Sodium in PDB 3usi: Crystal Structure of Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles

The structure of Crystal Structure of Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles, PDB code: 3usi was solved by H.Wang, J.Elferich, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.78 / 3.11
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.180, 84.389, 91.031, 90.00, 98.04, 90.00
R / Rfree (%)	23.7 / 25

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles (pdb code 3usi). 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 Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles, PDB code: 3usi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P2 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 Bound to L-Leucine in Space Group P2 From Lipid Bicelles within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:49.6 occ:1.00 O A:GLY20 2.2 80.6 1.0 O A:VAL23 2.2 47.1 1.0 OG1 A:THR354 2.4 35.4 1.0 OG A:SER355 2.4 40.1 1.0 O A:ALA351 2.5 47.2 1.0 N A:SER355 2.9 40.4 1.0 C A:THR354 3.3 33.8 1.0 CB A:THR354 3.3 35.7 1.0 C A:VAL23 3.3 47.2 1.0 C A:GLY20 3.4 81.6 1.0 CB A:SER355 3.4 39.4 1.0 CA A:SER355 3.5 39.8 1.0 C A:ALA351 3.5 47.5 1.0 CA A:THR354 3.7 34.6 1.0 CA A:GLY24 3.9 58.0 1.0 O A:THR354 3.9 34.1 1.0 CA A:ALA351 4.0 48.7 1.0 N A:GLY24 4.0 59.0 1.0 O A:ASN21 4.1 46.1 1.0 CA A:GLY20 4.1 83.1 1.0 N A:THR354 4.2 34.1 1.0 C A:ASN21 4.4 47.1 1.0 CA A:VAL23 4.4 48.2 1.0 N A:VAL23 4.4 48.1 1.0 N A:ASN21 4.4 48.6 1.0 CA A:ASN21 4.6 47.6 1.0 CG2 A:THR354 4.6 37.0 1.0 CB A:ALA351 4.7 48.9 1.0 N A:GLY352 4.7 30.2 1.0 O A:PHE350 4.7 51.6 1.0 C A:ALA22 4.8 48.4 1.0 O A:GLY352 4.9 28.6 1.0 O A:ALA19 4.9 45.1 1.0 C A:SER355 5.0 39.1 1.0 C A:GLY352 5.0 29.2 1.0 N A:ALA22 5.0 48.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P2 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 Bound to L-Leucine in Space Group P2 From Lipid Bicelles within 5.0Å range: probe atom residue distance (Å) B Occ A:Na752 b:72.2 occ:1.00 O A:ALA22 2.3 47.8 1.0 OD1 A:ASN27 2.4 61.1 1.0 O A:THR254 2.4 40.1 1.0 OG1 A:THR254 2.5 41.1 1.0 OD1 A:ASN286 2.5 52.7 1.0 OXT A:LEU601 2.6 56.5 1.0 C A:THR254 3.2 40.1 1.0 C A:ALA22 3.2 48.4 1.0 CA A:THR254 3.2 39.7 1.0 CB A:THR254 3.4 40.9 1.0 CG A:ASN27 3.4 62.1 1.0 CG A:ASN286 3.4 53.9 1.0 C A:LEU601 3.6 55.7 1.0 ND2 A:ASN286 3.7 54.3 1.0 CA A:VAL23 3.7 48.2 1.0 N A:LEU601 3.8 56.2 1.0 N A:VAL23 3.9 48.1 1.0 ND2 A:ASN27 3.9 63.4 1.0 N A:GLY24 4.1 59.0 1.0 CA A:ALA22 4.2 48.6 1.0 CA A:LEU601 4.3 55.3 1.0 O A:LEU601 4.3 55.4 1.0 C A:VAL23 4.4 47.2 1.0 N A:ASN27 4.4 60.3 1.0 CG2 A:THR254 4.4 42.3 1.0 N A:LEU255 4.4 48.7 1.0 CB A:ALA22 4.5 50.0 1.0 N A:THR254 4.6 39.4 1.0 CB A:ASN27 4.7 62.1 1.0 C A:GLY26 4.8 41.4 1.0 CB A:ASN286 4.8 55.2 1.0 O A:PHE253 4.9 45.8 1.0 CA A:GLY26 4.9 40.1 1.0 CA A:ASN27 4.9 61.6 1.0 OE1 A:GLU290 4.9 65.7 1.0 CB A:VAL23 4.9 49.6 1.0 O A:GLY24 5.0 58.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles


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 Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles within 5.0Å range: probe atom residue distance (Å) B Occ B:Na751 b:62.1 occ:1.00 O B:GLY20 2.2 56.7 1.0 O B:VAL23 2.2 48.1 1.0 OG1 B:THR354 2.4 57.3 1.0 OG B:SER355 2.4 54.9 1.0 O B:ALA351 2.5 74.2 1.0 N B:SER355 2.9 55.6 1.0 CB B:THR354 3.3 57.0 1.0 C B:THR354 3.3 53.3 1.0 C B:VAL23 3.3 47.9 1.0 C B:GLY20 3.4 57.3 1.0 CB B:SER355 3.5 53.6 1.0 CA B:SER355 3.5 53.8 1.0 C B:ALA351 3.5 75.6 1.0 CA B:THR354 3.7 55.4 1.0 CA B:GLY24 3.9 61.9 1.0 O B:THR354 3.9 52.6 1.0 CA B:ALA351 4.0 77.9 1.0 N B:GLY24 4.0 62.4 1.0 O B:ASN21 4.1 51.2 1.0 CA B:GLY20 4.1 59.6 1.0 N B:THR354 4.2 55.8 1.0 C B:ASN21 4.4 52.1 1.0 CA B:VAL23 4.4 48.3 1.0 N B:VAL23 4.4 46.9 1.0 N B:ASN21 4.4 54.4 1.0 CA B:ASN21 4.6 52.5 1.0 CG2 B:THR354 4.6 59.3 1.0 CB B:ALA351 4.7 78.4 1.0 N B:GLY352 4.7 50.9 1.0 O B:PHE350 4.7 79.6 1.0 C B:ALA22 4.9 43.4 1.0 O B:GLY352 4.9 46.7 1.0 O B:ALA19 4.9 60.4 1.0 C B:SER355 5.0 52.4 1.0 C B:GLY352 5.0 48.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles


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 Leut Bound to L-Leucine in Space Group P2 From Lipid Bicelles within 5.0Å range: probe atom residue distance (Å) B Occ B:Na752 b:49.1 occ:1.00 O B:ALA22 2.3 42.9 1.0 OD1 B:ASN27 2.4 73.8 1.0 O B:THR254 2.4 50.0 1.0 OG1 B:THR254 2.5 52.7 1.0 OD1 B:ASN286 2.5 60.9 1.0 OXT B:LEU601 2.6 55.7 1.0 C B:THR254 3.2 49.4 1.0 C B:ALA22 3.2 43.4 1.0 CA B:THR254 3.2 49.5 1.0 CB B:THR254 3.4 51.3 1.0 CG B:ASN27 3.4 75.7 1.0 CG B:ASN286 3.5 61.6 1.0 C B:LEU601 3.6 55.0 1.0 ND2 B:ASN286 3.7 61.6 1.0 CA B:VAL23 3.8 48.3 1.0 N B:LEU601 3.8 53.6 1.0 ND2 B:ASN27 3.9 76.9 1.0 N B:VAL23 3.9 46.9 1.0 N B:GLY24 4.0 62.4 1.0 CA B:ALA22 4.2 42.4 1.0 CA B:LEU601 4.3 53.5 1.0 O B:LEU601 4.3 55.6 1.0 C B:VAL23 4.4 47.9 1.0 N B:ASN27 4.4 73.9 1.0 CG2 B:THR254 4.4 51.9 1.0 N B:LEU255 4.4 59.9 1.0 CB B:ALA22 4.5 43.1 1.0 N B:THR254 4.6 48.2 1.0 CB B:ASN27 4.7 76.9 1.0 C B:GLY26 4.8 46.8 1.0 CB B:ASN286 4.9 62.9 1.0 O B:PHE253 4.9 59.9 1.0 CA B:GLY26 4.9 44.7 1.0 CA B:ASN27 4.9 76.1 1.0 OE1 B:GLU290 4.9 76.7 1.0 CB B:VAL23 4.9 50.6 1.0 O B:GLY24 5.0 63.4 1.0

H.Wang, J.Elferich, E.Gouaux. Structures of Leut in Bicelles Define Conformation and Substrate Binding in A Membrane-Like Context. Nat.Struct.Mol.Biol. V. 19 212 2012.
ISSN: ISSN 1545-9993
PubMed: 22245965
DOI: 10.1038/NSMB.2215