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Sodium in PDB 6m0f: X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in Substrate-Free Form

Protein crystallography data

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in Substrate-Free Form, PDB code: 6m0f 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) 48.99 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.978, 133.472, 162.088, 90, 90, 90
R / Rfree (%) 24.1 / 27.7

Other elements in 6m0f:

The structure of X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in Substrate-Free 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 Subsiteb Mutations (D121G/S426M) in Substrate-Free Form (pdb code 6m0f). 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) in Substrate-Free Form, PDB code: 6m0f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6m0f

Go back to Sodium Binding Sites List in 6m0f
Sodium binding site 1 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in Substrate-Free 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 Subsiteb Mutations (D121G/S426M) in Substrate-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:99.3
occ:1.00
OD1 A:ASP46 2.4 104.6 1.0
O A:ALA44 2.5 96.6 1.0
CA A:SER320 2.8 99.3 1.0
O A:SER320 2.8 103.5 1.0
OD1 A:ASN49 2.8 97.0 1.0
OG A:SER320 2.8 94.5 1.0
C A:SER320 3.1 99.7 1.0
CB A:SER320 3.3 96.0 1.0
CG A:ASP46 3.5 100.6 1.0
C A:ALA44 3.7 100.4 1.0
CG A:ASN49 3.7 97.4 1.0
O A:PHE319 3.8 118.2 1.0
O A:HOH702 3.9 84.2 1.0
OD1 A:ASN352 3.9 95.5 1.0
N A:SER320 4.0 105.1 1.0
N A:ASP46 4.0 97.8 1.0
OD2 A:ASP46 4.0 100.8 1.0
ND2 A:ASN49 4.1 99.3 1.0
CB A:ALA48 4.2 97.5 1.0
N A:LEU321 4.3 99.5 1.0
C A:PHE319 4.3 111.2 1.0
N A:ASN49 4.5 94.7 1.0
N A:VAL45 4.5 93.7 1.0
CA A:VAL45 4.5 91.7 1.0
CA A:ALA44 4.5 93.0 1.0
CB A:ASP46 4.6 92.3 1.0
C A:VAL45 4.8 98.3 1.0
CG A:ASN352 4.8 97.7 1.0
CA A:ASP46 4.8 93.5 1.0
CB A:ASN49 4.9 86.1 1.0
ND2 A:ASN352 5.0 97.0 1.0

Sodium binding site 2 out of 2 in 6m0f

Go back to Sodium Binding Sites List in 6m0f
Sodium binding site 2 out of 2 in the X-Ray Structure of Drosophila Dopamine Transporter with Subsiteb Mutations (D121G/S426M) in Substrate-Free 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 Subsiteb Mutations (D121G/S426M) in Substrate-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:107.9
occ:1.00
OD2 A:ASP420 2.6 99.2 1.0
OD1 A:ASP420 2.6 101.1 1.0
O A:VAL45 2.7 99.6 1.0
CG A:ASP420 3.0 100.2 1.0
O A:GLY42 3.1 87.8 1.0
CD2 A:LEU417 3.3 88.5 1.0
O A:LEU417 3.4 102.0 1.0
O A:THR416 3.4 96.1 1.0
CA A:LEU417 3.4 101.5 1.0
C A:LEU417 3.8 104.8 1.0
CA A:GLY42 3.8 95.3 1.0
C A:VAL45 3.8 98.3 1.0
C A:GLY42 3.9 93.5 1.0
O A:THR268 4.0 104.6 1.0
CB A:VAL45 4.1 96.8 1.0
OG A:SER421 4.2 104.7 1.0
C A:THR416 4.2 99.0 1.0
N A:LEU417 4.2 97.8 1.0
CB A:LEU417 4.3 95.9 1.0
CG A:LEU417 4.3 93.1 1.0
CG1 A:VAL45 4.4 93.4 1.0
CB A:ASP420 4.5 97.1 1.0
CA A:VAL45 4.5 91.7 1.0
CG A:PRO272 4.5 96.6 1.0
CA A:ALA269 4.8 102.6 1.0
N A:VAL45 4.9 93.7 1.0
N A:ASP46 4.9 97.8 1.0
O A:ILE41 4.9 92.4 1.0
C A:THR268 4.9 105.3 1.0
N A:SER421 4.9 100.5 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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