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Sodium in PDB 4mme: Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol

Protein crystallography data

The structure of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol, PDB code: 4mme was solved by H.Wang, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.98 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.258, 92.825, 87.530, 90.00, 93.75, 90.00
R / Rfree (%) 20.4 / 23.3

Other elements in 4mme:

The structure of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol (pdb code 4mme). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol, PDB code: 4mme:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4mme

Go back to Sodium Binding Sites List in 4mme
Sodium binding site 1 out of 4 in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:24.5
occ:1.00
O A:ALA351 2.2 22.4 1.0
O A:GLY20 2.2 26.3 1.0
O A:VAL23 2.2 28.3 1.0
OG A:SER355 2.3 23.1 1.0
OG1 A:THR354 2.3 22.8 1.0
N A:SER355 3.1 25.4 1.0
C A:ALA351 3.3 23.1 1.0
C A:VAL23 3.3 29.9 1.0
CB A:SER355 3.3 27.6 1.0
C A:GLY20 3.5 30.2 1.0
CB A:THR354 3.5 24.2 1.0
C A:THR354 3.6 25.7 1.0
CA A:SER355 3.6 24.7 1.0
O A:TYR21 3.7 27.2 1.0
CA A:ALA351 3.9 26.1 1.0
CA A:THR354 3.9 25.1 1.0
CA A:ASP24 4.1 27.9 1.0
N A:ASP24 4.1 26.4 1.0
N A:THR354 4.2 25.5 1.0
O A:THR354 4.3 26.0 1.0
C A:TYR21 4.3 28.2 1.0
CB A:ASP24 4.3 29.8 1.0
CA A:GLY20 4.3 24.9 1.0
CA A:VAL23 4.3 26.4 1.0
O A:PHE350 4.4 23.8 1.0
N A:VAL23 4.4 25.9 1.0
N A:TYR21 4.4 28.1 1.0
N A:GLY352 4.4 21.6 1.0
CA A:TYR21 4.5 24.8 1.0
CG2 A:THR354 4.7 22.9 1.0
CB A:ALA351 4.7 20.1 1.0
CB A:VAL23 4.7 25.7 1.0
O A:GLY352 4.8 23.1 1.0
C A:GLY352 4.8 23.5 1.0
CA A:GLY352 4.8 22.0 1.0
C A:ALA22 5.0 30.7 1.0
N A:ALA351 5.0 23.4 1.0

Sodium binding site 2 out of 4 in 4mme

Go back to Sodium Binding Sites List in 4mme
Sodium binding site 2 out of 4 in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:36.8
occ:1.00
O A:SER254 2.3 29.1 1.0
OD1 A:ASN27 2.4 30.8 1.0
O A:HOH713 2.4 34.1 1.0
O A:ALA22 2.4 30.4 1.0
OD1 A:ASN286 2.5 26.6 1.0
OG A:SER254 2.5 31.6 1.0
C A:SER254 3.1 30.0 1.0
CA A:SER254 3.2 27.6 1.0
CG A:ASN27 3.2 28.6 1.0
ND2 A:ASN27 3.3 32.3 1.0
C A:ALA22 3.4 30.7 1.0
CB A:SER254 3.4 30.1 1.0
CG A:ASN286 3.5 27.9 1.0
OD1 A:ASP24 3.7 36.6 1.0
ND2 A:ASN286 3.7 28.9 1.0
OE1 A:GLU290 3.9 43.0 1.0
N A:VAL23 4.1 25.9 1.0
CA A:VAL23 4.1 26.4 1.0
N A:ASP24 4.3 26.4 1.0
CA A:ALA22 4.3 28.8 1.0
N A:LEU255 4.3 27.8 1.0
CB A:ALA22 4.4 24.0 1.0
N A:SER254 4.6 28.9 1.0
CB A:ASN27 4.6 30.0 1.0
CG A:ASP24 4.7 35.5 1.0
C A:VAL23 4.7 29.9 1.0
N A:ASN27 4.8 30.6 1.0
CB A:ASN286 4.8 29.4 1.0
O A:PHE253 4.9 35.8 1.0
N1 A:29Q603 4.9 40.4 1.0
CD A:GLU290 5.0 40.8 1.0
C2 A:29Q603 5.0 35.8 1.0
CA A:LEU255 5.0 27.9 1.0

Sodium binding site 3 out of 4 in 4mme

Go back to Sodium Binding Sites List in 4mme
Sodium binding site 3 out of 4 in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:26.6
occ:1.00
O B:GLY20 2.1 30.0 1.0
O B:ALA351 2.2 34.0 1.0
O B:VAL23 2.3 33.2 1.0
OG B:SER355 2.4 29.7 1.0
OG1 B:THR354 2.4 29.6 1.0
N B:SER355 3.1 29.4 1.0
C B:ALA351 3.3 33.1 1.0
C B:GLY20 3.3 33.8 1.0
C B:VAL23 3.4 30.8 1.0
CB B:SER355 3.4 34.8 1.0
CB B:THR354 3.5 28.6 1.0
C B:THR354 3.5 31.1 1.0
CA B:SER355 3.6 33.1 1.0
O B:TYR21 3.7 34.9 1.0
CA B:ALA351 3.8 32.2 1.0
CA B:THR354 3.9 33.7 1.0
CA B:ASP24 4.1 33.6 1.0
N B:THR354 4.1 28.9 1.0
CA B:GLY20 4.1 31.9 1.0
C B:TYR21 4.2 37.2 1.0
N B:ASP24 4.2 32.8 1.0
O B:THR354 4.3 30.3 1.0
N B:TYR21 4.3 30.5 1.0
CB B:ASP24 4.3 33.9 1.0
O B:PHE350 4.3 28.2 1.0
CA B:VAL23 4.3 33.6 1.0
N B:VAL23 4.3 33.2 1.0
CA B:TYR21 4.4 32.3 1.0
N B:GLY352 4.4 28.7 1.0
CB B:ALA351 4.7 30.2 1.0
CG2 B:THR354 4.7 30.3 1.0
CB B:VAL23 4.7 31.7 1.0
O B:GLY352 4.8 34.1 1.0
C B:GLY352 4.8 30.1 1.0
CA B:GLY352 4.8 29.6 1.0
C B:ALA22 4.9 31.2 1.0
N B:ALA351 5.0 26.2 1.0
N B:ALA22 5.0 34.0 1.0

Sodium binding site 4 out of 4 in 4mme

Go back to Sodium Binding Sites List in 4mme
Sodium binding site 4 out of 4 in the Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Leubat (DELTA6 Mutant) in Complex with Mazindol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:40.0
occ:1.00
O B:SER254 2.4 34.8 1.0
OD1 B:ASN27 2.4 40.8 1.0
O B:ALA22 2.5 35.9 1.0
O B:HOH768 2.5 38.5 1.0
OD1 B:ASN286 2.5 34.5 1.0
OG B:SER254 2.5 37.0 1.0
C B:SER254 3.1 34.9 1.0
CG B:ASN27 3.2 37.5 1.0
CA B:SER254 3.2 36.6 1.0
ND2 B:ASN27 3.4 35.0 1.0
CB B:SER254 3.4 37.0 1.0
C B:ALA22 3.5 31.2 1.0
CG B:ASN286 3.5 34.5 1.0
OE1 B:GLU290 3.8 47.9 1.0
ND2 B:ASN286 3.8 32.0 1.0
OD1 B:ASP24 3.9 36.3 1.0
CA B:VAL23 4.2 33.6 1.0
N B:VAL23 4.2 33.2 1.0
N B:ASP24 4.3 32.8 1.0
CA B:ALA22 4.3 29.6 1.0
N B:LEU255 4.4 31.0 1.0
CB B:ALA22 4.5 29.3 1.0
C2 B:29Q603 4.5 44.0 1.0
CB B:ASN27 4.6 36.8 1.0
N B:SER254 4.6 36.1 1.0
N B:ASN27 4.7 39.3 1.0
CG B:ASP24 4.7 38.3 1.0
C B:VAL23 4.8 30.8 1.0
O B:PHE253 4.8 35.7 1.0
N1 B:29Q603 4.8 50.2 1.0
CB B:ASN286 4.8 35.5 1.0
CD B:GLU290 4.9 50.3 1.0
CA B:ASN27 4.9 37.5 1.0

Reference:

H.Wang, A.Goehring, K.H.Wang, A.Penmatsa, R.Ressler, E.Gouaux. Structural Basis For Action By Diverse Antidepressants on Biogenic Amine Transporters. Nature V. 503 141 2013.
ISSN: ISSN 0028-0836
PubMed: 24121440
DOI: 10.1038/NATURE12648
Page generated: Mon Oct 7 17:02:19 2024

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