Sodium in PDB 3gjd: Crystal Structure of Leut with Bound Og

The structure of Crystal Structure of Leut with Bound Og, PDB code: 3gjd was solved by A.M.L.Winther, M.Quick, J.A.Javitch, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.55 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.510, 86.570, 81.290, 90.00, 95.63, 90.00
R / Rfree (%)	16.9 / 19.9

The structure of Crystal Structure of Leut with Bound Og also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Leut with Bound Og (pdb code 3gjd). 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 with Bound Og, PDB code: 3gjd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut with Bound Og


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 with Bound Og within 5.0Å range: probe atom residue distance (Å) B Occ A:Na516 b:28.0 occ:1.00 O A:VAL23 2.4 22.6 1.0 OG1 A:THR354 2.4 23.2 1.0 O A:GLY20 2.4 27.0 1.0 O A:ALA351 2.4 21.4 1.0 OG A:SER355 2.7 23.7 1.0 N A:SER355 3.0 21.3 1.0 C A:THR354 3.3 27.2 1.0 C A:VAL23 3.3 24.9 1.0 CB A:THR354 3.4 25.8 1.0 CB A:SER355 3.4 24.4 1.0 C A:ALA351 3.5 26.7 1.0 C A:GLY20 3.5 31.5 1.0 CA A:SER355 3.6 20.9 1.0 CA A:THR354 3.7 24.5 1.0 CA A:GLY24 3.7 20.7 1.0 N A:GLY24 3.9 22.6 1.0 O A:THR354 3.9 28.2 1.0 CA A:ALA351 4.0 26.0 1.0 N A:THR354 4.0 26.1 1.0 CA A:GLY20 4.0 31.4 1.0 O A:ASN21 4.3 26.4 1.0 O A:PHE350 4.4 26.7 1.0 CA A:VAL23 4.4 21.6 1.0 N A:VAL23 4.4 23.3 1.0 C A:ASN21 4.6 28.0 1.0 N A:ASN21 4.6 26.4 1.0 O A:GLY352 4.6 23.2 1.0 N A:GLY352 4.6 23.9 1.0 CG2 A:THR354 4.7 25.8 1.0 C A:GLY352 4.7 22.3 1.0 C A:ALA22 4.8 24.2 1.0 CB A:ALA351 4.8 23.8 1.0 CB A:VAL23 4.9 25.4 1.0 CA A:GLY352 4.9 21.6 1.0 CA A:ASN21 4.9 24.5 1.0 O A:ALA22 5.0 23.4 1.0 C A:LEU353 5.0 28.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut with Bound Og


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 with Bound Og within 5.0Å range: probe atom residue distance (Å) B Occ A:Na517 b:26.7 occ:1.00 OD1 A:ASN27 2.4 24.3 1.0 O A:THR254 2.4 18.9 1.0 O A:ALA22 2.4 23.4 1.0 OD1 A:ASN286 2.6 21.2 1.0 OG1 A:THR254 2.6 24.6 1.0 OXT A:LEU519 2.6 23.7 1.0 C A:THR254 3.2 23.9 1.0 CA A:THR254 3.3 22.5 1.0 C A:ALA22 3.3 24.2 1.0 CG A:ASN27 3.3 27.1 1.0 CG A:ASN286 3.4 28.0 1.0 CB A:THR254 3.5 29.7 1.0 ND2 A:ASN286 3.6 25.9 1.0 ND2 A:ASN27 3.7 23.5 1.0 C A:LEU519 3.7 27.5 1.0 N A:LEU519 3.7 20.6 1.0 N A:GLY24 3.8 22.6 1.0 CA A:VAL23 3.9 21.6 1.0 N A:VAL23 4.0 23.3 1.0 OE2 A:GLU290 4.1 27.5 1.0 CA A:ALA22 4.2 22.2 1.0 CA A:LEU519 4.2 24.1 1.0 N A:ASN27 4.3 22.0 1.0 C A:VAL23 4.4 24.9 1.0 N A:LEU255 4.5 24.8 1.0 CB A:ALA22 4.5 23.5 1.0 CG2 A:THR254 4.5 26.4 1.0 O A:LEU519 4.6 23.8 1.0 CB A:ASN27 4.6 20.0 1.0 N A:THR254 4.6 19.5 1.0 O A:PHE253 4.7 23.0 1.0 C A:GLY26 4.8 29.0 1.0 CA A:ASN27 4.8 22.9 1.0 CB A:ASN286 4.8 25.9 1.0 CA A:GLY26 4.9 31.3 1.0 CA A:GLY24 4.9 20.7 1.0

M.Quick, A.M.L.Winther, L.Shi, P.Nissen, H.Weinstein, J.A.Javitch. Binding of An Octylglucoside Detergent Molecule in the Second Substrate (S2) Site of Leut Establishes An Inhibitor-Bound Conformation Proc.Natl.Acad.Sci.Usa V. 106 5563 2009.
ISSN: ISSN 0027-8424
PubMed: 19307590
DOI: 10.1073/PNAS.0811322106