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

Sodium Binding Sites:

The binding sites of Sodium atom in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel Dimer) (pdb code 8thj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel Dimer), PDB code: 8thj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8thj

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Sodium binding site 1 out of 4 in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel 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 (Antiparallel Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:85.0
occ:1.00
 O A:GLY337 2.1 77.5 1.0
O A:PRO342 2.2 77.0 1.0
O A:SER298 2.5 89.5 1.0
O A:VAL340 2.5 72.7 1.0
O A:SER295 3.0 85.5 1.0
C A:GLY337 3.2 73.2 1.0
C A:PRO342 3.4 74.9 1.0
C A:SER298 3.6 88.7 1.0
C A:VAL340 3.8 66.0 1.0
CA A:GLY299 3.8 80.3 1.0
CA A:GLY337 3.9 75.1 1.0
N A:PRO342 4.0 69.2 1.0
C A:SER295 4.0 82.5 1.0
C A:PRO341 4.1 65.9 1.0
N A:GLY299 4.2 85.3 1.0
CA A:PRO342 4.3 72.4 1.0
N A:PRO338 4.3 69.1 1.0
CD A:PRO342 4.3 78.0 1.0
N A:SER343 4.3 71.5 1.0
CA A:SER343 4.4 65.3 1.0
C A:GLY299 4.4 87.9 1.0
O A:PRO341 4.5 68.3 1.0
CA A:PRO341 4.5 67.2 1.0
CA A:SER295 4.5 80.4 1.0
CA A:PRO338 4.5 68.5 1.0
CB A:SER343 4.5 65.5 1.0
N A:PRO341 4.6 66.6 1.0
CG A:PRO342 4.6 73.5 1.0
CA A:VAL340 4.7 63.3 1.0
N A:VAL340 4.7 64.9 1.0
C A:PRO338 4.7 65.3 1.0
CB A:SER295 4.8 79.8 1.0
O A:GLY299 4.9 84.3 1.0
CA A:SER298 4.9 93.4 1.0
CB A:VAL340 4.9 65.2 1.0
N A:SER300 4.9 94.3 1.0
O A:ILE336 5.0 71.2 1.0

Sodium binding site 2 out of 4 in 8thj

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Sodium binding site 2 out of 4 in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel 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 (Antiparallel Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:74.4
occ:1.00
 O A:GLY558 2.2 62.0 1.0
O A:GLY517 2.4 61.6 1.0
O A:MET564 2.8 71.8 1.0
O A:THR561 3.1 67.5 1.0
C A:GLY558 3.1 52.5 1.0
OG1 A:THR561 3.2 70.3 1.0
C A:MET564 3.5 69.9 1.0
C A:GLY517 3.6 54.5 1.0
CA A:GLY558 3.9 50.5 1.0
CA A:GLY565 3.9 62.9 1.0
N A:ILE559 4.0 50.0 1.0
O A:MET518 4.0 65.8 1.0
N A:GLY565 4.0 68.9 1.0
CA A:MET518 4.0 54.4 1.0
CA A:ILE559 4.1 55.8 1.0
C A:THR561 4.1 63.9 1.0
N A:THR561 4.1 59.7 1.0
C A:MET518 4.1 61.5 1.0
CB A:THR561 4.3 64.0 1.0
N A:MET518 4.3 56.8 1.0
CA A:THR561 4.4 59.3 1.0
C A:ILE559 4.5 53.8 1.0
O A:ILE520 4.5 68.4 1.0
CA A:MET564 4.6 68.8 1.0
CA A:GLY517 4.7 49.7 1.0
CG2 A:THR561 4.7 56.2 1.0
N A:MET564 4.7 70.5 1.0
N A:LEU560 4.7 52.7 1.0
N A:PHE519 5.0 60.5 1.0

Sodium binding site 3 out of 4 in 8thj

Go back to Sodium Binding Sites List in 8thj
Sodium binding site 3 out of 4 in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel Dimer)


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 Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:84.3
occ:1.00
 O B:GLY337 2.2 76.5 1.0
O B:PRO342 2.2 77.9 1.0
O B:SER298 2.5 89.4 1.0
O B:VAL340 2.5 73.6 1.0
O B:SER295 2.9 86.4 1.0
C B:GLY337 3.2 73.7 1.0
C B:PRO342 3.4 74.8 1.0
C B:SER298 3.6 88.3 1.0
C B:VAL340 3.8 66.2 1.0
CA B:GLY299 3.8 80.4 1.0
CA B:GLY337 3.9 75.6 1.0
N B:PRO342 4.0 68.9 1.0
C B:SER295 4.0 82.2 1.0
C B:PRO341 4.1 66.6 1.0
N B:GLY299 4.2 84.7 1.0
CA B:PRO342 4.3 72.2 1.0
N B:PRO338 4.3 70.3 1.0
N B:SER343 4.3 70.0 1.0
CD B:PRO342 4.3 77.7 1.0
CA B:SER343 4.4 64.7 1.0
O B:PRO341 4.4 68.6 1.0
C B:GLY299 4.5 88.4 1.0
CA B:PRO341 4.5 68.0 1.0
CA B:SER295 4.5 79.4 1.0
CB B:SER343 4.5 64.5 1.0
CA B:PRO338 4.5 67.7 1.0
N B:PRO341 4.6 66.0 1.0
CG B:PRO342 4.6 73.8 1.0
CA B:VAL340 4.7 63.9 1.0
C B:PRO338 4.7 64.0 1.0
N B:VAL340 4.7 66.2 1.0
CB B:SER295 4.8 79.8 1.0
CA B:SER298 4.9 93.7 1.0
N B:SER300 4.9 94.0 1.0
O B:GLY299 4.9 84.6 1.0
CB B:VAL340 5.0 65.5 1.0
N B:SER298 5.0 98.2 1.0
O B:ILE336 5.0 70.0 1.0

Sodium binding site 4 out of 4 in 8thj

Go back to Sodium Binding Sites List in 8thj
Sodium binding site 4 out of 4 in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel Dimer)


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 Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Haemophilus Influenzae (Antiparallel Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:78.0
occ:1.00
 O B:GLY558 2.1 62.0 1.0
O B:GLY517 2.5 61.7 1.0
O B:MET564 2.8 71.6 1.0
O B:THR561 3.1 67.0 1.0
C B:GLY558 3.1 53.9 1.0
OG1 B:THR561 3.2 72.8 1.0
C B:MET564 3.5 68.1 1.0
C B:GLY517 3.6 55.1 1.0
O B:MET518 3.9 67.5 1.0
CA B:GLY565 3.9 62.4 1.0
CA B:GLY558 4.0 51.4 1.0
CA B:MET518 4.0 54.2 1.0
N B:GLY565 4.0 67.2 1.0
N B:ILE559 4.0 51.9 1.0
N B:THR561 4.1 59.5 1.0
C B:THR561 4.1 64.0 1.0
C B:MET518 4.1 62.0 1.0
CA B:ILE559 4.1 56.1 1.0
CB B:THR561 4.2 64.8 1.0
N B:MET518 4.2 57.3 1.0
CA B:THR561 4.3 59.8 1.0
C B:ILE559 4.5 53.5 1.0
O B:ILE520 4.5 69.8 1.0
CA B:MET564 4.6 67.9 1.0
CG2 B:THR561 4.6 56.8 1.0
N B:MET564 4.7 70.0 1.0
CA B:GLY517 4.7 51.5 1.0
N B:LEU560 4.7 53.5 1.0
CB B:MET564 4.9 71.3 1.0
N B:PHE519 4.9 61.6 1.0

Reference:

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
Page generated: Wed Oct 9 13:40:18 2024

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