Sodium in PDB 3f3a: Crystal Structure of Leut Bound to L-Tryptophan and Sodium

The structure of Crystal Structure of Leut Bound to L-Tryptophan and Sodium, PDB code: 3f3a 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)	48.23 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.566, 85.218, 82.274, 90.00, 93.33, 90.00
R / Rfree (%)	19.8 / 22.9

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Tryptophan and Sodium (pdb code 3f3a). 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 L-Tryptophan and Sodium, PDB code: 3f3a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to L-Tryptophan 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 L-Tryptophan and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:27.2 occ:1.00 O A:VAL23 2.3 27.1 1.0 OG A:SER355 2.3 26.8 1.0 O A:GLY20 2.3 30.6 1.0 O A:ALA351 2.3 26.2 1.0 OG1 A:THR354 2.4 29.9 1.0 N A:SER355 3.1 29.1 1.0 CB A:SER355 3.3 28.3 1.0 C A:VAL23 3.4 31.4 1.0 C A:THR354 3.4 25.8 1.0 C A:ALA351 3.5 29.3 1.0 C A:GLY20 3.5 33.5 1.0 CB A:THR354 3.5 27.1 1.0 CA A:SER355 3.6 29.4 1.0 CA A:THR354 3.8 24.6 1.0 O A:THR354 4.0 26.9 1.0 O A:ASN21 4.0 29.9 1.0 CA A:ALA351 4.1 27.1 1.0 CA A:GLY24 4.1 30.1 1.0 N A:GLY24 4.1 28.7 1.0 N A:THR354 4.1 28.0 1.0 CA A:GLY20 4.2 30.0 1.0 C A:ASN21 4.3 29.7 1.0 CA A:VAL23 4.3 21.9 1.0 N A:VAL23 4.3 29.7 1.0 O A:PHE350 4.4 27.5 1.0 N A:ASN21 4.4 31.2 1.0 O A:GLY352 4.5 30.1 1.0 CA A:ASN21 4.5 29.4 1.0 N A:GLY352 4.5 24.2 1.0 C A:GLY352 4.7 30.7 1.0 CB A:VAL23 4.7 34.1 1.0 CA A:GLY352 4.8 23.9 1.0 C A:ALA22 4.8 33.1 1.0 CG2 A:THR354 4.8 23.9 1.0 CB A:ALA351 4.9 26.5 1.0 N A:ALA22 5.0 30.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to L-Tryptophan 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 L-Tryptophan and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na752 b:28.9 occ:1.00 OD1 A:ASN286 2.4 29.9 1.0 O A:ALA22 2.4 26.2 1.0 O A:THR254 2.5 34.8 1.0 OXT A:TRP601 2.6 28.1 1.0 OD1 A:ASN27 2.6 36.4 1.0 OG1 A:THR254 2.7 33.2 1.0 C A:ALA22 3.2 33.1 1.0 C A:THR254 3.2 28.9 1.0 CG A:ASN286 3.3 34.7 1.0 CA A:THR254 3.3 30.2 1.0 CG A:ASN27 3.4 35.9 1.0 C A:TRP601 3.4 33.9 1.0 N A:TRP601 3.5 25.5 1.0 ND2 A:ASN286 3.6 33.2 1.0 CB A:THR254 3.6 31.3 1.0 ND2 A:ASN27 3.6 33.9 1.0 CA A:VAL23 3.8 21.9 1.0 N A:VAL23 3.8 29.7 1.0 O A:HOH539 3.9 31.8 1.0 N A:GLY24 4.0 28.7 1.0 CA A:TRP601 4.0 27.3 1.0 CA A:ALA22 4.1 31.9 1.0 OE1 A:GLU290 4.2 37.1 1.0 CB A:ALA22 4.3 28.8 1.0 O A:TRP601 4.3 33.2 1.0 C A:VAL23 4.4 31.4 1.0 CG2 A:THR254 4.5 30.8 1.0 N A:LEU255 4.5 30.3 1.0 CB A:ASN286 4.6 25.1 1.0 N A:THR254 4.7 32.2 1.0 CB A:ASN27 4.7 32.7 1.0 N A:ASN27 4.8 30.2 1.0 O A:PHE253 4.8 27.8 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