Sodium in PDB 8ft5: Crystal Structure of Leut Soaked with Crown-5

The structure of Crystal Structure of Leut Soaked with Crown-5, PDB code: 8ft5 was solved by A.Karasawa, H.Liu, M.Quick, A.H.Hendrickson, Q.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.44 / 3.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.442, 87.383, 80.798, 90, 95.06, 90
R / Rfree (%)	27.1 / 31.3

The structure of Crystal Structure of Leut Soaked with Crown-5 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Leut Soaked with Crown-5 (pdb code 8ft5). 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 Soaked with Crown-5, PDB code: 8ft5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut Soaked with Crown-5


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 Soaked with Crown-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:112.9 occ:0.00 O A:ALA351 2.3 110.1 1.0 OG A:SER355 2.3 119.2 1.0 O A:VAL23 2.3 110.1 1.0 O A:GLY20 2.3 112.1 1.0 OG1 A:THR354 2.4 108.9 1.0 N A:SER355 2.5 112.1 1.0 CB A:SER355 2.9 116.6 1.0 CA A:SER355 3.1 112.7 1.0 C A:THR354 3.1 112.3 1.0 C A:VAL23 3.2 114.6 1.0 CA A:GLY24 3.3 119.8 1.0 C A:ALA351 3.4 109.3 1.0 C A:GLY20 3.5 114.4 1.0 CB A:THR354 3.5 109.2 1.0 N A:GLY24 3.7 118.4 1.0 CA A:THR354 3.7 110.8 1.0 O A:THR354 3.7 112.7 1.0 CA A:ALA351 4.0 105.7 1.0 N A:THR354 4.0 108.8 1.0 CA A:GLY20 4.2 113.8 1.0 O A:ASN21 4.4 116.6 1.0 CA A:VAL23 4.5 117.7 1.0 N A:GLY352 4.5 112.5 1.0 C A:SER355 4.5 111.4 1.0 N A:ASN21 4.6 114.9 1.0 O A:PHE350 4.6 112.6 1.0 N A:VAL23 4.6 116.7 1.0 C A:ASN21 4.7 115.4 1.0 CG2 A:THR354 4.7 106.6 1.0 C A:GLY24 4.7 120.7 1.0 CB A:ALA351 4.7 110.0 1.0 CA A:GLY352 4.8 112.4 1.0 OH A:TYR108 4.8 114.9 1.0 CA A:ASN21 4.8 114.2 1.0 C A:GLY352 4.8 108.9 1.0 C A:LEU353 4.9 104.7 1.0 C A:ALA22 5.0 118.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut Soaked with Crown-5


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 Soaked with Crown-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:121.3 occ:0.00 OD1 A:ASN27 2.4 119.6 1.0 OG1 A:THR254 2.4 119.5 1.0 O A:THR254 2.4 122.0 1.0 O A:LEU604 2.4 120.8 0.0 O A:ALA22 2.4 121.0 1.0 OD1 A:ASN286 2.7 124.8 1.0 CG A:ASN27 2.9 121.4 1.0 CA A:THR254 2.9 126.4 1.0 ND2 A:ASN27 3.0 125.1 1.0 N A:LEU604 3.0 120.8 0.0 C A:THR254 3.0 125.8 1.0 CB A:THR254 3.2 121.4 1.0 C A:LEU604 3.3 120.2 0.0 C A:ALA22 3.4 118.5 1.0 CG A:ASN286 3.6 123.3 1.0 CA A:LEU604 3.7 120.2 0.0 ND2 A:ASN286 3.7 124.0 1.0 N A:GLY24 3.9 118.4 1.0 N A:ASN27 4.1 121.6 1.0 CA A:VAL23 4.1 117.7 1.0 N A:VAL23 4.2 116.7 1.0 CB A:ASN27 4.2 118.9 1.0 OXT A:LEU604 4.3 119.3 0.0 N A:THR254 4.3 127.2 1.0 N A:LEU255 4.4 127.8 1.0 CA A:ALA22 4.4 117.5 1.0 OE2 A:GLU290 4.4 126.5 1.0 CG2 A:THR254 4.4 121.7 1.0 C A:VAL23 4.5 114.6 1.0 O A:PHE253 4.6 120.5 1.0 CA A:ASN27 4.6 118.0 1.0 C A:GLY26 4.6 123.4 1.0 CB A:ALA22 4.8 119.5 1.0 CA A:GLY26 4.8 120.2 1.0 CA A:GLY24 4.8 119.8 1.0 C A:PHE253 4.9 120.8 1.0 N A:GLY26 4.9 119.9 1.0 CB A:LEU604 5.0 120.1 0.0 CB A:ASN286 5.0 117.0 1.0

A.Karasawa, H.Liu, M.Quick, W.A.Hendrickson, Q.Liu. Crystallographic Characterization of Sodium Ions in A Bacterial Leucine/Sodium Symporter To Be Published.