Sodium in PDB 4hmk: Crystal Structure of Leut-E290S with Bound Br

The structure of Crystal Structure of Leut-E290S with Bound Br, PDB code: 4hmk was solved by A.K.Kantcheva, M.Quick, L.Shi, A.M.L.Winther, S.Stolzenberg, H.Weinstein, J.A.Javitch, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.30 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.140, 92.320, 87.210, 90.00, 94.25, 90.00
R / Rfree (%)	20.5 / 26.1

The structure of Crystal Structure of Leut-E290S with Bound Br also contains other interesting chemical elements:

Bromine

(Br)

11 atoms

The binding sites of Sodium atom in the Crystal Structure of Leut-E290S with Bound Br (pdb code 4hmk). 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 Leut-E290S with Bound Br, PDB code: 4hmk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Leut-E290S with Bound Br


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 Leut-E290S with Bound Br within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:40.6 occ:1.00 O A:VAL23 2.7 40.2 1.0 O A:GLY20 2.7 41.7 1.0 O A:ALA351 2.8 45.3 1.0 OG1 A:THR354 2.9 41.0 1.0 N A:SER355 3.3 44.0 1.0 OG A:SER355 3.3 38.9 1.0 C A:VAL23 3.5 41.3 1.0 C A:THR354 3.6 42.0 1.0 CB A:THR354 3.6 41.9 1.0 C A:ALA351 3.6 46.3 1.0 CB A:SER355 3.6 31.9 1.0 C A:GLY20 3.7 48.6 1.0 CA A:GLY24 3.8 41.5 1.0 CA A:SER355 3.8 37.3 1.0 CA A:THR354 3.9 41.5 1.0 CA A:ALA351 3.9 40.9 1.0 CA A:GLY20 4.0 41.3 1.0 N A:GLY24 4.0 42.7 1.0 N A:THR354 4.1 44.1 1.0 O A:PHE350 4.2 35.5 1.0 O A:THR354 4.2 43.4 1.0 O A:ASN21 4.3 47.8 1.0 CA A:VAL23 4.5 44.1 1.0 O A:ALA22 4.6 46.8 1.0 N A:GLY352 4.6 40.5 1.0 N A:VAL23 4.7 38.9 1.0 C A:GLY352 4.7 36.9 1.0 CB A:ALA351 4.7 36.5 1.0 C A:ASN21 4.7 42.6 1.0 CA A:GLY352 4.8 37.3 1.0 O A:GLY352 4.8 38.7 1.0 N A:ASN21 4.8 43.7 1.0 C A:ALA22 4.8 41.4 1.0 CB A:VAL23 4.8 47.7 1.0 CG2 A:THR354 4.9 39.0 1.0 N A:ALA351 4.9 41.1 1.0 C A:PHE350 5.0 40.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Leut-E290S with Bound Br


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 Leut-E290S with Bound Br within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:46.6 occ:1.00 OXT A:LEU601 2.9 44.5 1.0 OD1 A:ASN27 3.0 49.4 1.0 O A:THR254 3.0 50.3 1.0 OG1 A:THR254 3.1 52.3 1.0 O A:ALA22 3.1 46.8 1.0 OD1 A:ASN286 3.1 45.7 1.0 N A:GLY24 3.4 42.7 1.0 CG A:ASN27 3.4 50.9 1.0 ND2 A:ASN27 3.4 46.5 1.0 CA A:THR254 3.5 49.5 1.0 C A:ALA22 3.5 41.4 1.0 CA A:VAL23 3.5 44.1 1.0 C A:THR254 3.6 50.1 1.0 C A:LEU601 3.6 43.8 1.0 N A:VAL23 3.8 38.9 1.0 CB A:THR254 3.8 44.5 1.0 N A:LEU601 3.9 42.3 1.0 C A:VAL23 3.9 41.3 1.0 N A:ASN27 3.9 43.6 1.0 CG A:ASN286 4.0 45.6 1.0 ND2 A:ASN286 4.2 48.1 1.0 CA A:LEU601 4.3 45.3 1.0 O A:LEU601 4.3 43.5 1.0 CA A:ALA22 4.4 41.8 1.0 CA A:GLY26 4.5 44.8 1.0 C A:GLY26 4.5 45.6 1.0 CB A:ASN27 4.6 44.7 1.0 CA A:GLY24 4.6 41.5 1.0 CA A:ASN27 4.6 42.7 1.0 N A:THR254 4.7 48.5 1.0 CB A:ALA22 4.7 42.6 1.0 O A:PHE253 4.8 45.7 1.0 O A:GLY24 4.8 39.9 1.0 CB A:VAL23 4.9 47.7 1.0 N A:LEU255 4.9 47.3 1.0 N A:GLY26 4.9 42.1 1.0 CG2 A:THR254 4.9 42.9 1.0 C A:GLY24 5.0 43.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Leut-E290S with Bound Br


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 Leut-E290S with Bound Br within 5.0Å range: probe atom residue distance (Å) B Occ B:Na604 b:49.2 occ:1.00 O B:GLY20 2.7 42.3 1.0 O B:VAL23 2.7 45.3 1.0 O B:ALA351 2.8 45.5 1.0 OG1 B:THR354 2.9 41.5 1.0 N B:SER355 3.2 46.4 1.0 OG B:SER355 3.3 40.9 1.0 CB B:THR354 3.5 43.2 1.0 C B:THR354 3.6 44.1 1.0 C B:ALA351 3.6 45.8 1.0 C B:VAL23 3.6 43.8 1.0 CB B:SER355 3.6 35.5 1.0 C B:GLY20 3.7 52.7 1.0 CA B:THR354 3.8 42.9 1.0 CA B:GLY24 3.8 41.0 1.0 CA B:SER355 3.8 40.0 1.0 CA B:ALA351 3.9 42.8 1.0 N B:THR354 3.9 41.4 1.0 CA B:GLY20 4.0 43.1 1.0 O B:PHE350 4.1 39.6 1.0 N B:GLY24 4.1 46.8 1.0 O B:ASN21 4.3 49.1 1.0 O B:THR354 4.3 41.7 1.0 O B:ALA22 4.6 48.6 1.0 C B:GLY352 4.6 42.3 1.0 N B:GLY352 4.6 40.0 1.0 O B:GLY352 4.6 43.1 1.0 CA B:VAL23 4.7 41.3 1.0 CA B:GLY352 4.8 38.2 1.0 CB B:ALA351 4.8 37.2 1.0 C B:ASN21 4.8 44.3 1.0 N B:VAL23 4.8 38.4 1.0 N B:ASN21 4.8 46.1 1.0 CG2 B:THR354 4.9 40.8 1.0 N B:ALA351 4.9 42.7 1.0 C B:PHE350 4.9 43.0 1.0 CB B:VAL23 4.9 46.3 1.0 C B:ALA22 4.9 41.4 1.0 N B:LEU353 5.0 43.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Leut-E290S with Bound Br


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 Leut-E290S with Bound Br within 5.0Å range: probe atom residue distance (Å) B Occ B:Na605 b:55.5 occ:1.00 OD1 B:ASN27 3.0 50.5 1.0 O B:THR254 3.0 48.7 1.0 OXT B:LEU603 3.0 54.5 1.0 OG1 B:THR254 3.1 55.2 1.0 O B:ALA22 3.1 48.6 1.0 OD1 B:ASN286 3.2 51.9 1.0 ND2 B:ASN27 3.3 47.6 1.0 CG B:ASN27 3.4 54.2 1.0 N B:GLY24 3.4 46.8 1.0 C B:ALA22 3.4 41.4 1.0 CA B:THR254 3.4 47.5 1.0 C B:LEU603 3.5 48.0 1.0 CA B:VAL23 3.5 41.3 1.0 N B:LEU603 3.6 38.7 1.0 C B:THR254 3.6 49.2 1.0 N B:VAL23 3.7 38.4 1.0 CB B:THR254 3.8 48.8 1.0 C B:VAL23 3.9 43.8 1.0 N B:ASN27 3.9 41.9 1.0 CG B:ASN286 4.0 51.3 1.0 CA B:LEU603 4.1 49.8 1.0 O B:LEU603 4.2 45.1 1.0 ND2 B:ASN286 4.2 51.6 1.0 CA B:ALA22 4.3 43.6 1.0 C B:GLY26 4.5 46.9 1.0 CB B:ASN27 4.5 47.8 1.0 CB B:ALA22 4.5 44.1 1.0 CA B:GLY24 4.6 41.0 1.0 CA B:ASN27 4.6 41.8 1.0 CA B:GLY26 4.6 44.9 1.0 N B:THR254 4.6 46.2 1.0 O B:PHE253 4.6 51.6 1.0 O B:GLY24 4.7 41.1 1.0 N B:LEU255 4.9 49.6 1.0 CG2 B:THR254 4.9 44.8 1.0 CB B:VAL23 4.9 46.3 1.0 C B:GLY24 4.9 42.4 1.0

A.K.Kantcheva, M.Quick, L.Shi, A.M.L.Winther, S.Stolzenberg, H.Weinstein, J.A.Javitch, P.Nissen. The Chloride Binding Site of Neurotransmitter Sodium Symporters Proc.Natl.Acad.Sci.Usa 2013.
ISSN: ESSN 1091-6490