Sodium in PDB 7dix: Crystal Structure of Leut in Lipidic Cubic Phase at pH 5

The structure of Crystal Structure of Leut in Lipidic Cubic Phase at pH 5, PDB code: 7dix was solved by J.Fan, Y.Xiao, Z.Sun, X.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.66 / 3.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.162, 115.07, 80.819, 90, 102.89, 90
R / Rfree (%)	22.1 / 25

The binding sites of Sodium atom in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 5 (pdb code 7dix). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 5, PDB code: 7dix:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 5


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 in Lipidic Cubic Phase at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:46.0 occ:1.00 OG1 A:THR254 2.3 52.0 1.0 OD1 A:ASN27 2.3 46.1 1.0 O A:ALA22 2.3 44.5 1.0 O A:THR254 2.4 49.7 1.0 OXT A:MSE601 2.5 51.9 1.0 OD1 A:ASN286 2.7 49.2 1.0 CA A:THR254 2.9 55.8 1.0 C A:THR254 3.0 53.1 1.0 CB A:THR254 3.1 53.6 1.0 CG A:ASN27 3.2 46.6 1.0 C A:ALA22 3.4 44.6 1.0 C A:MSE601 3.5 49.4 1.0 ND2 A:ASN27 3.5 47.7 1.0 CG A:ASN286 3.7 49.2 1.0 N A:GLY24 3.8 44.6 1.0 N A:MSE601 3.8 50.3 1.0 OE2 A:GLU290 4.0 53.9 1.0 CA A:VAL23 4.0 42.0 1.0 ND2 A:ASN286 4.0 49.5 1.0 N A:VAL23 4.1 42.2 1.0 CA A:MSE601 4.2 48.2 1.0 N A:THR254 4.3 60.4 1.0 N A:ASN27 4.3 47.5 1.0 CG2 A:THR254 4.3 55.3 1.0 C A:VAL23 4.3 41.7 1.0 N A:LEU255 4.4 50.6 1.0 CA A:ALA22 4.4 44.1 1.0 O A:MSE601 4.4 46.8 1.0 CB A:ASN27 4.5 47.1 1.0 O A:PHE253 4.6 52.7 1.0 CA A:GLY24 4.7 43.1 1.0 CA A:ASN27 4.7 48.4 1.0 C A:GLY26 4.8 49.6 1.0 CB A:ALA22 4.8 44.6 1.0 C A:PHE253 4.9 53.1 1.0 CA A:GLY26 5.0 48.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 5


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 in Lipidic Cubic Phase at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:46.5 occ:1.00 O A:ALA351 2.3 44.6 1.0 O A:GLY20 2.3 42.2 1.0 OG1 A:THR354 2.3 40.6 1.0 O A:VAL23 2.3 41.9 1.0 OG A:SER355 2.4 41.4 1.0 N A:SER355 2.7 42.2 1.0 C A:THR354 3.1 42.0 1.0 CB A:THR354 3.2 41.8 1.0 CB A:SER355 3.2 41.4 1.0 C A:ALA351 3.3 44.4 1.0 CA A:SER355 3.4 41.9 1.0 C A:GLY20 3.4 44.3 1.0 C A:VAL23 3.4 41.7 1.0 CA A:THR354 3.5 42.9 1.0 CA A:GLY24 3.8 43.1 1.0 O A:THR354 3.8 40.8 1.0 CA A:ALA351 3.8 44.8 1.0 N A:THR354 3.9 40.8 1.0 CA A:GLY20 4.0 44.3 1.0 N A:GLY24 4.1 44.6 1.0 O A:PHE350 4.3 45.3 1.0 N A:GLY352 4.5 42.9 1.0 N A:ASN21 4.5 42.4 1.0 CG2 A:THR354 4.6 43.2 1.0 CA A:VAL23 4.6 42.0 1.0 O A:ASN21 4.6 43.3 1.0 CB A:ALA351 4.7 44.4 1.0 N A:VAL23 4.7 42.2 1.0 C A:ASN21 4.7 43.0 1.0 C A:GLY352 4.8 44.5 1.0 CA A:ASN21 4.8 43.2 1.0 C A:SER355 4.8 41.9 1.0 C A:LEU353 4.9 39.4 1.0 CA A:GLY352 4.9 42.9 1.0 O A:GLY352 4.9 44.6 1.0 N A:ALA351 5.0 44.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 5


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 in Lipidic Cubic Phase at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:45.5 occ:1.00 O B:GLY20 2.2 49.3 1.0 O B:ALA351 2.2 45.2 1.0 O B:VAL23 2.3 49.4 1.0 OG1 B:THR354 2.3 43.3 1.0 OG B:SER355 2.5 44.0 1.0 N B:SER355 3.0 44.5 1.0 C B:ALA351 3.3 43.7 1.0 CB B:THR354 3.3 43.8 1.0 C B:THR354 3.4 43.2 1.0 C B:GLY20 3.4 50.7 1.0 CB B:SER355 3.4 43.9 1.0 C B:VAL23 3.5 49.2 1.0 CA B:SER355 3.6 44.3 1.0 CA B:ALA351 3.7 43.8 1.0 CA B:THR354 3.7 43.5 1.0 CA B:GLY20 4.0 50.6 1.0 N B:THR354 4.1 43.2 1.0 O B:THR354 4.1 43.6 1.0 CA B:GLY24 4.2 50.6 1.0 N B:GLY24 4.3 52.1 1.0 O B:PHE350 4.3 45.0 1.0 N B:GLY352 4.5 44.4 1.0 N B:ASN21 4.5 52.5 1.0 CA B:VAL23 4.5 49.5 1.0 CB B:ALA351 4.5 45.2 1.0 O B:ASN21 4.5 54.5 1.0 N B:VAL23 4.6 50.0 1.0 CG2 B:THR354 4.6 44.3 1.0 C B:ASN21 4.6 52.0 1.0 CA B:ASN21 4.7 51.8 1.0 C B:GLY352 4.9 45.5 1.0 CB B:VAL23 4.9 49.7 1.0 CA B:GLY352 4.9 44.0 1.0 N B:ALA351 4.9 42.3 1.0

J.Fan, Y.Xiao, M.Quick, Y.Yang, Z.Sun, J.A.Javitch, X.Zhou. Crystal Structures of Leut Reveal Conformational Dynamics in the Outward-Facing States J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X