Sodium in PDB 3usp: Crystal Structure of Leut in Heptyl-Beta-D-Selenoglucoside

The structure of Crystal Structure of Leut in Heptyl-Beta-D-Selenoglucoside, PDB code: 3usp 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)	47.56 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.697, 86.359, 81.399, 90.00, 96.15, 90.00
R / Rfree (%)	22.3 / 23.2

The structure of Crystal Structure of Leut in Heptyl-Beta-D-Selenoglucoside also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Leut in Heptyl-Beta-D-Selenoglucoside (pdb code 3usp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Leut in Heptyl-Beta-D-Selenoglucoside, PDB code: 3usp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut in Heptyl-Beta-D-Selenoglucoside


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 Heptyl-Beta-D-Selenoglucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:17.7 occ:1.00 O A:GLY20 2.2 18.7 1.0 O A:ALA351 2.3 23.1 1.0 O A:VAL23 2.3 18.4 1.0 OG1 A:THR354 2.3 18.8 1.0 OG A:SER355 2.4 17.3 1.0 N A:SER355 2.7 21.4 1.0 C A:THR354 3.1 19.8 1.0 CB A:SER355 3.3 18.3 1.0 CB A:THR354 3.3 20.5 1.0 C A:VAL23 3.3 17.1 1.0 CA A:SER355 3.3 17.1 1.0 C A:ALA351 3.3 16.3 1.0 C A:GLY20 3.4 21.9 1.0 CA A:THR354 3.6 19.1 1.0 CA A:GLY24 3.7 18.4 1.0 O A:THR354 3.8 20.4 1.0 CA A:ALA351 3.9 24.2 1.0 N A:GLY24 3.9 16.8 1.0 CA A:GLY20 4.0 17.3 1.0 N A:THR354 4.0 17.8 1.0 CA A:VAL23 4.4 18.9 1.0 N A:ASN21 4.4 21.4 1.0 O A:ASN21 4.4 21.6 1.0 N A:VAL23 4.5 16.7 1.0 N A:GLY352 4.5 18.1 1.0 O A:GLY352 4.5 22.3 1.0 O A:PHE350 4.6 18.8 1.0 C A:ASN21 4.6 21.5 1.0 CB A:ALA351 4.6 17.7 1.0 CG2 A:THR354 4.6 19.4 1.0 CA A:ASN21 4.7 20.2 1.0 C A:GLY352 4.8 18.9 1.0 C A:SER355 4.8 18.3 1.0 C A:ALA22 4.8 18.2 1.0 C A:LEU353 4.9 22.4 1.0 CA A:GLY352 5.0 19.0 1.0 CB A:VAL23 5.0 20.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut in Heptyl-Beta-D-Selenoglucoside


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 Heptyl-Beta-D-Selenoglucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:22.4 occ:1.00 O A:ALA22 2.3 18.9 1.0 O A:THR254 2.3 20.4 1.0 OD1 A:ASN27 2.4 18.6 1.0 OG1 A:THR254 2.4 23.4 1.0 OD1 A:ASN286 2.4 19.1 1.0 OXT A:LEU604 2.6 21.2 1.0 C A:THR254 3.1 20.0 1.0 C A:ALA22 3.1 18.2 1.0 CA A:THR254 3.1 23.3 1.0 CG A:ASN27 3.2 19.7 1.0 CG A:ASN286 3.3 21.3 1.0 CB A:THR254 3.3 23.3 1.0 ND2 A:ASN27 3.5 20.3 1.0 ND2 A:ASN286 3.5 20.2 1.0 C A:LEU604 3.5 19.0 1.0 N A:LEU604 3.6 16.6 1.0 N A:VAL23 3.9 16.7 1.0 CA A:VAL23 3.9 18.9 1.0 N A:GLY24 4.0 16.8 1.0 CA A:ALA22 4.0 17.6 1.0 CA A:LEU604 4.1 18.8 1.0 OE2 A:GLU290 4.3 22.6 1.0 CB A:ALA22 4.3 17.6 1.0 N A:LEU255 4.3 18.4 1.0 CG2 A:THR254 4.4 18.9 1.0 O A:LEU604 4.4 18.2 1.0 C A:VAL23 4.5 17.1 1.0 N A:ASN27 4.5 20.3 1.0 N A:THR254 4.5 16.6 1.0 CB A:ASN27 4.6 19.2 1.0 CB A:ASN286 4.7 17.4 1.0 O A:PHE253 4.8 16.6 1.0 C A:GLY26 4.9 19.7 1.0 CA A:ASN27 5.0 22.7 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