C A:PRO338 4.9 94.2 1.0 OG A:SER295 4.9 97.4 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Parallel Dimer)


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 Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Parallel Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:104.2 occ:1.00 O B:SER295 2.3 100.8 1.0 O B:VAL340 2.5 100.5 1.0 O B:SER298 2.5 104.0 1.0 O B:GLY337 2.7 102.3 1.0 O B:PRO342 2.8 96.0 1.0 C B:SER295 3.4 100.8 1.0 C B:VAL340 3.5 99.0 1.0 C B:SER298 3.6 100.8 1.0 C B:GLY337 3.7 102.3 1.0 C B:PRO341 3.9 92.9 1.0 CA B:SER295 3.9 102.4 1.0 C B:PRO342 3.9 92.8 1.0 N B:PRO342 4.0 91.0 1.0 CB B:SER295 4.0 104.2 1.0 O B:PRO341 4.0 99.4 1.0 CA B:GLY299 4.1 102.7 1.0 CA B:GLY337 4.1 103.7 1.0 CD B:PRO342 4.2 94.7 1.0 CB B:VAL340 4.3 97.2 1.0 N B:GLY299 4.3 100.9 1.0 CA B:VAL340 4.4 98.7 1.0 N B:PRO341 4.4 95.1 1.0 CA B:PRO341 4.4 92.5 1.0 N B:GLY296 4.5 104.3 1.0 CA B:PRO342 4.6 91.5 1.0 N B:VAL340 4.6 101.7 1.0 CG1 B:VAL340 4.6 98.6 1.0 OG B:SER295 4.7 105.5 1.0 N B:SER298 4.7 104.4 1.0 CA B:SER298 4.8 101.8 1.0 CG B:PRO342 4.8 95.7 1.0 N B:PRO338 4.8 100.9 1.0 O B:ILE336 4.8 104.3 1.0 CA B:GLY296 4.9 106.0 1.0 C B:GLY296 4.9 105.2 1.0 N B:SER343 5.0 90.1 1.0

M.J.Currie, J.S.Davies, M.Scalise, A.Gulati, J.D.Wright, M.C.Newton-Vesty, G.S.Abeysekera, R.Subramanian, W.Y.Wahlgren, R.Friemann, J.R.Allison, P.D.Mace, M.D.W.Griffin, B.Demeler, S.Wakatsuki, D.Drew, C.Indiveri, R.C.J.Dobson, R.A.North. Structural and Biophysical Analysis of A Haemophilus Influenzae Tripartite Atp-Independent Periplasmic (Trap) Transporter Elife 2023.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.92307.1