Atomistry » Sodium » PDB 6lfw-6mc0 » 6m38
Atomistry »
  Sodium »
    PDB 6lfw-6mc0 »
      6m38 »

Sodium in PDB 6m38: X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form

Protein crystallography data

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form, PDB code: 6m38 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) 48.64 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.288, 140.641, 167.818, 90, 90, 90
R / Rfree (%) 21.5 / 24.4

Other elements in 6m38:

The structure of X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine 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 A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form (pdb code 6m38). 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 A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form, PDB code: 6m38:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6m38

Go back to Sodium Binding Sites List in 6m38
Sodium binding site 1 out of 2 in the X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine 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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:69.7
occ:1.00
OD1 A:ASN49 2.4 68.5 1.0
O A:ALA44 2.4 62.8 1.0
O A:SER320 2.5 72.5 1.0
OG A:SER320 2.5 72.4 1.0
C A:29E601 2.9 79.2 1.0
CA A:SER320 2.9 74.6 1.0
C A:SER320 3.0 70.8 1.0
OD1 A:ASN352 3.2 67.0 1.0
CB A:SER320 3.2 69.4 1.0
CG A:ASN49 3.4 63.8 1.0
OD1 A:ASP46 3.5 71.9 1.0
C A:ALA44 3.6 64.3 1.0
ND2 A:ASN49 3.7 61.8 1.0
N A:29E601 3.8 73.5 1.0
CG A:ASN352 4.1 68.8 1.0
O A:HOH706 4.2 76.7 1.0
N A:SER320 4.3 73.8 1.0
N A:LEU321 4.3 69.7 1.0
N A:ASP46 4.3 66.5 1.0
ND2 A:ASN352 4.3 68.8 1.0
O A:PHE319 4.4 69.1 1.0
CA A:VAL45 4.5 62.2 1.0
N A:VAL45 4.5 64.9 1.0
CG A:ASP46 4.6 73.9 1.0
CA A:ALA44 4.6 63.8 1.0
N A:ASN49 4.6 69.5 1.0
CB A:ALA48 4.7 70.2 1.0
CB A:ASN49 4.7 67.1 1.0
C A:PHE319 4.8 71.4 1.0
C A:VAL45 4.9 66.6 1.0

Sodium binding site 2 out of 2 in 6m38

Go back to Sodium Binding Sites List in 6m38
Sodium binding site 2 out of 2 in the X-Ray Structure of A Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine 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 Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in S-Duloxetine Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:66.5
occ:1.00
O A:GLY42 2.2 63.5 1.0
O A:LEU417 2.3 74.9 1.0
OG A:SER421 2.3 68.7 1.0
OD1 A:ASP420 2.3 71.5 1.0
O A:VAL45 2.5 68.7 1.0
N A:SER421 3.2 64.0 1.0
CB A:SER421 3.3 63.6 1.0
C A:VAL45 3.3 66.6 1.0
C A:LEU417 3.4 70.0 1.0
CG A:ASP420 3.4 70.8 1.0
C A:GLY42 3.5 66.1 1.0
CB A:ASP46 3.5 66.0 1.0
CA A:ASP46 3.7 66.6 1.0
CA A:SER421 3.7 62.1 1.0
N A:ASP46 3.9 66.5 1.0
O A:PHE43 4.0 67.7 1.0
C A:ASP420 4.0 63.1 1.0
OD2 A:ASP420 4.2 67.7 1.0
CA A:LEU417 4.2 67.4 1.0
N A:GLY418 4.3 68.1 1.0
CA A:GLY42 4.3 66.2 1.0
CA A:GLY418 4.3 66.7 1.0
C A:PHE43 4.3 64.2 1.0
CB A:ASP420 4.4 61.2 1.0
N A:VAL45 4.4 64.9 1.0
N A:PHE43 4.4 67.7 1.0
C A:GLY418 4.4 64.4 1.0
O A:GLY418 4.4 63.0 1.0
CA A:PHE43 4.5 61.4 1.0
CA A:VAL45 4.5 62.2 1.0
CA A:ASP420 4.5 64.7 1.0
N A:ASP420 4.5 68.7 1.0
O A:THR416 4.6 68.8 1.0
O A:ASP420 4.8 65.9 1.0
CG A:ASP46 4.9 73.9 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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy