Sodium in PDB 8b01: Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Photobacterium Profundum in A Nanodisc

The binding sites of Sodium atom in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Photobacterium Profundum in A Nanodisc (pdb code 8b01). 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 Photobacterium Profundum in A Nanodisc, PDB code: 8b01:
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 Photobacterium Profundum in A Nanodisc


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 Photobacterium Profundum in A Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:150.1 occ:1.00 O B:GLY145 2.3 139.8 1.0 O B:SER103 2.4 134.9 1.0 O B:VAL148 2.5 123.7 1.0 O B:SER106 2.5 148.3 1.0 O B:PRO150 2.7 138.4 1.0 C B:GLY145 3.3 135.6 1.0 C B:SER106 3.6 147.2 1.0 C B:SER103 3.6 132.8 1.0 C B:VAL148 3.7 120.6 1.0 CA B:GLY145 3.7 136.1 1.0 CA B:GLY107 3.8 150.3 1.0 C B:PRO150 3.9 135.2 1.0 C B:PRO149 4.1 131.4 1.0 N B:PRO150 4.1 130.9 1.0 N B:GLY107 4.1 150.8 1.0 O B:PRO149 4.2 136.2 1.0 CA B:SER103 4.3 131.8 1.0 CD B:PRO150 4.3 132.4 1.0 N B:PRO146 4.4 130.3 1.0 CA B:VAL148 4.5 119.2 1.0 CB B:VAL148 4.6 120.0 1.0 N B:PRO149 4.6 131.2 1.0 CA B:PRO149 4.6 132.0 1.0 CA B:PRO150 4.6 131.0 1.0 N B:VAL148 4.6 117.8 1.0 CB B:SER103 4.7 132.5 1.0 N B:GLY104 4.7 132.0 1.0 C B:GLY107 4.7 151.5 1.0 CA B:PRO146 4.7 130.0 1.0 CG B:PRO150 4.8 129.2 1.0 CA B:SER106 4.8 146.7 1.0 N B:SER106 4.8 145.2 1.0 O B:ILE144 4.8 139.6 1.0 N B:SER151 4.9 137.7 1.0 CA B:GLY104 4.9 133.7 1.0 C B:PRO146 5.0 130.7 1.0 C B:GLY104 5.0 134.8 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of the Tripartite Atp-Independent Periplasmic (Trap) Transporter Siaqm From Photobacterium Profundum in A Nanodisc


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 Photobacterium Profundum in A Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:158.0 occ:1.00 O B:MET372 2.3 152.2 1.0 O B:GLY366 2.5 137.0 1.0 O B:THR369 2.5 138.2 1.0 OG1 B:THR369 2.7 132.7 1.0 O B:GLY325 3.0 125.0 1.0 C B:THR369 3.4 135.0 1.0 C B:MET372 3.5 152.0 1.0 N B:THR369 3.6 134.9 1.0 C B:GLY366 3.6 131.7 1.0 CA B:THR326 3.7 127.6 1.0 CB B:THR369 3.8 134.7 1.0 CA B:THR369 3.8 132.7 1.0 C B:GLY325 3.9 124.6 1.0 O B:THR326 4.0 138.9 1.0 C B:THR326 4.1 133.8 1.0 CA B:GLY373 4.1 148.5 1.0 N B:GLY373 4.2 151.4 1.0 N B:THR326 4.3 127.1 1.0 C B:ILE367 4.3 126.5 1.0 CA B:ILE367 4.4 126.3 1.0 O B:ILE367 4.4 129.6 1.0 N B:ILE367 4.5 128.2 1.0 CA B:MET372 4.5 149.2 1.0 N B:MET372 4.5 146.2 1.0 CA B:GLY366 4.6 129.7 1.0 N B:PRO370 4.6 142.7 1.0 O B:PRO370 4.6 150.4 1.0 C B:LEU368 4.7 130.1 1.0 N B:LEU368 4.7 126.8 1.0 C B:PRO370 4.8 145.5 1.0 CB B:THR326 4.8 126.6 1.0 CG2 B:THR326 4.9 127.1 1.0 CG2 B:THR369 4.9 136.4 1.0 CB B:MET372 4.9 147.4 1.0

J.S.Davies, M.J.Currie, R.A.North, M.Scalise, J.D.Wright, J.M.Copping, D.M.Remus, A.Gulati, D.R.Morado, S.A.Jamieson, M.C.Newton-Vesty, G.S.Abeysekera, S.Ramaswamy, R.Friemann, S.Wakatsuki, J.R.Allison, C.Indiveri, D.Drew, P.D.Mace, R.C.J.Dobson. Structure and Mechanism of A Tripartite Atp-Independent Periplasmic Trap Transporter. Nat Commun V. 14 1120 2023.
ISSN: ESSN 2041-1723
PubMed: 36849793
DOI: 10.1038/S41467-023-36590-1