Sodium in PDB 6nle: X-Ray Structure of Leut with V269 Deletion

The structure of X-Ray Structure of Leut with V269 Deletion, PDB code: 6nle was solved by V.Navratna, D.Yang, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.26 / 2.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.540, 86.140, 81.530, 90.00, 110.72, 90.00
R / Rfree (%)	22.4 / 26

The binding sites of Sodium atom in the X-Ray Structure of Leut with V269 Deletion (pdb code 6nle). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Leut with V269 Deletion, PDB code: 6nle:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Leut with V269 Deletion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Leut with V269 Deletion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:42.0 occ:1.00 O A:GLY20 2.3 48.0 1.0 O A:ALA351 2.3 45.1 1.0 OG1 A:THR354 2.4 31.0 1.0 O A:VAL23 2.5 59.0 1.0 OG A:SER355 2.5 50.4 1.0 N A:SER355 2.8 41.0 1.0 C A:THR354 2.9 41.5 1.0 CB A:THR354 3.0 35.9 1.0 CA A:THR354 3.3 40.0 1.0 CB A:SER355 3.3 45.7 1.0 C A:GLY20 3.4 51.0 1.0 C A:ALA351 3.4 42.9 1.0 CA A:SER355 3.5 43.8 1.0 O A:THR354 3.5 40.1 1.0 C A:VAL23 3.6 52.7 1.0 N A:THR354 3.7 42.5 1.0 CA A:GLY20 4.0 52.6 1.0 CA A:GLY24 4.1 47.4 1.0 CA A:ALA351 4.1 45.5 1.0 O A:PHE350 4.2 43.1 1.0 N A:GLY24 4.3 48.5 1.0 N A:GLY352 4.5 36.6 1.0 CG2 A:THR354 4.5 36.7 1.0 N A:ASN21 4.5 50.4 1.0 C A:GLY352 4.6 44.0 1.0 CA A:GLY352 4.7 38.4 1.0 O A:ASN21 4.7 49.2 1.0 O A:GLY352 4.7 52.2 1.0 C A:LEU353 4.7 46.4 1.0 CA A:VAL23 4.8 47.9 1.0 C A:ASN21 4.8 51.7 1.0 CA A:ASN21 4.8 47.2 1.0 N A:VAL23 4.9 46.7 1.0 C A:SER355 4.9 47.1 1.0 N A:LEU353 4.9 42.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Leut with V269 Deletion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Leut with V269 Deletion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:40.1 occ:1.00 OD1 A:ASN27 2.4 65.9 1.0 O A:ALA22 2.4 50.1 1.0 OG1 A:THR254 2.4 62.1 1.0 O A:THR254 2.5 42.2 1.0 OD1 A:ASN286 2.8 42.5 1.0 CA A:THR254 2.8 44.7 1.0 O A:LEU601 2.9 56.8 1.0 CB A:THR254 3.0 51.9 1.0 C A:THR254 3.0 40.9 1.0 CG A:ASN27 3.1 61.5 1.0 N A:LEU601 3.3 51.2 1.0 ND2 A:ASN27 3.3 56.4 1.0 C A:ALA22 3.4 48.4 1.0 C A:LEU601 3.7 56.6 1.0 CG A:ASN286 3.7 44.9 1.0 OE1 A:GLU290 3.8 56.7 1.0 ND2 A:ASN286 4.0 47.9 1.0 N A:GLY24 4.0 48.5 1.0 CA A:LEU601 4.1 52.2 1.0 CA A:VAL23 4.2 47.9 1.0 N A:VAL23 4.2 46.7 1.0 N A:THR254 4.2 43.2 1.0 N A:ASN27 4.2 48.2 1.0 CA A:ALA22 4.3 51.9 1.0 N A:LEU255 4.4 36.3 1.0 CG2 A:THR254 4.4 50.6 1.0 CB A:ASN27 4.5 59.3 1.0 C A:VAL23 4.5 52.7 1.0 O A:PHE253 4.5 47.5 1.0 C A:GLY26 4.6 48.7 1.0 OXT A:LEU601 4.7 60.1 1.0 CA A:GLY26 4.7 45.4 1.0 CB A:ALA22 4.7 56.8 1.0 CA A:ASN27 4.8 56.5 1.0 C A:PHE253 4.8 40.6 1.0 N A:GLY26 4.9 46.7 1.0 CA A:GLY24 5.0 47.4 1.0 CD A:GLU290 5.0 57.1 1.0

V.Navratna, D.Yang, E.Gouaux. X-Ray Structure of Leut with V269 Deletion To Be Published.