Sodium in PDB 6m47: X-Ray Structure of A Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in Tramadol Bound Form

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in Tramadol Bound Form, PDB code: 6m47 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)	48.50 / 3.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.004, 140.956, 167.795, 90, 90, 90
R / Rfree (%)	24.1 / 27.5

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in Tramadol 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 Net-Like Mutations (D121G/S426M/F471L) in Tramadol Bound Form (pdb code 6m47). 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 Net-Like Mutations (D121G/S426M/F471L) in Tramadol Bound Form, PDB code: 6m47:
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 Net-Like Mutations (D121G/S426M/F471L) in Tramadol 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 Net-Like Mutations (D121G/S426M/F471L) in Tramadol Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:85.7 occ:1.00 OD1 A:ASN352 2.3 86.4 1.0 OG A:SER320 2.4 84.1 1.0 OD1 A:ASN49 2.4 77.8 1.0 ND2 A:ASN49 2.6 86.8 1.0 ND2 A:ASN352 2.8 83.8 1.0 CG A:ASN49 2.8 80.2 1.0 O A:ALA44 2.8 85.5 1.0 CG A:ASN352 2.8 80.1 1.0 O A:SER320 3.0 76.4 1.0 O A:HOH708 3.1 80.2 1.0 CB A:SER320 3.6 87.7 1.0 C A:SER320 3.8 85.8 1.0 C A:ALA44 3.8 79.9 1.0 CA A:SER320 3.9 84.9 1.0 CL A:CL605 4.1 80.3 1.0 CA A:VAL45 4.2 80.4 1.0 OG A:SER356 4.2 77.7 1.0 CB A:ASN49 4.2 72.2 1.0 CB A:ASN352 4.3 77.6 1.0 N A:VAL45 4.4 80.0 1.0 CG2 A:VAL45 4.6 80.3 1.0 O A:ASN352 4.7 77.9 1.0 CA A:ASN352 4.7 76.2 1.0 C A:ASN352 4.7 80.1 1.0 CA A:ALA44 4.8 71.7 1.0 CA A:ASN49 4.8 77.1 1.0 N A:ASP46 4.8 86.0 1.0 CB A:ALA44 4.9 78.6 1.0 N A:ASN49 4.9 80.3 1.0 N A:LEU321 5.0 85.5 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of A Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in Tramadol 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 Net-Like Mutations (D121G/S426M/F471L) in Tramadol Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:85.7 occ:1.00 O A:GLY42 2.4 87.3 1.0 O A:HOH701 2.6 75.8 1.0 O A:VAL45 2.6 80.3 1.0 O A:LEU417 2.8 86.1 1.0 OD2 A:ASP420 2.9 82.3 1.0 CB A:ASP420 3.1 75.4 1.0 OG A:SER421 3.3 81.0 1.0 C A:GLY42 3.4 87.8 1.0 CG A:ASP420 3.4 83.3 1.0 C A:LEU417 3.5 79.9 1.0 O A:THR416 3.6 72.8 1.0 N A:SER421 3.7 85.7 1.0 CA A:GLY42 3.7 87.7 1.0 C A:VAL45 3.8 85.7 1.0 CA A:LEU417 3.8 78.3 1.0 CA A:ASP420 3.9 78.3 1.0 N A:ASP420 4.0 88.9 1.0 C A:ASP420 4.2 83.4 1.0 CB A:SER421 4.4 87.3 1.0 N A:GLY418 4.4 81.2 1.0 N A:PHE43 4.6 85.9 1.0 C A:THR416 4.6 76.5 1.0 OD1 A:ASP420 4.6 87.5 1.0 CA A:SER421 4.6 86.7 1.0 CA A:ASP46 4.6 82.4 1.0 N A:ASP46 4.7 86.0 1.0 N A:LEU417 4.7 80.1 1.0 O A:THR268 4.7 77.5 1.0 CA A:VAL45 4.8 80.4 1.0 N A:VAL45 4.8 80.0 1.0 CB A:ASP46 4.8 83.6 1.0 C A:GLY418 4.9 82.0 1.0 CA A:GLY418 4.9 82.8 1.0 N A:LEU419 4.9 79.2 1.0 CD2 A:LEU417 4.9 64.3 1.0 CB A:LEU417 5.0 71.6 1.0 CA A:PHE43 5.0 78.3 1.0

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