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

The structure of Crystal Structure of Leut in Lipidic Cubic Phase at pH 7, PDB code: 7dii 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)	32.10 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.588, 72.184, 80.806, 100.89, 97.58, 115.16
R / Rfree (%)	19.2 / 21.3

The binding sites of Sodium atom in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 7 (pdb code 7dii). 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 in Lipidic Cubic Phase at pH 7, PDB code: 7dii:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:41.1 occ:1.00 OD1 A:ASN27 2.3 40.9 1.0 O A:ALA22 2.3 38.1 1.0 O A:THR254 2.3 38.5 1.0 OG1 A:THR254 2.4 41.4 1.0 OD1 A:ASN286 2.5 38.9 1.0 OXT A:LEU601 2.5 42.5 1.0 CG A:ASN27 3.0 42.2 1.0 C A:THR254 3.1 35.0 1.0 CA A:THR254 3.1 32.2 1.0 C A:ALA22 3.2 39.1 1.0 ND2 A:ASN27 3.2 37.8 1.0 CB A:THR254 3.3 36.9 1.0 CG A:ASN286 3.3 35.7 1.0 ND2 A:ASN286 3.5 34.2 1.0 C A:LEU601 3.6 43.1 1.0 N A:LEU601 3.7 39.7 1.0 N A:VAL23 3.9 37.8 1.0 CA A:VAL23 3.9 38.1 1.0 N A:GLY24 3.9 38.3 1.0 OE1 A:GLU290 4.0 43.6 1.0 CA A:ALA22 4.1 36.4 1.0 CA A:LEU601 4.2 41.0 1.0 CB A:ALA22 4.4 34.8 1.0 CG2 A:THR254 4.4 34.8 1.0 N A:LEU255 4.4 36.0 1.0 CB A:ASN27 4.4 43.9 1.0 C A:VAL23 4.4 36.9 1.0 O A:LEU601 4.5 43.6 1.0 N A:ASN27 4.5 39.0 1.0 N A:THR254 4.5 32.4 1.0 O A:PHE253 4.7 39.3 1.0 CB A:ASN286 4.8 38.0 1.0 CA A:ASN27 4.8 43.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:32.6 occ:1.00 O A:ALA351 2.3 40.4 1.0 O A:GLY20 2.3 34.2 1.0 O A:VAL23 2.3 35.9 1.0 OG A:SER355 2.3 37.5 1.0 OG1 A:THR354 2.4 35.3 1.0 N A:SER355 2.8 35.9 1.0 CB A:SER355 3.1 29.2 1.0 C A:VAL23 3.3 36.9 1.0 C A:THR354 3.3 36.7 1.0 CA A:SER355 3.4 36.4 1.0 C A:ALA351 3.4 41.6 1.0 C A:GLY20 3.4 47.2 1.0 CB A:THR354 3.4 39.2 1.0 CA A:GLY24 3.6 41.4 1.0 CA A:THR354 3.8 36.1 1.0 N A:GLY24 3.8 38.3 1.0 CA A:ALA351 4.0 41.9 1.0 O A:THR354 4.0 38.3 1.0 N A:THR354 4.1 34.0 1.0 CA A:GLY20 4.1 48.5 1.0 O A:ASN21 4.3 42.2 1.0 CA A:VAL23 4.4 38.1 1.0 O A:PHE350 4.4 44.9 1.0 N A:VAL23 4.4 37.8 1.0 N A:GLY352 4.5 37.7 1.0 N A:ASN21 4.5 44.0 1.0 C A:ASN21 4.5 39.0 1.0 O A:GLY352 4.7 36.0 1.0 C A:GLY352 4.7 32.9 1.0 CA A:ASN21 4.7 41.1 1.0 CG2 A:THR354 4.7 35.1 1.0 CA A:GLY352 4.8 34.9 1.0 CB A:ALA351 4.8 38.0 1.0 C A:ALA22 4.8 39.1 1.0 C A:SER355 4.8 35.9 1.0 CB A:VAL23 4.9 38.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:38.8 occ:1.00 OD1 B:ASN27 2.3 39.7 1.0 O B:ALA22 2.3 38.4 1.0 O B:THR254 2.4 40.7 1.0 OG1 B:THR254 2.4 41.3 1.0 OD1 B:ASN286 2.5 31.9 1.0 O B:LEU601 2.7 37.7 1.0 CG B:ASN27 3.1 38.0 1.0 C B:THR254 3.1 38.7 1.0 CA B:THR254 3.1 37.6 1.0 C B:ALA22 3.2 37.5 1.0 ND2 B:ASN27 3.3 35.0 1.0 CB B:THR254 3.3 38.1 1.0 CG B:ASN286 3.3 34.7 1.0 ND2 B:ASN286 3.5 33.7 1.0 C B:LEU601 3.7 43.4 1.0 N B:LEU601 3.8 37.3 1.0 N B:VAL23 3.9 38.3 1.0 CA B:VAL23 3.9 38.5 1.0 OE1 B:GLU290 4.0 42.5 1.0 N B:GLY24 4.0 37.0 1.0 CA B:ALA22 4.1 38.2 1.0 CB B:ALA22 4.3 37.7 1.0 CG2 B:THR254 4.3 37.1 1.0 N B:LEU255 4.4 33.0 1.0 CA B:LEU601 4.4 45.6 1.0 CB B:ASN27 4.4 38.3 1.0 N B:ASN27 4.5 39.5 1.0 C B:VAL23 4.5 40.4 1.0 N B:THR254 4.5 35.5 1.0 OXT B:LEU601 4.6 44.4 1.0 CB B:ASN286 4.7 36.1 1.0 CA B:ASN27 4.8 41.3 1.0 O B:PHE253 4.8 38.4 1.0 CD B:GLU290 5.0 45.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Leut in Lipidic Cubic Phase at pH 7


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 in Lipidic Cubic Phase at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:38.3 occ:1.00 O B:GLY20 2.3 35.6 1.0 O B:ALA351 2.3 33.8 1.0 O B:VAL23 2.3 41.4 1.0 OG1 B:THR354 2.3 35.6 1.0 OG B:SER355 2.4 37.4 1.0 N B:SER355 2.7 34.3 1.0 CB B:SER355 3.1 33.6 1.0 C B:THR354 3.2 35.8 1.0 CA B:SER355 3.3 34.1 1.0 C B:VAL23 3.3 40.4 1.0 CB B:THR354 3.4 36.6 1.0 C B:ALA351 3.4 38.2 1.0 C B:GLY20 3.4 37.2 1.0 CA B:GLY24 3.6 36.5 1.0 CA B:THR354 3.7 36.5 1.0 N B:GLY24 3.9 37.0 1.0 O B:THR354 3.9 36.2 1.0 CA B:ALA351 4.0 37.9 1.0 N B:THR354 4.0 38.4 1.0 CA B:GLY20 4.1 39.0 1.0 O B:ASN21 4.3 37.3 1.0 CA B:VAL23 4.4 38.5 1.0 O B:PHE350 4.5 34.0 1.0 N B:VAL23 4.5 38.3 1.0 N B:ASN21 4.5 39.1 1.0 C B:ASN21 4.5 37.6 1.0 N B:GLY352 4.5 38.4 1.0 O B:GLY352 4.6 37.9 1.0 C B:GLY352 4.7 35.6 1.0 CG2 B:THR354 4.7 30.9 1.0 CA B:ASN21 4.7 40.0 1.0 CA B:GLY352 4.8 35.4 1.0 C B:SER355 4.8 35.8 1.0 CB B:ALA351 4.9 36.5 1.0 C B:ALA22 4.9 37.5 1.0 C B:LEU353 5.0 38.4 1.0 CB B:VAL23 5.0 37.2 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