Sodium in PDB 6m2r: X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form

The structure of X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form, PDB code: 6m2r 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)	48.40 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.8, 141.27, 167.711, 90, 90, 90
R / Rfree (%)	21.1 / 24.7

The structure of X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine 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 Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form (pdb code 6m2r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form, PDB code: 6m2r:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine 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 Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:65.7 occ:1.00 OG A:SER320 2.3 56.2 1.0 O A:HOH808 2.5 62.4 1.0 O A:SER320 2.5 58.0 1.0 O A:ALA44 2.5 58.6 1.0 OD1 A:ASN49 2.8 63.0 1.0 OD1 A:ASN352 3.0 56.6 1.0 CA A:SER320 3.1 59.1 1.0 CB A:SER320 3.2 55.4 1.0 C A:SER320 3.2 60.3 1.0 ND2 A:ASN49 3.3 55.1 1.0 CG A:ASN49 3.3 61.3 1.0 C A:ALA44 3.7 58.5 1.0 CG A:ASN352 3.8 58.1 1.0 ND2 A:ASN352 3.8 52.3 1.0 OD1 A:ASP46 4.3 63.8 1.0 HNAB A:LNR704 4.4 98.1 1.0 N A:LEU321 4.5 58.2 1.0 CA A:VAL45 4.5 61.0 1.0 N A:SER320 4.5 63.8 1.0 N A:VAL45 4.6 56.5 1.0 N A:ASP46 4.6 56.3 1.0 CA A:ALA44 4.6 58.5 1.0 CB A:ASN49 4.7 59.6 1.0 N A:ASN49 4.7 60.4 1.0 CL A:CL705 4.8 55.6 1.0 O A:PHE319 4.8 67.2 1.0 CA A:ASN49 4.9 56.5 1.0 CB A:ALA44 5.0 50.7 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine 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 Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:56.8 occ:1.00 O A:LEU417 2.2 64.6 1.0 O A:GLY42 2.3 59.4 1.0 O A:VAL45 2.4 58.4 1.0 OG A:SER421 2.6 58.3 1.0 CB A:ASP420 2.9 56.5 1.0 N A:SER421 3.2 56.4 1.0 O A:HOH801 3.3 58.0 1.0 C A:LEU417 3.3 59.0 1.0 C A:VAL45 3.4 59.3 1.0 C A:GLY42 3.5 58.9 1.0 CB A:SER421 3.5 59.2 1.0 CB A:ASP46 3.6 63.4 1.0 CA A:ASP46 3.8 59.7 1.0 CA A:ASP420 3.8 57.5 1.0 C A:ASP420 3.8 57.4 1.0 OD2 A:ASP420 3.8 59.7 1.0 CG A:ASP420 3.9 63.8 1.0 CA A:SER421 3.9 56.1 1.0 N A:ASP46 4.0 56.3 1.0 N A:ASP420 4.1 63.8 1.0 CA A:LEU417 4.1 53.6 1.0 N A:GLY418 4.2 57.6 1.0 O A:PHE43 4.3 56.9 1.0 O A:GLY418 4.3 57.2 1.0 CA A:GLY42 4.3 56.0 1.0 CA A:GLY418 4.4 53.0 1.0 C A:GLY418 4.4 59.1 1.0 O A:THR416 4.4 58.8 1.0 N A:PHE43 4.5 58.8 1.0 C A:PHE43 4.5 55.8 1.0 CA A:PHE43 4.5 59.9 1.0 N A:VAL45 4.5 56.5 1.0 CA A:VAL45 4.5 61.0 1.0 O A:ASP420 4.8 59.1 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:60.3 occ:1.00 OG L:SER101 2.6 53.8 1.0 O L:GLY102 3.0 47.5 1.0 O L:GLN6 3.3 54.8 1.0 CB L:SER101 3.4 52.0 1.0 CB L:ALA9 3.8 43.6 1.0 O L:SER101 3.8 48.8 1.0 CA L:ALA9 3.9 47.7 1.0 C L:SER101 3.9 45.2 1.0 C L:GLY102 4.2 48.8 1.0 C L:GLN6 4.2 53.3 1.0 CA L:SER101 4.3 44.8 1.0 N L:GLY102 4.3 46.0 1.0 CB L:GLN6 4.4 49.4 1.0 N L:GLN6 4.5 51.1 1.0 N L:ALA9 4.6 56.1 1.0 CA L:GLN6 4.6 50.1 1.0 CA L:GLY102 4.8 50.4 1.0 O L:PRO8 4.9 46.9 1.0 C L:PRO8 5.0 48.9 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of A Functional Drosophila Dopamine Transporter in L- Norepinephrine Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ L:Na302 b:56.9 occ:1.00 NE2 L:GLN6 2.6 52.4 1.0 OG1 L:THR103 2.6 48.2 1.0 O L:THR22 2.9 51.4 1.0 CE L:MET21 3.3 61.4 1.0 CB L:GLN6 3.3 49.4 1.0 CB L:MET21 3.4 56.4 1.0 CD L:GLN6 3.5 49.4 1.0 N L:THR22 3.5 58.5 1.0 CG L:MET21 3.5 56.0 1.0 CG L:GLN6 3.6 47.2 1.0 CB L:THR103 3.6 47.9 1.0 C L:THR22 3.8 57.1 1.0 O L:SER7 3.8 51.2 1.0 C L:MET21 3.9 54.4 1.0 N L:SER7 4.0 54.7 1.0 CZ3 L:TRP36 4.1 47.9 1.0 CA L:GLN6 4.1 50.1 1.0 CA L:MET21 4.2 55.0 1.0 CA L:THR22 4.2 57.3 1.0 CH2 L:TRP36 4.2 46.6 1.0 SD L:MET21 4.3 51.7 1.0 C L:GLN6 4.4 53.3 1.0 C L:SER7 4.4 54.7 1.0 O L:MET21 4.5 53.0 1.0 N L:THR103 4.5 44.2 1.0 CG2 L:THR103 4.6 48.1 1.0 OE1 L:GLN6 4.7 49.2 1.0 CA L:THR103 4.7 45.7 1.0 O L:PRO8 4.8 46.9 1.0 N L:CYS23 4.8 58.3 1.0 CA L:SER7 4.8 55.1 1.0 O L:TYR87 4.9 48.6 1.0 C L:GLY102 4.9 48.8 1.0

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