Sodium in PDB 3f4j: Crystal Structure of Leut Bound to Glycine and Sodium

The structure of Crystal Structure of Leut Bound to Glycine and Sodium, PDB code: 3f4j was solved by S.K.Singh, C.L.Piscitelli, A.Yamashita, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.94 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.060, 86.550, 81.450, 90.00, 95.27, 90.00
R / Rfree (%)	20.4 / 22.7

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to Glycine and Sodium (pdb code 3f4j). 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 Bound to Glycine and Sodium, PDB code: 3f4j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to Glycine and Sodium


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 Bound to Glycine and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:44.6 occ:1.00 O A:ALA351 2.4 35.0 1.0 OG1 A:THR354 2.5 38.9 1.0 O A:GLY20 2.6 39.3 1.0 O A:VAL23 2.6 40.2 1.0 N A:SER355 2.8 40.0 1.0 OG A:SER355 2.9 36.3 1.0 C A:THR354 3.1 36.4 1.0 CB A:SER355 3.3 41.9 1.0 CB A:THR354 3.3 41.1 1.0 C A:ALA351 3.4 38.3 1.0 CA A:SER355 3.4 37.3 1.0 CA A:THR354 3.5 37.1 1.0 C A:VAL23 3.6 35.4 1.0 C A:GLY20 3.7 39.4 1.0 N A:THR354 3.7 36.1 1.0 O A:THR354 3.8 35.5 1.0 CA A:GLY24 3.9 36.8 1.0 CA A:ALA351 3.9 36.9 1.0 O A:PHE350 4.1 36.0 1.0 N A:GLY24 4.2 36.2 1.0 CA A:GLY20 4.3 34.0 1.0 O A:GLY352 4.3 39.2 1.0 N A:GLY352 4.4 37.9 1.0 C A:GLY352 4.4 37.9 1.0 O A:ASN21 4.6 36.0 1.0 C A:LEU353 4.7 37.4 1.0 CG2 A:THR354 4.7 38.6 1.0 CA A:GLY352 4.7 35.5 1.0 N A:ASN21 4.8 39.4 1.0 CA A:VAL23 4.8 37.7 1.0 N A:VAL23 4.8 38.2 1.0 C A:ASN21 4.8 35.2 1.0 C A:SER355 4.9 36.1 1.0 CB A:ALA351 4.9 36.7 1.0 N A:LEU353 4.9 35.5 1.0 CA A:ASN21 5.0 38.2 1.0 N A:ALA351 5.0 35.9 1.0 C A:PHE350 5.0 36.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to Glycine and Sodium


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 Bound to Glycine and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na752 b:52.3 occ:1.00 OD1 A:ASN27 2.6 42.6 1.0 O A:ALA22 2.7 37.6 1.0 OG1 A:THR254 2.7 44.4 1.0 O A:THR254 2.8 36.7 1.0 OXT A:GLY601 2.8 33.3 1.0 OD1 A:ASN286 2.9 35.9 1.0 CG A:ASN27 3.2 46.8 1.0 CA A:THR254 3.3 38.3 1.0 ND2 A:ASN27 3.3 39.0 1.0 C A:THR254 3.4 36.8 1.0 CB A:THR254 3.6 39.6 1.0 C A:ALA22 3.6 39.0 1.0 CG A:ASN286 3.7 38.8 1.0 ND2 A:ASN286 3.7 35.8 1.0 OE2 A:GLU290 3.8 40.0 1.0 C A:GLY601 3.8 36.6 1.0 N A:GLY24 3.8 36.2 1.0 N A:GLY601 3.9 34.2 1.0 N A:ASN27 3.9 39.0 1.0 CA A:VAL23 4.0 37.7 1.0 N A:VAL23 4.3 38.2 1.0 C A:GLY26 4.4 39.5 1.0 CA A:GLY601 4.4 34.5 1.0 C A:VAL23 4.4 35.4 1.0 CA A:GLY26 4.4 43.3 1.0 CB A:ASN27 4.4 40.5 1.0 CA A:ASN27 4.5 40.5 1.0 N A:THR254 4.6 37.5 1.0 O A:GLY601 4.6 39.8 1.0 CA A:ALA22 4.7 33.2 1.0 CG2 A:THR254 4.7 40.8 1.0 N A:LEU255 4.7 40.0 1.0 O A:PHE253 4.7 36.2 1.0 CD A:GLU290 4.9 42.8 1.0 N A:GLY26 4.9 42.2 1.0 CA A:GLY24 4.9 36.8 1.0 O A:GLY24 5.0 35.0 1.0

S.K.Singh, C.L.Piscitelli, A.Yamashita, E.Gouaux. A Competitive Inhibitor Traps Leut in An Open-to-Out Conformation. Science V. 322 1655 2008.
ISSN: ISSN 0036-8075
PubMed: 19074341
DOI: 10.1126/SCIENCE.1166777