Sodium in PDB 6m38: X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form, PDB code: 6m38 was solved by P.Shabareesh, A.K.Mallela, D.Joseph, A.Penmatsa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.64 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.288, 140.641, 167.818, 90, 90, 90
R / Rfree (%)	21.5 / 24.4

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form (pdb code 6m38). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form, PDB code: 6m38:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:69.7 occ:1.00 OD1 A:ASN49 2.4 68.5 1.0 O A:ALA44 2.4 62.8 1.0 O A:SER320 2.5 72.5 1.0 OG A:SER320 2.5 72.4 1.0 C A:29E601 2.9 79.2 1.0 CA A:SER320 2.9 74.6 1.0 C A:SER320 3.0 70.8 1.0 OD1 A:ASN352 3.2 67.0 1.0 CB A:SER320 3.2 69.4 1.0 CG A:ASN49 3.4 63.8 1.0 OD1 A:ASP46 3.5 71.9 1.0 C A:ALA44 3.6 64.3 1.0 ND2 A:ASN49 3.7 61.8 1.0 N A:29E601 3.8 73.5 1.0 CG A:ASN352 4.1 68.8 1.0 O A:HOH706 4.2 76.7 1.0 N A:SER320 4.3 73.8 1.0 N A:LEU321 4.3 69.7 1.0 N A:ASP46 4.3 66.5 1.0 ND2 A:ASN352 4.3 68.8 1.0 O A:PHE319 4.4 69.1 1.0 CA A:VAL45 4.5 62.2 1.0 N A:VAL45 4.5 64.9 1.0 CG A:ASP46 4.6 73.9 1.0 CA A:ALA44 4.6 63.8 1.0 N A:ASN49 4.6 69.5 1.0 CB A:ALA48 4.7 70.2 1.0 CB A:ASN49 4.7 67.1 1.0 C A:PHE319 4.8 71.4 1.0 C A:VAL45 4.9 66.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:66.5 occ:1.00 O A:GLY42 2.2 63.5 1.0 O A:LEU417 2.3 74.9 1.0 OG A:SER421 2.3 68.7 1.0 OD1 A:ASP420 2.3 71.5 1.0 O A:VAL45 2.5 68.7 1.0 N A:SER421 3.2 64.0 1.0 CB A:SER421 3.3 63.6 1.0 C A:VAL45 3.3 66.6 1.0 C A:LEU417 3.4 70.0 1.0 CG A:ASP420 3.4 70.8 1.0 C A:GLY42 3.5 66.1 1.0 CB A:ASP46 3.5 66.0 1.0 CA A:ASP46 3.7 66.6 1.0 CA A:SER421 3.7 62.1 1.0 N A:ASP46 3.9 66.5 1.0 O A:PHE43 4.0 67.7 1.0 C A:ASP420 4.0 63.1 1.0 OD2 A:ASP420 4.2 67.7 1.0 CA A:LEU417 4.2 67.4 1.0 N A:GLY418 4.3 68.1 1.0 CA A:GLY42 4.3 66.2 1.0 CA A:GLY418 4.3 66.7 1.0 C A:PHE43 4.3 64.2 1.0 CB A:ASP420 4.4 61.2 1.0 N A:VAL45 4.4 64.9 1.0 N A:PHE43 4.4 67.7 1.0 C A:GLY418 4.4 64.4 1.0 O A:GLY418 4.4 63.0 1.0 CA A:PHE43 4.5 61.4 1.0 CA A:VAL45 4.5 62.2 1.0 CA A:ASP420 4.5 64.7 1.0 N A:ASP420 4.5 68.7 1.0 O A:THR416 4.6 68.8 1.0 O A:ASP420 4.8 65.9 1.0 CG A:ASP46 4.9 73.9 1.0

P.Shabareesh, A.K.Mallela, D.Joseph. Structural Basis of Norepinephrine Recognition and Transport Inhibition in Neurotransmitter Transporters To Be Published.