Sodium in PDB 6xwm: Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation

The structure of Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation, PDB code: 6xwm was solved by T.Boesen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.05 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	77.848, 83.985, 86.939, 65.38, 89.77, 64.56
R / Rfree (%)	21.1 / 23.3

The binding sites of Sodium atom in the Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation (pdb code 6xwm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation, PDB code: 6xwm:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:74.0 occ:1.00 O A:GLY20 2.3 0.1 1.0 O A:ALA351 2.3 62.5 1.0 O A:VAL23 2.4 70.2 1.0 OG A:SER355 2.4 63.1 1.0 OG1 A:THR354 2.4 71.9 1.0 N A:SER355 3.3 63.0 1.0 C A:VAL23 3.4 70.1 1.0 C A:ALA351 3.4 62.4 1.0 C A:GLY20 3.4 0.9 1.0 CB A:SER355 3.5 62.2 1.0 CA A:ASN21 3.7 0.3 1.0 CB A:THR354 3.7 65.2 1.0 C A:THR354 3.8 64.8 1.0 CA A:SER355 3.8 63.5 1.0 C A:ASN21 3.9 0.5 1.0 O A:ASN21 3.9 0.4 1.0 CA A:ALA351 3.9 63.7 1.0 CA A:GLY24 4.0 61.8 1.0 N A:ASN21 4.0 0.8 1.0 N A:GLY24 4.1 67.6 1.0 CA A:THR354 4.2 65.9 1.0 N A:VAL23 4.4 63.8 1.0 O A:THR354 4.4 70.1 1.0 CA A:VAL23 4.5 65.4 1.0 N A:THR354 4.5 65.5 1.0 CB A:ALA351 4.5 62.2 1.0 N A:GLY352 4.6 52.4 1.0 CA A:GLY20 4.6 0.4 1.0 N A:ALA22 4.7 78.7 1.0 O A:PHE350 4.8 69.7 1.0 CG2 A:THR354 4.8 64.0 1.0 CA A:GLY352 4.9 53.2 1.0 C A:ALA22 4.9 70.3 1.0

Sodium binding site 2 out of 4 in the Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:71.7 occ:1.00 OG1 A:THR254 2.4 58.7 1.0 OD1 A:ASN27 2.4 77.1 1.0 O A:ALA22 2.4 72.6 1.0 O A:THR254 2.4 58.4 1.0 O A:PHE601 2.5 60.4 1.0 CG A:ASN27 2.9 78.4 1.0 CA A:THR254 3.0 58.0 1.0 ND2 A:ASN27 3.1 82.8 1.0 OD1 A:ASN286 3.1 83.3 1.0 C A:THR254 3.1 55.1 1.0 CB A:THR254 3.2 55.2 1.0 ND2 A:ASN286 3.3 80.5 1.0 C A:PHE601 3.4 60.1 1.0 C A:ALA22 3.5 70.3 1.0 CG A:ASN286 3.6 75.8 1.0 N A:PHE601 3.8 58.7 1.0 CA A:PHE601 4.1 58.0 1.0 N A:ASN27 4.1 66.4 1.0 OXT A:PHE601 4.2 59.9 1.0 N A:GLY24 4.2 67.6 1.0 CA A:VAL23 4.2 65.4 1.0 CB A:ASN27 4.3 73.7 1.0 N A:VAL23 4.3 63.8 1.0 N A:THR254 4.4 55.5 1.0 N A:LEU255 4.4 64.3 1.0 CG2 A:THR254 4.4 53.0 1.0 C A:GLY26 4.4 57.8 1.0 CA A:ALA22 4.5 69.2 1.0 CA A:ASN27 4.5 71.7 1.0 O A:PHE253 4.6 57.7 1.0 CA A:GLY26 4.6 57.9 1.0 C A:VAL23 4.7 70.1 1.0 OE1 A:GLU290 4.8 80.2 1.0 CB A:ALA22 4.9 65.1 1.0 N A:GLY26 4.9 53.2 1.0 C A:PHE253 5.0 61.1 1.0

Sodium binding site 3 out of 4 in the Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:65.8 occ:1.00 O B:VAL23 2.4 70.0 1.0 OG1 B:THR354 2.4 63.5 1.0 OG B:SER355 2.4 65.6 1.0 O B:ALA351 2.4 61.7 1.0 O B:GLY20 2.5 99.2 1.0 N B:SER355 3.3 56.0 1.0 CB B:SER355 3.4 57.3 1.0 C B:ALA351 3.5 61.8 1.0 C B:VAL23 3.5 71.0 1.0 C B:GLY20 3.5 98.5 1.0 CB B:THR354 3.7 61.1 1.0 CA B:SER355 3.7 60.7 1.0 C B:THR354 3.7 60.6 1.0 CA B:ALA351 4.0 56.6 1.0 CA B:GLY24 4.1 52.5 1.0 CA B:THR354 4.2 64.7 1.0 CA B:GLY20 4.2 93.3 1.0 O B:ASN21 4.2 0.4 1.0 N B:GLY24 4.2 60.2 1.0 O B:THR354 4.4 62.6 1.0 N B:THR354 4.5 63.4 1.0 C B:ASN21 4.5 0.4 1.0 N B:ASN21 4.6 0.8 1.0 CB B:ALA351 4.6 51.3 1.0 CA B:VAL23 4.6 67.5 1.0 N B:GLY352 4.6 59.1 1.0 N B:VAL23 4.7 70.2 1.0 CA B:ASN21 4.8 0.9 1.0 CE B:MET199 4.8 0.6 1.0 CG2 B:THR354 4.8 62.6 1.0 O B:ALA19 4.8 80.4 1.0 O B:PHE350 4.8 66.6 1.0 CA B:GLY352 5.0 58.7 1.0

Sodium binding site 4 out of 4 in the Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mechanism of Substrate Release in Neurotransmitter:Sodium Symporters: the Structure of Leut in An Inward-Facing Occluded Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:78.0 occ:1.00 O B:ALA22 2.4 76.7 1.0 OG1 B:THR254 2.4 67.5 1.0 OD1 B:ASN27 2.4 67.5 1.0 O B:THR254 2.4 65.7 1.0 OXT B:PHE601 2.6 63.2 1.0 OD1 B:ASN286 3.0 80.2 1.0 CG B:ASN27 3.1 70.0 1.0 C B:THR254 3.1 58.9 1.0 CA B:THR254 3.1 59.7 1.0 ND2 B:ASN286 3.2 73.3 1.0 C B:ALA22 3.2 78.7 1.0 CB B:THR254 3.3 55.6 1.0 ND2 B:ASN27 3.3 70.8 1.0 C B:PHE601 3.4 59.9 1.0 CG B:ASN286 3.5 67.8 1.0 N B:PHE601 3.6 66.5 1.0 N B:VAL23 4.0 70.2 1.0 CA B:VAL23 4.0 67.5 1.0 N B:GLY24 4.0 60.2 1.0 CA B:PHE601 4.0 62.8 1.0 CA B:ALA22 4.1 80.7 1.0 O B:PHE601 4.3 61.0 1.0 N B:ASN27 4.4 64.0 1.0 CB B:ALA22 4.4 74.4 1.0 C B:VAL23 4.4 71.0 1.0 N B:LEU255 4.4 67.8 1.0 CB B:ASN27 4.5 65.4 1.0 CG2 B:THR254 4.5 54.2 1.0 N B:THR254 4.5 59.5 1.0 C B:GLY26 4.8 52.9 1.0 CA B:ASN27 4.8 65.0 1.0 O B:PHE253 4.8 56.1 1.0 CA B:GLY26 4.9 48.6 1.0 CB B:ASN286 4.9 71.1 1.0 CA B:GLY24 5.0 52.5 1.0

K.Gotfryd, T.Boesen, J.S.Mortensen, G.Khelashvili, M.Quick, D.S.Terry, J.W.Missel, M.V.Levine, P.Gourdon, S.C.Blanchard, J.A.Javitch, H.Weinstein, C.J.Loland, P.Nissen, U.Gether. X-Ray Structure of Leut in An Inward-Facing Occluded Conformation Reveals Mechanism of Substrate Release. Nat Commun V. 11 1005 2020.
ISSN: ESSN 2041-1723
PubMed: 32081981
DOI: 10.1038/S41467-020-14735-W