Sodium in PDB 6m3z: X-Ray Structure of A Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in Milnacipran Bound Form

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in Milnacipran Bound Form, PDB code: 6m3z 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)	48.55 / 3.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.997, 141.599, 168.249, 90, 90, 90
R / Rfree (%)	22.2 / 26.4

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in Milnacipran 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 Milnacipran Bound Form (pdb code 6m3z). 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 Milnacipran Bound Form, PDB code: 6m3z:
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 Milnacipran 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 Milnacipran Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:83.4 occ:1.00 O A:ALA44 2.5 83.4 1.0 O A:SER320 2.6 89.0 1.0 OD1 A:ASN49 2.7 74.9 1.0 OG A:SER320 3.0 75.5 1.0 OD1 A:ASP46 3.0 80.8 1.0 CA A:SER320 3.3 78.9 1.0 C A:SER320 3.3 85.4 1.0 N12 A:F0F701 3.6 78.3 1.0 CB A:SER320 3.6 73.9 1.0 C A:ALA44 3.7 81.9 1.0 CG A:ASN49 3.8 74.4 1.0 O A:HOH805 3.8 75.3 1.0 CG A:ASP46 4.0 80.6 1.0 ND2 A:ASN49 4.2 74.9 1.0 OD1 A:ASN352 4.2 87.8 1.0 N A:ASP46 4.3 74.8 1.0 ND2 A:ASN352 4.4 81.0 1.0 O A:PHE319 4.5 86.2 1.0 OD2 A:ASP46 4.5 80.7 1.0 N A:VAL45 4.5 81.0 1.0 CA A:VAL45 4.5 81.3 1.0 CB A:ALA48 4.6 72.4 1.0 N A:SER320 4.6 78.6 1.0 CA A:ALA44 4.6 79.7 1.0 N A:LEU321 4.6 84.4 1.0 CG A:ASN352 4.7 81.1 1.0 N A:ASN49 4.8 82.6 1.0 C A:VAL45 4.9 79.1 1.0 C11 A:F0F701 4.9 80.2 1.0 C A:PHE319 5.0 81.3 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 Milnacipran 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 Milnacipran Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:73.0 occ:1.00 O A:LEU417 2.4 78.1 1.0 O A:GLY42 2.4 92.4 1.0 O A:VAL45 2.4 75.4 1.0 OG A:SER421 2.6 78.4 1.0 CB A:ASP420 2.7 76.3 1.0 OD2 A:ASP420 3.2 75.7 1.0 N A:SER421 3.3 78.6 1.0 CG A:ASP420 3.5 80.8 1.0 C A:VAL45 3.5 79.1 1.0 C A:LEU417 3.5 73.3 1.0 C A:GLY42 3.5 83.7 1.0 CA A:ASP420 3.7 77.4 1.0 CB A:SER421 3.8 77.7 1.0 C A:ASP420 3.8 79.8 1.0 N A:ASP420 4.0 86.0 1.0 CA A:SER421 4.1 75.4 1.0 CB A:ASP46 4.1 77.8 1.0 CA A:ASP46 4.2 79.2 1.0 N A:ASP46 4.2 74.8 1.0 CA A:LEU417 4.2 77.1 1.0 CA A:GLY42 4.3 77.4 1.0 N A:VAL45 4.4 81.0 1.0 N A:GLY418 4.4 75.3 1.0 N A:PHE43 4.5 83.3 1.0 CA A:VAL45 4.5 81.3 1.0 CA A:GLY418 4.5 74.6 1.0 O A:THR416 4.5 80.0 1.0 O A:PHE43 4.5 87.8 1.0 C A:GLY418 4.5 79.8 1.0 CA A:PHE43 4.6 77.9 1.0 C A:PHE43 4.6 84.7 1.0 OD1 A:ASP420 4.7 84.1 1.0 O A:GLY418 4.7 76.4 1.0 O A:ASP420 4.8 83.5 1.0 N A:LEU419 4.9 78.8 1.0

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