Sodium in PDB 7dj1: Crystal Structure of the G26C Mutant of Leut

The structure of Crystal Structure of the G26C Mutant of Leut, PDB code: 7dj1 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)	46.87 / 3.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.853, 94.115, 94.248, 90, 95.93, 90
R / Rfree (%)	24.7 / 27.2

The binding sites of Sodium atom in the Crystal Structure of the G26C Mutant of Leut (pdb code 7dj1). 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 the G26C Mutant of Leut, PDB code: 7dj1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the G26C Mutant of Leut


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 the G26C Mutant of Leut within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:82.2 occ:1.00 O A:ALA22 2.3 78.4 1.0 OD1 A:ASN27 2.3 81.3 1.0 O A:THR254 2.4 83.0 1.0 OG1 A:THR254 2.4 81.9 1.0 OXT A:LEU601 2.6 76.4 1.0 OD1 A:ASN286 2.7 82.9 1.0 CA A:THR254 3.0 82.5 1.0 C A:THR254 3.1 83.2 1.0 CG A:ASN27 3.1 82.0 1.0 CB A:THR254 3.2 83.0 1.0 C A:ALA22 3.4 78.2 1.0 ND2 A:ASN27 3.4 83.6 1.0 CG A:ASN286 3.7 84.6 1.0 C A:LEU601 3.7 74.8 1.0 N A:LEU601 3.8 75.1 1.0 ND2 A:ASN286 3.9 86.1 1.0 CA A:VAL23 4.1 76.3 1.0 N A:VAL23 4.2 75.9 1.0 OE2 A:GLU290 4.3 76.7 1.0 CA A:ALA22 4.3 77.3 1.0 CA A:LEU601 4.4 74.9 1.0 N A:LEU255 4.4 85.1 1.0 N A:THR254 4.4 83.1 1.0 N A:GLY24 4.4 73.5 1.0 CG2 A:THR254 4.4 84.3 1.0 CB A:ASN27 4.5 81.3 1.0 N A:ASN27 4.5 76.4 1.0 O A:PHE253 4.6 79.6 1.0 CB A:ALA22 4.6 78.8 1.0 O A:LEU601 4.7 74.7 1.0 CB A:CYS26 4.7 74.9 1.0 C A:VAL23 4.7 73.4 1.0 CA A:ASN27 4.8 79.2 1.0 C A:PHE253 4.9 80.7 1.0 CD A:GLU290 5.0 77.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the G26C Mutant of Leut


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 the G26C Mutant of Leut within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:69.4 occ:1.00 OG1 A:THR354 2.2 67.2 1.0 O A:VAL23 2.2 71.9 1.0 O A:ALA351 2.3 66.8 1.0 O A:GLY20 2.3 76.2 1.0 N A:SER355 2.7 64.7 1.0 OG A:SER355 2.8 66.7 1.0 C A:THR354 2.9 64.8 1.0 CB A:THR354 2.9 66.4 1.0 CA A:THR354 3.3 64.8 1.0 C A:ALA351 3.3 66.2 1.0 C A:GLY20 3.4 77.2 1.0 C A:VAL23 3.4 73.4 1.0 CA A:SER355 3.4 65.1 1.0 CB A:SER355 3.5 65.7 1.0 O A:THR354 3.6 65.4 1.0 N A:THR354 3.7 64.0 1.0 CA A:ALA351 3.7 66.5 1.0 CA A:GLY24 3.8 70.7 1.0 CA A:GLY20 3.9 77.6 1.0 N A:GLY24 4.1 73.5 1.0 O A:PHE350 4.3 67.6 1.0 CG2 A:THR354 4.3 66.5 1.0 N A:GLY352 4.5 65.7 1.0 CB A:ALA351 4.5 66.4 1.0 N A:ASN21 4.5 77.2 1.0 CA A:VAL23 4.5 76.3 1.0 O A:ASN21 4.7 72.0 1.0 N A:VAL23 4.7 75.9 1.0 C A:LEU353 4.7 62.7 1.0 C A:ASN21 4.9 74.8 1.0 C A:GLY352 4.9 64.6 1.0 N A:ALA351 4.9 65.4 1.0 CA A:ASN21 4.9 75.3 1.0 C A:SER355 4.9 64.4 1.0 CA A:GLY352 4.9 65.0 1.0 CB A:VAL23 5.0 78.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the G26C Mutant of Leut


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 the G26C Mutant of Leut within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:78.2 occ:1.00 OD1 B:ASN27 2.3 79.8 1.0 O B:ALA22 2.3 72.9 1.0 OG1 B:THR254 2.4 79.5 1.0 OD1 B:ASN286 2.5 79.7 1.0 O B:THR254 2.5 80.5 1.0 O B:LEU601 2.7 71.2 1.0 CG B:ASN27 2.8 80.3 1.0 ND2 B:ASN27 2.9 82.8 1.0 CA B:THR254 3.2 79.9 1.0 C B:THR254 3.2 80.7 1.0 CB B:THR254 3.3 80.5 1.0 C B:ALA22 3.4 73.3 1.0 N B:LEU601 3.5 71.2 1.0 CG B:ASN286 3.5 81.8 1.0 C B:LEU601 3.7 70.6 1.0 ND2 B:ASN286 3.8 83.5 1.0 CA B:VAL23 4.0 72.7 1.0 N B:VAL23 4.1 71.7 1.0 CA B:LEU601 4.1 71.5 1.0 CB B:ASN27 4.2 78.3 1.0 N B:GLY24 4.3 72.5 1.0 CA B:ALA22 4.4 72.9 1.0 N B:ASN27 4.4 73.8 1.0 N B:LEU255 4.5 81.0 1.0 CG2 B:THR254 4.5 82.3 1.0 N B:THR254 4.6 80.4 1.0 C B:VAL23 4.6 70.4 1.0 CA B:ASN27 4.6 75.6 1.0 CB B:ALA22 4.7 75.0 1.0 O B:PHE253 4.8 76.2 1.0 OXT B:LEU601 4.8 70.8 1.0 OE1 B:GLU290 4.8 73.1 1.0 CB B:CYS26 4.8 75.3 1.0 CB B:ASN286 4.9 83.2 1.0 CD B:GLU290 4.9 73.5 1.0 OE2 B:GLU290 4.9 74.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the G26C Mutant of Leut


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 the G26C Mutant of Leut within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:68.3 occ:1.00 O B:VAL23 2.2 70.3 1.0 OG1 B:THR354 2.2 64.7 1.0 O B:ALA351 2.3 65.8 1.0 O B:GLY20 2.3 70.3 1.0 N B:SER355 2.5 63.9 1.0 OG B:SER355 2.7 62.6 1.0 C B:THR354 2.8 64.8 1.0 CB B:THR354 2.9 65.0 1.0 CA B:THR354 3.3 64.5 1.0 CA B:SER355 3.3 64.5 1.0 C B:ALA351 3.3 64.7 1.0 CB B:SER355 3.3 63.4 1.0 C B:VAL23 3.3 70.4 1.0 C B:GLY20 3.4 71.5 1.0 O B:THR354 3.5 65.9 1.0 N B:THR354 3.7 63.5 1.0 CA B:GLY24 3.7 70.0 1.0 CA B:ALA351 3.8 63.9 1.0 N B:GLY24 4.0 72.5 1.0 CA B:GLY20 4.0 72.0 1.0 CG2 B:THR354 4.4 65.2 1.0 O B:PHE350 4.4 65.0 1.0 N B:GLY352 4.5 63.0 1.0 N B:ASN21 4.5 73.3 1.0 CA B:VAL23 4.5 72.7 1.0 CB B:ALA351 4.6 62.6 1.0 O B:ASN21 4.6 69.6 1.0 N B:VAL23 4.7 71.7 1.0 C B:LEU353 4.7 63.1 1.0 C B:SER355 4.7 65.8 1.0 C B:ASN21 4.8 71.4 1.0 C B:GLY352 4.8 64.2 1.0 CA B:ASN21 4.8 71.5 1.0 CA B:GLY352 4.9 63.4 1.0 N B:ALA351 5.0 63.1 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