Sodium in PDB 4xp1: X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine, PDB code: 4xp1 was solved by E.Gouaux, A.Penmatsa, K.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.98 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.797, 140.181, 166.195, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.6

The structure of X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine (pdb code 4xp1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine, PDB code: 4xp1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine


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 Bound to Neurotransmitter Dopamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:69.6 occ:1.00 OD1 A:ASN49 2.4 66.9 1.0 O A:ALA44 2.5 62.5 1.0 OG A:SER320 2.5 62.9 1.0 OD1 A:ASN352 2.5 61.7 1.0 O A:SER320 2.6 69.1 1.0 O A:HOH814 2.9 74.8 1.0 CG A:ASN49 3.1 66.2 1.0 ND2 A:ASN49 3.2 66.7 1.0 C A:SER320 3.3 68.6 1.0 CA A:SER320 3.5 72.2 1.0 CG A:ASN352 3.5 67.0 1.0 CB A:SER320 3.5 66.5 1.0 C A:ALA44 3.5 67.9 1.0 ND2 A:ASN352 3.8 72.9 1.0 CA A:VAL45 4.3 66.3 1.0 N A:VAL45 4.3 67.1 1.0 CA A:ALA44 4.4 66.0 1.0 N A:ASP46 4.5 71.6 1.0 N A:LEU321 4.5 67.0 1.0 CB A:ASN49 4.6 62.3 1.0 CB A:ALA44 4.6 62.1 1.0 CB A:ASP46 4.7 71.6 1.0 CB A:ASN352 4.8 67.1 1.0 N A:ASN49 4.9 72.3 1.0 N A:SER320 4.9 75.2 1.0 C A:VAL45 4.9 69.0 1.0 O A:HOH812 4.9 68.8 1.0 CL A:CL703 5.0 72.0 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine


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 Bound to Neurotransmitter Dopamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:69.6 occ:1.00 O A:LEU417 2.3 70.9 1.0 O A:GLY42 2.3 69.0 1.0 O A:VAL45 2.5 67.0 1.0 OG A:SER421 2.8 72.9 1.0 OD2 A:ASP420 3.0 66.1 1.0 N A:SER421 3.1 66.0 1.0 CB A:ASP420 3.2 69.8 1.0 C A:LEU417 3.5 68.1 1.0 C A:GLY42 3.5 69.8 1.0 CG A:ASP420 3.6 68.7 1.0 CB A:SER421 3.6 63.7 1.0 C A:VAL45 3.6 69.0 1.0 O A:HOH803 3.7 62.0 1.0 C A:ASP420 3.7 68.8 1.0 CA A:SER421 3.8 60.0 1.0 CA A:ASP420 3.8 66.6 1.0 N A:ASP420 3.9 68.1 1.0 O A:PHE43 3.9 67.2 1.0 CA A:ASP46 4.2 64.8 1.0 C A:PHE43 4.3 65.4 1.0 N A:ASP46 4.4 71.6 1.0 CA A:PHE43 4.4 64.4 1.0 N A:PHE43 4.4 71.8 1.0 N A:GLY418 4.4 65.9 1.0 C A:GLY418 4.4 65.3 1.0 CA A:LEU417 4.4 64.5 1.0 CA A:GLY418 4.4 64.8 1.0 OD1 A:ASP46 4.5 80.5 1.0 CA A:GLY42 4.5 66.1 1.0 O A:GLY418 4.5 65.4 1.0 CB A:ASP46 4.6 71.6 1.0 N A:VAL45 4.7 67.1 1.0 CA A:VAL45 4.7 66.3 1.0 O A:ASP420 4.7 72.1 1.0 O A:THR416 4.7 67.9 1.0 OD1 A:ASP420 4.8 72.6 1.0 N A:LEU419 4.8 63.8 1.0 C A:LEU419 4.8 66.2 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure of Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine


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 Drosophila Dopamine Transporter Bound to Neurotransmitter Dopamine within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:95.6 occ:1.00 OG1 L:THR194 2.4 91.0 1.0 O L:ASP152 2.4 0.8 1.0 CB L:THR194 3.2 87.2 1.0 O L:LYS150 3.3 89.9 1.0 C L:ASP152 3.5 0.1 1.0 OG L:SER192 3.6 98.0 1.0 N L:THR194 3.8 86.2 1.0 O L:SER192 3.8 95.2 1.0 N L:ASP152 3.9 0.3 1.0 C L:LYS150 4.0 86.9 1.0 CA L:ASP152 4.1 0.2 1.0 CA L:THR194 4.1 86.7 1.0 C L:TYR193 4.1 87.6 1.0 C L:SER192 4.2 0.1 1.0 CB L:LYS150 4.2 85.8 1.0 C L:ILE151 4.3 99.6 1.0 CG2 L:THR194 4.3 85.7 1.0 CA L:TYR193 4.4 84.5 1.0 N L:TYR193 4.4 94.5 1.0 CA L:ILE151 4.6 96.9 1.0 N L:ILE151 4.6 91.6 1.0 OG L:SER209 4.7 94.9 1.0 N L:GLY153 4.7 0.3 1.0 O L:TYR193 4.7 86.5 1.0 CB L:SER192 4.7 0.6 1.0 CA L:LYS150 4.7 86.6 1.0

K.H.Wang, A.Penmatsa, E.Gouaux. Neurotransmitter and Psychostimulant Recognition By the Dopamine Transporter. Nature 2015.
ISSN: ESSN 1476-4687
PubMed: 25970245
DOI: 10.1038/NATURE14431