Sodium in PDB 4xpf: X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55, PDB code: 4xpf was solved by A.Penmatsa, K.H.Wang, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.32 / 3.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.415, 140.312, 166.962, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 29.6

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55 also contains other interesting chemical elements:

Iodine	(I)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55 (pdb code 4xpf). 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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55, PDB code: 4xpf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55


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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:0.4 occ:1.00 OG A:SER320 2.5 0.9 1.0 ND2 A:ASN49 2.7 0.0 1.0 O A:ALA44 2.8 92.2 1.0 O A:SER320 3.0 97.1 1.0 OD1 A:ASN49 3.1 0.0 1.0 CG A:ASN49 3.2 0.7 1.0 OD1 A:ASN352 3.3 0.2 1.0 OD1 A:ASP46 3.5 0.8 1.0 CB A:SER320 3.5 95.5 1.0 CA A:SER320 3.7 99.4 1.0 C A:SER320 3.7 0.2 1.0 C A:ALA44 3.9 95.1 1.0 C A:42F603 4.2 0.7 1.0 CG A:ASN352 4.3 0.4 1.0 CB A:ALA48 4.4 0.3 1.0 CA A:VAL45 4.5 90.0 1.0 ND2 A:ASN352 4.5 0.8 1.0 N A:ASN49 4.5 0.1 1.0 N A:ASP46 4.5 97.6 1.0 CB A:ASN49 4.6 0.6 1.0 CG A:ASP46 4.6 1.0 1.0 N A:VAL45 4.7 96.8 1.0 CA A:ASN49 4.9 0.3 1.0 C A:ALA48 4.9 0.9 1.0 N A:LEU321 4.9 0.0 1.0 C A:VAL45 5.0 97.0 1.0 CA A:ALA44 5.0 93.1 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55


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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to Rti-55 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:0.4 occ:1.00 O A:VAL45 2.0 0.8 1.0 OG A:SER421 2.1 96.8 1.0 O A:GLY42 2.3 88.8 1.0 OD1 A:ASP420 2.3 99.3 1.0 O A:LEU417 2.3 0.1 1.0 N A:SER421 2.9 0.5 1.0 CG A:ASP420 3.0 99.5 1.0 CB A:SER421 3.0 99.1 1.0 C A:VAL45 3.3 97.0 1.0 C A:GLY42 3.4 91.4 1.0 CA A:SER421 3.4 97.1 1.0 C A:LEU417 3.4 97.2 1.0 OD2 A:ASP420 3.7 98.5 1.0 C A:ASP420 3.7 97.7 1.0 CB A:ASP420 3.7 95.8 1.0 CA A:ASP420 4.1 97.5 1.0 O A:GLY418 4.1 97.1 1.0 O A:PHE43 4.1 95.5 1.0 N A:ASP420 4.2 98.1 1.0 CA A:LEU417 4.2 90.1 1.0 CA A:VAL45 4.2 90.0 1.0 N A:ASP46 4.2 97.6 1.0 N A:VAL45 4.2 96.8 1.0 CA A:GLY42 4.3 95.4 1.0 N A:PHE43 4.3 88.3 1.0 CA A:ASP46 4.3 98.4 1.0 C A:PHE43 4.4 93.4 1.0 C A:GLY418 4.4 0.3 1.0 CA A:PHE43 4.4 92.8 1.0 CB A:ASP46 4.4 0.1 1.0 N A:GLY418 4.4 0.2 1.0 O A:THR416 4.5 89.9 1.0 CB A:VAL45 4.5 91.6 1.0 CA A:GLY418 4.6 0.0 1.0 O A:ASP420 4.6 93.4 1.0 C A:SER421 4.8 98.2 1.0 CG1 A:VAL45 4.9 96.7 1.0 C A:LEU419 5.0 97.9 1.0

A.Penmatsa, K.H.Wang, E.Gouaux. Structural Basis For Neurotransmitter and Psycho Stimulant Recognition By the Drosophila Dopamine Transporter Nature 2015.
ISSN: ESSN 1476-4687