Sodium in PDB 6yu6: Crystal Structure of Mhst in Complex with L-Leucine

The structure of Crystal Structure of Mhst in Complex with L-Leucine, PDB code: 6yu6 was solved by D.Focht, C.Neumann, J.Lyons, A.Eguskiza Bilbao, R.Blunck, L.Malinauskaite, I.O.Schwarz, J.A.Javitch, M.Quick, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.48 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.230, 215.560, 50.170, 90.00, 90.05, 90.00
R / Rfree (%)	18.5 / 22.2

The binding sites of Sodium atom in the Crystal Structure of Mhst in Complex with L-Leucine (pdb code 6yu6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Mhst in Complex with L-Leucine, PDB code: 6yu6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Mhst in Complex with L-Leucine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:32.6 occ:1.00 O A:ALA320 2.0 30.6 1.0 O A:VAL27 2.1 30.8 1.0 O A:GLY24 2.3 41.2 1.0 OG A:SER324 2.4 28.2 1.0 OG A:SER323 2.4 35.4 1.0 C A:ALA320 3.0 31.9 1.0 N A:SER324 3.1 35.8 1.0 C A:VAL27 3.1 29.7 1.0 C A:GLY24 3.4 32.0 1.0 CB A:SER324 3.4 28.2 1.0 CA A:ALA320 3.5 33.3 1.0 CB A:SER323 3.6 29.0 1.0 CA A:SER324 3.7 32.0 1.0 C A:SER323 3.7 31.4 1.0 CA A:GLY28 3.8 36.6 1.0 N A:GLY28 3.9 30.6 1.0 CB A:ALA320 3.9 34.4 1.0 CA A:SER323 4.1 28.2 1.0 CA A:GLY24 4.1 35.0 1.0 N A:ALA321 4.2 31.5 1.0 CA A:VAL27 4.2 28.2 1.0 N A:VAL27 4.2 30.4 1.0 N A:SER323 4.2 31.6 1.0 O A:SER25 4.4 37.7 1.0 N A:SER25 4.4 28.9 1.0 C A:SER25 4.4 34.6 1.0 O A:SER323 4.6 29.5 1.0 CA A:SER25 4.6 28.8 1.0 CA A:ALA321 4.6 31.6 1.0 CB A:VAL27 4.7 32.3 1.0 O A:MET23 4.8 32.0 1.0 O A:ALA319 4.8 33.2 1.0 C A:ALA321 4.9 31.7 1.0 N A:ALA320 4.9 34.4 1.0 C A:ALA26 4.9 29.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Mhst in Complex with L-Leucine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:38.0 occ:1.00 O A:ALA26 2.2 41.0 1.0 OXT A:LEU503 2.4 33.9 1.0 OG1 A:THR231 2.4 38.9 1.0 OD1 A:ASP263 2.4 37.7 1.0 O A:THR231 2.4 39.9 1.0 OD1 A:ASN31 2.4 36.3 1.0 ND2 A:ASN31 2.9 30.2 1.0 CG A:ASN31 3.0 30.6 1.0 C A:THR231 3.2 40.9 1.0 CA A:THR231 3.3 41.8 1.0 CG A:ASP263 3.3 38.3 1.0 C A:ALA26 3.3 29.4 1.0 CB A:THR231 3.4 36.6 1.0 C A:LEU503 3.5 34.5 1.0 OD2 A:ASP263 3.5 43.8 1.0 N A:LEU503 3.9 37.3 1.0 N A:VAL27 4.1 30.4 1.0 CA A:VAL27 4.2 28.2 1.0 CA A:ALA26 4.2 28.2 1.0 O A:LEU503 4.3 36.3 1.0 N A:GLY28 4.3 30.6 1.0 CA A:LEU503 4.3 39.9 1.0 CB A:ASN31 4.3 30.2 1.0 N A:ASN31 4.4 36.2 1.0 CG2 A:THR231 4.4 35.2 1.0 N A:LEU232 4.5 37.4 1.0 CB A:ALA26 4.6 28.2 1.0 CB A:ASP263 4.6 38.2 1.0 N A:THR231 4.7 36.7 1.0 CA A:ASN31 4.7 34.5 1.0 C A:GLY30 4.7 31.4 1.0 C A:VAL27 4.8 29.7 1.0 O A:PHE230 5.0 39.7 1.0 CA A:GLY30 5.0 31.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Mhst in Complex with L-Leucine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:32.8 occ:1.00 O B:ALA26 2.2 36.5 1.0 OG1 B:THR231 2.3 38.2 1.0 OD1 B:ASP263 2.4 40.0 1.0 OXT B:LEU503 2.4 34.0 1.0 O B:THR231 2.4 43.0 1.0 OD1 B:ASN31 2.4 38.2 1.0 CG B:ASN31 3.0 35.4 1.0 C B:ALA26 3.2 31.3 1.0 C B:THR231 3.2 36.1 1.0 ND2 B:ASN31 3.2 43.1 1.0 CA B:THR231 3.2 34.6 1.0 CG B:ASP263 3.3 41.0 1.0 CB B:THR231 3.3 37.2 1.0 OD2 B:ASP263 3.4 45.4 1.0 C B:LEU503 3.5 33.9 1.0 N B:LEU503 3.9 35.2 1.0 N B:VAL27 4.0 35.2 1.0 CA B:VAL27 4.1 28.6 1.0 CA B:ALA26 4.1 30.4 1.0 N B:ASN31 4.2 37.2 1.0 CB B:ASN31 4.3 31.9 1.0 O B:LEU503 4.3 32.3 1.0 N B:GLY28 4.3 29.5 1.0 CA B:LEU503 4.3 32.4 1.0 CG2 B:THR231 4.4 35.0 1.0 CB B:ALA26 4.5 29.4 1.0 N B:LEU232 4.5 36.5 1.0 C B:VAL27 4.6 28.2 1.0 CA B:ASN31 4.6 36.9 1.0 N B:THR231 4.7 35.5 1.0 CB B:ASP263 4.7 35.8 1.0 C B:GLY30 4.7 36.3 1.0 CA B:GLY30 4.9 28.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Mhst in Complex with L-Leucine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:29.6 occ:1.00 O B:ALA320 2.1 30.3 1.0 O B:VAL27 2.1 30.0 1.0 O B:GLY24 2.2 36.4 1.0 OG B:SER323 2.4 38.3 1.0 OG B:SER324 2.4 33.8 1.0 C B:ALA320 3.0 34.3 1.0 N B:SER324 3.2 35.9 1.0 C B:VAL27 3.3 28.2 1.0 C B:GLY24 3.3 33.2 1.0 CA B:ALA320 3.4 32.0 1.0 CB B:SER324 3.5 30.1 1.0 CB B:SER323 3.6 32.5 1.0 CA B:SER324 3.8 32.2 1.0 CB B:ALA320 3.8 35.4 1.0 C B:SER323 3.8 30.4 1.0 CA B:GLY24 4.0 36.6 1.0 CA B:GLY28 4.1 28.9 1.0 CA B:SER323 4.1 29.2 1.0 N B:GLY28 4.2 29.5 1.0 N B:ALA321 4.2 33.5 1.0 N B:SER323 4.4 34.8 1.0 CA B:VAL27 4.4 28.6 1.0 N B:SER25 4.4 32.7 1.0 N B:VAL27 4.5 35.2 1.0 O B:SER25 4.6 34.0 1.0 O B:SER323 4.6 30.5 1.0 C B:SER25 4.7 29.8 1.0 CA B:SER25 4.7 28.2 1.0 CB B:VAL27 4.7 32.0 1.0 O B:ALA319 4.7 42.4 1.0 CA B:ALA321 4.7 28.2 1.0 N B:ALA320 4.8 31.6 1.0 O B:MET23 5.0 40.9 1.0 C B:ALA321 5.0 31.7 1.0

D.Focht, C.Neumann, J.Lyons, A.Eguskiza Bilbao, R.Blunck, L.Malinauskaite, I.O.Schwarz, J.A.Javitch, M.Quick, P.Nissen. Role of A Non-Helical Region of Transmembrane Helix 6 in the Substrate Recognition Mechanism of the Hydrophobic Amino Acid Transporter Mhst. To Be Published.