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Sodium in PDB 6m0z: X-Ray Structure of Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in L-Norepinephrine Bound Form

Protein crystallography data

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in L-Norepinephrine Bound Form, PDB code: 6m0z 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) 48.61 / 2.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.292, 142.801, 168.35, 90, 90, 90
R / Rfree (%) 21.3 / 24.3

Other elements in 6m0z:

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in L-Norepinephrine Bound Form also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in L-Norepinephrine Bound Form (pdb code 6m0z). 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 Net-Like Mutations (D121G/S426M/F471L) in L-Norepinephrine Bound Form, PDB code: 6m0z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6m0z

Go back to Sodium Binding Sites List in 6m0z
Sodium binding site 1 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) 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 Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in L-Norepinephrine Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:88.2
occ:1.00
OG A:SER320 2.3 73.7 1.0
OD1 A:ASN49 2.4 85.6 1.0
O A:ALA44 2.5 88.7 1.0
O A:HOH802 2.7 92.6 1.0
O A:SER320 2.8 80.0 1.0
OD1 A:ASN352 3.3 79.1 1.0
CB A:SER320 3.3 72.3 1.0
CA A:SER320 3.3 77.1 1.0
CG A:ASN49 3.4 81.5 1.0
C A:SER320 3.5 78.2 1.0
OD1 A:ASP46 3.5 91.8 1.0
C A:ALA44 3.7 85.7 1.0
ND2 A:ASN49 3.7 86.2 1.0
HNAA A:LNR707 4.2 114.4 1.0
CG A:ASN352 4.2 83.8 1.0
N A:ASP46 4.3 85.1 1.0
ND2 A:ASN352 4.3 83.0 1.0
CA A:VAL45 4.4 79.6 1.0
N A:VAL45 4.5 79.0 1.0
N A:ASN49 4.6 82.9 1.0
CG A:ASP46 4.6 95.1 1.0
CA A:ALA44 4.7 83.1 1.0
CB A:ASN49 4.7 79.3 1.0
N A:SER320 4.7 78.3 1.0
CB A:ALA48 4.7 82.6 1.0
CL A:CL706 4.7 83.7 1.0
N A:LEU321 4.8 77.8 1.0
HNAB A:LNR707 4.8 114.4 1.0
NAA A:LNR707 4.8 95.3 1.0
C A:VAL45 4.8 82.3 1.0
CA A:ASN49 4.9 78.5 1.0

Sodium binding site 2 out of 2 in 6m0z

Go back to Sodium Binding Sites List in 6m0z
Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) 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 Drosophila Dopamine Transporter with Net-Like Mutations (D121G/S426M/F471L) in L-Norepinephrine Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:80.9
occ:1.00
O A:GLY42 2.2 85.9 1.0
O A:LEU417 2.3 88.9 1.0
O A:VAL45 2.4 83.0 1.0
OG A:SER421 2.9 80.3 1.0
CB A:ASP420 2.9 77.7 1.0
O A:HOH801 3.2 83.0 1.0
N A:SER421 3.2 79.5 1.0
C A:GLY42 3.3 86.4 1.0
C A:LEU417 3.5 83.0 1.0
C A:VAL45 3.5 82.3 1.0
OD2 A:ASP420 3.7 87.7 1.0
CA A:ASP420 3.8 77.1 1.0
CG A:ASP420 3.8 87.2 1.0
CB A:SER421 3.8 84.8 1.0
C A:ASP420 3.9 81.5 1.0
CB A:ASP46 4.0 90.1 1.0
CA A:SER421 4.0 80.1 1.0
CA A:ASP46 4.0 83.1 1.0
N A:ASP420 4.1 90.1 1.0
CA A:GLY42 4.1 85.3 1.0
N A:ASP46 4.2 85.1 1.0
CA A:LEU417 4.2 79.7 1.0
N A:PHE43 4.3 85.9 1.0
O A:PHE43 4.4 85.0 1.0
N A:GLY418 4.4 80.4 1.0
CA A:PHE43 4.4 81.5 1.0
C A:PHE43 4.4 83.4 1.0
O A:THR416 4.5 82.4 1.0
N A:VAL45 4.5 79.0 1.0
O A:GLY418 4.6 79.5 1.0
CA A:VAL45 4.6 79.6 1.0
C A:GLY418 4.6 78.9 1.0
CA A:GLY418 4.6 76.6 1.0
O A:ASP420 4.9 81.9 1.0

Reference:

P.Shabareesh, A.K.Mallela, D.Joseph. Structural Basis of Norepinephrine Recognition and Transport Inhibition in Neurotransmitter Transporters To Be Published.
Page generated: Wed Mar 3 15:25:42 2021

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