Sodium in PDB 3f3d: Crystal Structure of Leut Bound to L-Methionine and Sodium

The structure of Crystal Structure of Leut Bound to L-Methionine and Sodium, PDB code: 3f3d 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)	43.96 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.333, 86.636, 81.166, 90.00, 95.57, 90.00
R / Rfree (%)	19.7 / 22.4

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Methionine and Sodium (pdb code 3f3d). 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-Methionine and Sodium, PDB code: 3f3d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to L-Methionine 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-Methionine and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:29.9 occ:1.00 O A:VAL23 2.1 34.5 1.0 O A:GLY20 2.2 37.4 1.0 O A:ALA351 2.4 33.1 1.0 OG1 A:THR354 2.4 32.3 1.0 OG A:SER355 2.6 32.6 1.0 N A:SER355 3.1 32.8 1.0 C A:VAL23 3.1 34.5 1.0 C A:GLY20 3.4 37.0 1.0 CB A:THR354 3.4 32.7 1.0 C A:ALA351 3.5 33.2 1.0 C A:THR354 3.5 32.5 1.0 CB A:SER355 3.5 32.7 1.0 CA A:GLY24 3.7 34.6 1.0 CA A:SER355 3.7 32.8 1.0 N A:GLY24 3.8 34.4 1.0 CA A:THR354 3.8 32.6 1.0 CA A:ALA351 4.0 33.3 1.0 CA A:GLY20 4.0 36.9 1.0 N A:THR354 4.2 32.5 1.0 O A:THR354 4.2 32.5 1.0 CA A:VAL23 4.2 34.5 1.0 N A:VAL23 4.3 34.7 1.0 O A:ASN21 4.4 36.4 1.0 N A:ASN21 4.5 36.6 1.0 O A:PHE350 4.5 34.2 1.0 C A:ASN21 4.6 36.2 1.0 N A:GLY352 4.6 33.0 1.0 CG2 A:THR354 4.7 32.6 1.0 CB A:VAL23 4.7 34.6 1.0 CA A:ASN21 4.8 36.4 1.0 CB A:ALA351 4.8 33.1 1.0 O A:GLY352 4.8 33.5 1.0 C A:GLY352 4.9 33.0 1.0 C A:ALA22 4.9 34.9 1.0 CA A:GLY352 4.9 32.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to L-Methionine 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-Methionine and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na752 b:34.8 occ:1.00 O A:ALA22 2.1 34.7 1.0 OD1 A:ASN27 2.2 34.3 1.0 O A:THR254 2.4 35.7 1.0 OD1 A:ASN286 2.6 40.0 1.0 OG1 A:THR254 2.7 35.4 1.0 OXT A:MET601 2.8 35.5 1.0 C A:ALA22 3.1 34.9 1.0 CG A:ASN27 3.2 36.0 1.0 C A:THR254 3.2 35.8 1.0 CA A:THR254 3.4 35.8 1.0 CG A:ASN286 3.6 41.4 1.0 CB A:THR254 3.6 35.8 1.0 ND2 A:ASN27 3.6 35.9 1.0 N A:MET601 3.7 35.8 1.0 N A:GLY24 3.7 34.4 1.0 C A:MET601 3.8 35.7 1.0 CA A:VAL23 3.8 34.5 1.0 N A:VAL23 3.8 34.7 1.0 ND2 A:ASN286 3.9 40.3 1.0 OE2 A:GLU290 4.1 45.2 1.0 CA A:ALA22 4.1 35.1 1.0 N A:ASN27 4.3 36.2 1.0 C A:VAL23 4.3 34.5 1.0 CA A:MET601 4.3 35.7 1.0 CB A:ALA22 4.5 34.7 1.0 N A:LEU255 4.5 35.9 1.0 CB A:ASN27 4.5 36.2 1.0 CG2 A:THR254 4.6 35.3 1.0 O A:MET601 4.7 35.6 1.0 N A:THR254 4.7 35.9 1.0 O A:PHE253 4.8 35.9 1.0 C A:GLY26 4.8 35.9 1.0 CA A:ASN27 4.8 36.5 1.0 CA A:GLY26 4.8 35.8 1.0 CA A:GLY24 4.8 34.6 1.0 CB A:ASN286 5.0 41.6 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