Sodium in PDB 3f4i: Crystal Structure of Leut Bound to L-Selenomethionine and Sodium

The structure of Crystal Structure of Leut Bound to L-Selenomethionine and Sodium, PDB code: 3f4i 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)	31.11 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.777, 86.703, 81.692, 90.00, 95.85, 90.00
R / Rfree (%)	19.2 / 21.8

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Selenomethionine and Sodium (pdb code 3f4i). 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-Selenomethionine and Sodium, PDB code: 3f4i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to L-Selenomethionine 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-Selenomethionine and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:27.0 occ:1.00 O A:VAL23 2.4 23.9 1.0 O A:GLY20 2.5 26.6 1.0 O A:ALA351 2.5 22.6 1.0 OG1 A:THR354 2.6 25.7 1.0 OG A:SER355 2.7 24.5 1.0 N A:SER355 3.1 26.6 1.0 C A:VAL23 3.3 30.5 1.0 CB A:SER355 3.4 29.3 1.0 C A:THR354 3.4 25.0 1.0 C A:ALA351 3.5 25.3 1.0 CB A:THR354 3.6 28.3 1.0 C A:GLY20 3.6 28.9 1.0 CA A:SER355 3.6 25.9 1.0 CA A:GLY24 3.7 25.4 1.0 CA A:THR354 3.9 23.6 1.0 N A:GLY24 3.9 25.8 1.0 CA A:ALA351 4.0 25.4 1.0 O A:THR354 4.1 25.3 1.0 CA A:GLY20 4.1 26.8 1.0 N A:THR354 4.1 24.4 1.0 O A:ASN21 4.3 27.5 1.0 CA A:VAL23 4.3 26.9 1.0 N A:VAL23 4.4 26.0 1.0 O A:PHE350 4.5 24.9 1.0 C A:ASN21 4.6 31.7 1.0 N A:ASN21 4.7 25.8 1.0 C A:ALA22 4.7 32.4 1.0 N A:GLY352 4.7 21.4 1.0 O A:ALA22 4.7 24.1 1.0 O A:GLY352 4.8 26.1 1.0 CB A:VAL23 4.8 27.4 1.0 CB A:ALA351 4.9 25.3 1.0 C A:GLY352 4.9 23.0 1.0 CG2 A:THR354 4.9 24.9 1.0 CA A:ASN21 5.0 30.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to L-Selenomethionine 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-Selenomethionine and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na752 b:33.0 occ:1.00 OD1 A:ASN27 2.5 24.1 1.0 O A:THR254 2.6 23.6 1.0 O A:ALA22 2.6 24.1 1.0 OD1 A:ASN286 2.7 23.5 1.0 OG1 A:THR254 2.8 31.5 1.0 OXT A:MSE601 2.8 23.8 1.0 CG A:ASN27 3.3 30.8 1.0 C A:THR254 3.3 26.0 1.0 C A:ALA22 3.3 32.4 1.0 CA A:THR254 3.4 28.6 1.0 ND2 A:ASN27 3.5 28.1 1.0 CG A:ASN286 3.5 28.9 1.0 ND2 A:ASN286 3.6 25.8 1.0 CB A:THR254 3.7 30.9 1.0 N A:GLY24 3.7 25.8 1.0 N A:MSE601 3.8 23.8 1.0 CA A:VAL23 3.8 26.9 1.0 C A:MSE601 3.8 27.9 1.0 N A:VAL23 3.9 26.0 1.0 OE2 A:GLU290 4.0 28.4 1.0 C A:VAL23 4.2 30.5 1.0 N A:ASN27 4.2 25.4 1.0 CA A:ALA22 4.3 27.3 1.0 CA A:MSE601 4.4 31.0 1.0 CB A:ALA22 4.5 25.7 1.0 CB A:ASN27 4.5 24.5 1.0 N A:LEU255 4.6 25.8 1.0 CG2 A:THR254 4.7 27.4 1.0 N A:THR254 4.7 25.4 1.0 O A:MSE601 4.7 25.4 1.0 C A:GLY26 4.7 28.1 1.0 CA A:GLY24 4.7 25.4 1.0 CA A:ASN27 4.8 27.2 1.0 O A:PHE253 4.8 23.7 1.0 CA A:GLY26 4.8 28.6 1.0 CB A:ASN286 4.9 24.2 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