Sodium in PDB 4llh: Substrate Bound Outward-Open State of the Symporter Betp

The structure of Substrate Bound Outward-Open State of the Symporter Betp, PDB code: 4llh was solved by C.Perez, B.Faust, C.Ziegler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.30 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.470, 129.690, 164.650, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 29

The structure of Substrate Bound Outward-Open State of the Symporter Betp also contains other interesting chemical elements:

Arsenic	(As)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Substrate Bound Outward-Open State of the Symporter Betp (pdb code 4llh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Substrate Bound Outward-Open State of the Symporter Betp, PDB code: 4llh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Substrate Bound Outward-Open State of the Symporter Betp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Substrate Bound Outward-Open State of the Symporter Betp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:62.9 occ:1.00 OG A:SER468 2.3 81.1 1.0 O A:ALA147 2.8 66.5 1.0 O A:PHE464 2.8 90.6 1.0 O A:MET150 3.1 88.4 1.0 OG1 A:THR467 3.1 55.1 1.0 CA A:GLY151 3.3 89.0 1.0 C A:MET150 3.4 88.8 1.0 CB A:SER468 3.5 83.1 1.0 N A:GLY151 3.6 89.1 1.0 N A:SER468 3.9 90.5 1.0 C A:ALA147 4.0 65.8 1.0 C A:GLY151 4.0 87.0 1.0 C A:PHE464 4.0 90.5 1.0 CA A:SER468 4.2 84.8 1.0 O A:GLY151 4.2 83.9 1.0 CD1 A:PHE464 4.2 85.0 1.0 CB A:THR467 4.4 54.7 1.0 N A:MET150 4.4 84.3 1.0 C A:THR467 4.5 96.0 1.0 CA A:MET150 4.5 87.4 1.0 O A:PHE465 4.6 98.0 1.0 CE1 A:PHE464 4.6 80.5 1.0 CA A:ALA147 4.7 64.9 1.0 CA A:PHE464 4.7 86.8 1.0 C A:ALA148 4.7 69.9 1.0 CG A:PHE464 4.8 85.8 1.0 O A:PHE146 4.8 63.5 1.0 O A:ALA148 4.8 74.5 1.0 N A:ILE152 4.9 87.7 1.0 CA A:THR467 4.9 98.1 1.0 N A:ALA148 4.9 65.0 1.0 CA A:ALA148 4.9 60.9 1.0 C A:GLY149 4.9 79.4 1.0 N A:PHE465 5.0 94.8 1.0 CA A:PHE465 5.0 95.3 1.0

Sodium binding site 2 out of 2 in the Substrate Bound Outward-Open State of the Symporter Betp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Substrate Bound Outward-Open State of the Symporter Betp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:96.6 occ:1.00 OG B:SER468 2.4 75.2 1.0 O B:ALA147 2.4 67.7 1.0 OG1 B:THR467 2.5 66.9 1.0 O B:PHE464 2.8 50.4 1.0 O B:MET150 2.9 83.3 1.0 N B:SER468 3.1 68.9 1.0 C B:ALA147 3.3 60.8 1.0 CB B:SER468 3.4 74.9 1.0 CB B:THR467 3.4 71.8 1.0 C B:THR467 3.5 71.5 1.0 C B:PHE464 3.6 54.8 1.0 CA B:SER468 3.6 71.5 1.0 CA B:ALA147 3.8 58.2 1.0 CA B:THR467 3.9 74.2 1.0 CA B:PHE464 4.0 60.2 1.0 C B:MET150 4.1 80.2 1.0 N B:THR467 4.2 74.3 1.0 O B:THR467 4.2 71.1 1.0 N B:ALA148 4.2 55.1 1.0 O B:THR463 4.3 63.2 1.0 CB B:ALA147 4.4 56.1 1.0 CD2 B:PHE464 4.5 48.4 1.0 CA B:ALA148 4.6 52.5 1.0 O B:PHE465 4.6 66.1 1.0 N B:PHE465 4.7 59.5 1.0 CG2 B:THR467 4.8 74.2 1.0 C B:PHE465 4.8 69.0 1.0 CA B:GLY151 4.8 77.0 1.0 C B:ALA148 4.9 58.6 1.0 N B:GLY151 4.9 78.8 1.0 O B:PHE146 4.9 56.2 1.0 CB B:PHE464 5.0 57.3 1.0 CA B:PHE465 5.0 64.3 1.0 CG B:PHE464 5.0 51.5 1.0 O B:GLY151 5.0 79.8 1.0

C.Perez, B.Faust, A.R.Mehdipour, K.A.Francesconi, L.R.Forrest, C.Ziegler. Substrate-Bound Outward-Open State of the Betaine Transporter Betp Provides Insights Into Na(+) Coupling. Nat Commun V. 5 4231 2014.
ISSN: ESSN 2041-1723
PubMed: 25023443
DOI: 10.1038/NCOMMS5231