Atomistry » Sodium » PDB 4mfc-4mzx » 4mm5
Atomistry »
  Sodium »
    PDB 4mfc-4mzx »
      4mm5 »

Sodium in PDB 4mm5: Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Sertraline

Protein crystallography data

The structure of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Sertraline, PDB code: 4mm5 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) 31.57 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.076, 87.927, 81.960, 90.00, 95.53, 90.00
R / Rfree (%) 21.3 / 26.4

Other elements in 4mm5:

The structure of Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Sertraline 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 (DELTA13 Mutant) in Complex with Sertraline (pdb code 4mm5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Sertraline, PDB code: 4mm5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4mm5

Go back to Sodium Binding Sites List in 4mm5
Sodium binding site 1 out of 2 in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Sertraline


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 (DELTA13 Mutant) in Complex with Sertraline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:28.8
occ:1.00
O A:GLY20 2.1 31.6 1.0
O A:VAL23 2.1 31.2 1.0
O A:ALA351 2.3 28.7 1.0
OG1 A:THR354 2.3 32.2 1.0
OG A:SER355 2.4 32.7 1.0
C A:ALA351 3.3 30.1 1.0
C A:GLY20 3.3 34.9 1.0
C A:VAL23 3.3 32.5 1.0
CB A:THR354 3.4 27.2 1.0
N A:SER355 3.4 29.9 1.0
CB A:SER355 3.5 26.9 1.0
C A:THR354 3.6 32.2 1.0
CA A:ALA351 3.8 33.0 1.0
CA A:SER355 3.9 27.2 1.0
CA A:THR354 3.9 30.3 1.0
O A:TYR21 3.9 35.4 1.0
O A:THR354 4.1 32.4 1.0
O A:PHE350 4.2 33.1 1.0
N A:THR354 4.2 27.8 1.0
CA A:GLY20 4.2 32.6 1.0
C A:TYR21 4.2 30.6 1.0
N A:ASP24 4.2 33.5 1.0
N A:TYR21 4.3 34.8 1.0
CA A:ASP24 4.3 34.9 1.0
CA A:VAL23 4.3 37.5 1.0
N A:GLY352 4.3 28.8 1.0
CA A:TYR21 4.4 35.9 1.0
N A:VAL23 4.4 37.4 1.0
CB A:VAL23 4.6 34.1 1.0
CB A:ASP24 4.6 37.2 1.0
CG2 A:THR354 4.6 26.8 1.0
CB A:ALA351 4.7 28.3 1.0
CA A:GLY352 4.7 26.0 1.0
O A:HOH701 4.8 32.2 1.0
C A:GLY352 4.8 27.6 1.0
O A:GLY352 4.8 29.6 1.0
N A:ALA351 4.9 31.6 1.0
CG1 A:VAL23 4.9 33.4 1.0
C A:PHE350 5.0 31.7 1.0
N A:ALA22 5.0 32.6 1.0
C A:ALA22 5.0 38.1 1.0

Sodium binding site 2 out of 2 in 4mm5

Go back to Sodium Binding Sites List in 4mm5
Sodium binding site 2 out of 2 in the Crystal Structure of Leubat (DELTA13 Mutant) in Complex with Sertraline


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 (DELTA13 Mutant) in Complex with Sertraline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:44.2
occ:1.00
OD1 A:ASN286 2.4 46.6 1.0
OD1 A:ASN27 2.4 39.2 1.0
O A:SER254 2.4 33.6 1.0
OG A:SER254 2.5 51.0 1.0
O A:ALA22 2.6 37.0 1.0
C A:SER254 3.1 38.0 1.0
CA A:SER254 3.1 40.4 1.0
OD1 A:ASP24 3.2 45.2 1.0
CG A:ASN27 3.2 44.0 1.0
CG A:ASN286 3.3 42.7 1.0
CB A:SER254 3.4 50.6 1.0
ND2 A:ASN286 3.4 44.1 1.0
ND2 A:ASN27 3.4 49.3 1.0
C A:ALA22 3.7 38.1 1.0
N A:LEU255 4.3 42.5 1.0
CG A:ASP24 4.4 41.7 1.0
N11 A:SRE603 4.5 44.1 1.0
N A:SER254 4.5 42.7 1.0
CA A:ALA22 4.5 37.1 1.0
N A:VAL23 4.5 37.4 1.0
CB A:ALA22 4.5 42.1 1.0
CB A:ASN27 4.6 39.7 1.0
CA A:VAL23 4.6 37.5 1.0
N A:ASP24 4.7 33.5 1.0
CB A:ASN286 4.7 43.5 1.0
OG A:SER290 4.7 46.5 1.0
N A:ASN27 4.7 37.6 1.0
O A:PHE253 4.7 47.9 1.0
CA A:ASN27 4.9 41.1 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: Tue Dec 15 06:54:19 2020

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