Sodium in PDB 4fy0: Crystal Structure of Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles

The structure of Crystal Structure of Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles, PDB code: 4fy0 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)	29.93 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.840, 90.497, 81.969, 90.00, 103.15, 90.00
R / Rfree (%)	19.9 / 21.9

The binding sites of Sodium atom in the Crystal Structure of Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles (pdb code 4fy0). 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 Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles, PDB code: 4fy0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles


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 Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:59.8 occ:1.00 O A:VAL23 2.1 58.0 1.0 O A:GLY20 2.2 53.6 1.0 O A:ALA351 2.3 62.7 1.0 OG1 A:THR354 2.4 66.9 1.0 OG A:SER355 2.4 60.0 1.0 C A:VAL23 3.1 61.2 1.0 N A:SER355 3.3 63.3 1.0 C A:ALA351 3.4 61.5 1.0 C A:GLY20 3.4 56.0 1.0 CB A:THR354 3.4 58.9 1.0 CB A:SER355 3.4 59.1 1.0 C A:THR354 3.4 64.3 1.0 CA A:GLY24 3.6 56.2 1.0 N A:GLY24 3.7 58.8 1.0 CA A:SER355 3.8 60.2 1.0 CA A:THR354 3.9 58.5 1.0 O A:THR354 3.9 65.8 1.0 CA A:ALA351 3.9 54.4 1.0 O A:ASN21 4.1 58.5 1.0 CA A:GLY20 4.1 55.8 1.0 N A:THR354 4.2 56.9 1.0 CA A:VAL23 4.3 58.3 1.0 O A:PHE350 4.4 62.3 1.0 N A:VAL23 4.5 58.8 1.0 N A:ASN21 4.5 62.3 1.0 C A:ASN21 4.5 58.4 1.0 N A:GLY352 4.5 57.2 1.0 O A:GLY352 4.6 67.6 1.0 CA A:ASN21 4.7 58.6 1.0 CG2 A:THR354 4.7 65.9 1.0 CB A:VAL23 4.8 57.4 1.0 C A:GLY352 4.8 64.5 1.0 CB A:ALA351 4.8 51.0 1.0 C A:ALA22 4.9 59.2 1.0 CA A:GLY352 4.9 56.2 1.0 C A:GLY24 5.0 60.3 1.0 O A:ALA19 5.0 58.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles


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 Leut-F253A Bound to L-Selenomethionine From Lipid Bicelles within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:60.1 occ:1.00 O A:ALA22 2.3 61.9 1.0 O A:THR254 2.4 57.6 1.0 OD1 A:ASN27 2.4 67.0 1.0 OD1 A:ASN286 2.4 65.5 1.0 OG1 A:THR254 2.4 64.9 1.0 O A:MSE603 2.6 64.8 1.0 C A:ALA22 3.1 59.2 1.0 C A:THR254 3.1 65.2 1.0 CA A:THR254 3.2 63.1 1.0 CG A:ASN27 3.3 62.9 1.0 CG A:ASN286 3.3 65.1 1.0 CB A:THR254 3.3 63.8 1.0 ND2 A:ASN27 3.4 65.1 1.0 ND2 A:ASN286 3.5 65.1 1.0 N A:MSE603 3.6 68.9 1.0 C A:MSE603 3.6 64.2 1.0 N A:VAL23 3.7 58.8 1.0 CA A:VAL23 3.8 58.3 1.0 N A:GLY24 3.9 58.8 1.0 CA A:ALA22 4.0 55.0 1.0 OE2 A:GLU290 4.1 63.0 1.0 CA A:MSE603 4.2 59.4 1.0 CB A:ALA22 4.3 52.6 1.0 N A:LEU255 4.4 65.9 1.0 C A:VAL23 4.4 61.2 1.0 CG2 A:THR254 4.5 55.9 1.0 N A:THR254 4.6 58.0 1.0 OXT A:MSE603 4.6 65.4 1.0 CB A:ASN27 4.7 64.1 1.0 CB A:ASN286 4.7 62.4 1.0 N A:ASN27 4.7 63.4 1.0 O A:ALA253 4.9 62.9 1.0

H.Wang, E.Gouaux. Substrate Binds in the S1 Site of the F253A Mutant of Leut, A Neurotransmitter Sodium Symporter Homologue. Embo Rep. V. 13 861 2012.
ISSN: ISSN 1469-221X
PubMed: 22836580
DOI: 10.1038/EMBOR.2012.110