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Sodium in PDB 4xph: X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE

Protein crystallography data

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE, PDB code: 4xph was solved by A.Penmatsa, K.Wang, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.11 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.968, 144.665, 165.666, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27.7

Other elements in 4xph:

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE (pdb code 4xph). 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 with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE, PDB code: 4xph:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4xph

Go back to Sodium Binding Sites List in 4xph
Sodium binding site 1 out of 3 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE


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 3,4DICHLOROPHENETHYLAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:85.2
occ:1.00
OD1 A:ASN49 2.3 80.8 1.0
OG A:SER320 2.4 80.3 1.0
O A:ALA44 2.4 81.1 1.0
O A:SER320 2.7 91.2 1.0
OD1 A:ASP46 2.9 87.2 1.0
OD1 A:ASN352 2.9 81.1 1.0
CA A:SER320 3.0 87.6 1.0
C A:SER320 3.1 86.0 1.0
CG A:ASN49 3.1 77.3 1.0
CB A:SER320 3.2 84.4 1.0
ND2 A:ASN49 3.4 77.5 1.0
C A:ALA44 3.6 82.2 1.0
CG A:ASN352 3.9 77.4 1.0
ND2 A:ASN352 4.0 77.2 1.0
N A:ASP46 4.0 79.6 1.0
CG A:ASP46 4.1 88.1 1.0
CA A:VAL45 4.2 80.4 1.0
N A:SER320 4.3 88.7 1.0
N A:LEU321 4.4 81.5 1.0
N A:VAL45 4.4 80.2 1.0
CB A:ASN49 4.5 75.5 1.0
N A:42J602 4.5 83.2 1.0
CA A:ALA44 4.6 75.0 1.0
C A:VAL45 4.7 80.3 1.0
N A:ASN49 4.7 85.7 1.0
O A:PHE319 4.7 87.3 1.0
CB A:ASP46 4.8 79.4 1.0
CL A:CL605 4.9 82.6 1.0
CA A:ASN49 4.9 76.3 1.0
C A:42J602 4.9 92.3 1.0
CA A:ASP46 4.9 75.3 1.0
C A:PHE319 5.0 90.0 1.0
OD2 A:ASP46 5.0 99.0 1.0

Sodium binding site 2 out of 3 in 4xph

Go back to Sodium Binding Sites List in 4xph
Sodium binding site 2 out of 3 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE


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 3,4DICHLOROPHENETHYLAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:79.0
occ:1.00
OD1 A:ASP420 2.3 88.8 1.0
O A:GLY42 2.3 84.4 1.0
O A:VAL45 2.3 81.7 1.0
O A:LEU417 2.3 78.2 1.0
OG A:SER421 2.4 75.0 1.0
CG A:ASP420 2.9 84.1 1.0
N A:SER421 3.1 83.3 1.0
CB A:SER421 3.3 75.4 1.0
C A:VAL45 3.4 80.3 1.0
C A:LEU417 3.4 74.7 1.0
OD2 A:ASP420 3.4 82.8 1.0
C A:GLY42 3.5 83.2 1.0
CA A:SER421 3.6 80.8 1.0
CA A:ASP46 3.7 75.3 1.0
C A:ASP420 3.8 81.6 1.0
O A:HOH701 3.8 81.8 1.0
CB A:ASP420 3.8 71.2 1.0
N A:ASP46 4.0 79.6 1.0
O A:PHE43 4.0 80.8 1.0
CA A:LEU417 4.1 71.9 1.0
CB A:ASP46 4.2 79.4 1.0
CA A:ASP420 4.2 74.3 1.0
N A:ASP420 4.3 82.3 1.0
N A:PHE43 4.3 81.0 1.0
CA A:PHE43 4.3 78.0 1.0
C A:PHE43 4.3 81.0 1.0
CA A:GLY42 4.4 82.2 1.0
O A:GLY418 4.4 76.4 1.0
N A:GLY418 4.4 73.9 1.0
O A:THR416 4.5 81.8 1.0
C A:GLY418 4.5 75.5 1.0
CA A:VAL45 4.5 80.4 1.0
N A:VAL45 4.6 80.2 1.0
O A:ASP420 4.7 82.0 1.0
CA A:GLY418 4.7 74.1 1.0
C A:ASP46 5.0 75.2 1.0

Sodium binding site 3 out of 3 in 4xph

Go back to Sodium Binding Sites List in 4xph
Sodium binding site 3 out of 3 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE


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 with Subsiteb Mutations (D121G/S426M) Bound to 3,4DICHLOROPHENETHYLAMINE within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na301

b:81.0
occ:1.00
OG1 L:THR103 2.5 70.1 1.0
NE2 L:GLN6 2.7 72.8 1.0
O L:THR22 3.0 79.7 1.0
CB L:MET21 3.2 71.6 1.0
CB L:GLN6 3.4 74.6 1.0
CB L:THR103 3.5 72.5 1.0
N L:THR22 3.5 79.8 1.0
CG L:MET21 3.5 75.5 1.0
CD L:GLN6 3.7 79.1 1.0
C L:MET21 3.7 79.3 1.0
C L:THR22 3.7 82.5 1.0
CG L:GLN6 3.8 76.8 1.0
O L:SER7 3.8 80.6 1.0
CZ3 L:TRP36 3.9 72.3 1.0
CA L:MET21 4.0 76.3 1.0
SD L:MET21 4.0 75.1 1.0
N L:SER7 4.0 81.0 1.0
CH2 L:TRP36 4.0 70.9 1.0
CA L:GLN6 4.1 72.7 1.0
CA L:THR22 4.2 81.7 1.0
O L:MET21 4.3 79.3 1.0
CG2 L:THR103 4.4 65.3 1.0
C L:GLN6 4.4 71.5 1.0
C L:SER7 4.4 76.0 1.0
N L:THR103 4.6 69.4 1.0
CA L:THR103 4.6 73.5 1.0
N L:CYS23 4.7 77.7 1.0
OE1 L:GLN6 4.8 79.6 1.0
CA L:SER7 4.8 78.3 1.0
O L:TYR87 4.9 73.5 1.0
O L:PRO8 4.9 79.1 1.0

Reference:

K.Wang, A.Penmatsa, E.Gouaux. Structural Basis For Neurotransmitter and Psychostimulant Recognition By the Drosophila Dopamine Transporter Nature 2015.
ISSN: ESSN 1476-4687
Page generated: Tue Dec 15 10:00:29 2020

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