Sodium in PDB 6hpp: X-Ray Structure of Glic in Complex with Propionate

The structure of X-Ray Structure of Glic in Complex with Propionate, PDB code: 6hpp was solved by Z.Fourati, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.690, 133.730, 158.890, 90.00, 101.38, 90.00
R / Rfree (%)	19.4 / 20.1

The structure of X-Ray Structure of Glic in Complex with Propionate also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the X-Ray Structure of Glic in Complex with Propionate (pdb code 6hpp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the X-Ray Structure of Glic in Complex with Propionate, PDB code: 6hpp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the X-Ray Structure of Glic in Complex with Propionate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Glic in Complex with Propionate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:0.5 occ:1.00 O A:ILE71 2.9 0.4 1.0 O A:PRO68 3.4 0.7 1.0 N A:ILE73 3.5 0.3 1.0 CA A:TRP72 3.8 0.3 1.0 C A:ILE71 3.9 0.9 1.0 C A:TRP72 4.1 0.5 1.0 CG2 A:VAL5 4.3 0.8 1.0 N A:TRP72 4.3 0.0 1.0 CB A:ILE73 4.3 0.1 1.0 CA A:ILE73 4.4 0.7 1.0 C A:PRO68 4.5 0.8 1.0 CD1 A:ILE73 4.6 0.4 1.0 O A:ILE73 4.6 0.9 1.0 CG1 A:ILE73 4.7 0.5 1.0 CB A:VAL5 4.9 0.7 1.0 O A:GLU69 4.9 0.1 1.0 CA A:GLU69 4.9 0.8 1.0

Sodium binding site 2 out of 6 in the X-Ray Structure of Glic in Complex with Propionate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Glic in Complex with Propionate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:0.8 occ:1.00 OG1 B:THR226 3.7 95.6 1.0 OG1 C:THR226 3.9 0.8 1.0 OG1 A:THR226 4.0 0.0 1.0 CG2 B:THR226 4.5 93.3 1.0 OG1 E:THR226 4.6 97.8 1.0 OG1 D:THR226 4.6 0.9 1.0 CG2 A:THR226 4.7 86.5 1.0 CB B:THR226 4.7 98.3 1.0 CG2 C:THR226 4.9 95.4 1.0 CB A:THR226 5.0 94.3 1.0

Sodium binding site 3 out of 6 in the X-Ray Structure of Glic in Complex with Propionate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of Glic in Complex with Propionate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:0.6 occ:1.00 O B:ILE71 2.5 0.7 1.0 N B:ILE73 3.4 0.9 1.0 C B:ILE71 3.5 0.8 1.0 CA B:TRP72 3.5 0.5 1.0 O B:PRO68 3.5 0.4 1.0 N B:TRP72 3.8 0.3 1.0 C B:TRP72 3.9 0.8 1.0 CG2 B:VAL5 4.0 0.7 1.0 CB B:ILE73 4.5 0.9 1.0 CB B:VAL5 4.5 0.3 1.0 CA B:ILE73 4.5 0.6 1.0 C B:PRO68 4.6 0.1 1.0 CG1 B:VAL5 4.6 0.7 1.0 O B:GLU69 4.6 0.7 1.0 CB B:TRP72 4.7 0.4 1.0 CD1 B:ILE73 4.7 0.8 1.0 CG1 B:ILE73 4.7 0.8 1.0 O B:ILE73 4.7 0.3 1.0 CA B:ILE71 4.8 0.0 1.0 C B:GLU69 4.9 0.9 1.0 CA B:GLU69 4.9 0.8 1.0 N B:ILE71 5.0 0.1 1.0 O B:TRP72 5.0 0.8 1.0

Sodium binding site 4 out of 6 in the X-Ray Structure of Glic in Complex with Propionate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of Glic in Complex with Propionate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:0.5 occ:1.00 O C:ILE71 2.6 0.4 1.0 O C:PRO68 3.0 0.3 1.0 C C:ILE71 3.6 0.6 1.0 N C:ILE73 3.7 0.8 1.0 CA C:TRP72 3.9 0.1 1.0 C C:PRO68 4.1 0.3 1.0 C C:TRP72 4.2 0.8 1.0 N C:TRP72 4.2 0.4 1.0 CD1 C:ILE73 4.4 0.3 1.0 CB C:ILE73 4.4 0.1 1.0 CG2 C:VAL5 4.4 0.9 1.0 CA C:GLU69 4.5 0.8 1.0 O C:GLU69 4.5 0.8 1.0 CG1 C:ILE73 4.6 0.2 1.0 CA C:ILE73 4.6 0.6 1.0 C C:GLU69 4.6 0.5 1.0 N C:GLU69 4.7 0.5 1.0 CA C:ILE71 4.9 0.6 1.0 N C:ILE71 4.9 0.5 1.0 CB C:VAL5 5.0 0.1 1.0 O C:ILE73 5.0 0.1 1.0

Sodium binding site 5 out of 6 in the X-Ray Structure of Glic in Complex with Propionate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of Glic in Complex with Propionate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na402 b:0.8 occ:1.00 O D:ILE71 3.0 0.4 1.0 N D:ILE73 3.2 0.7 1.0 CA D:TRP72 3.6 0.0 1.0 O D:PRO68 3.8 0.2 1.0 C D:TRP72 3.9 0.5 1.0 C D:ILE71 3.9 0.2 1.0 N D:TRP72 4.2 0.9 1.0 CA D:ILE73 4.2 0.1 1.0 CB D:ILE73 4.2 0.1 1.0 O D:ILE73 4.3 0.0 1.0 CG2 D:VAL5 4.3 1.0 1.0 CG1 D:ILE73 4.7 0.7 1.0 CD1 D:ILE73 4.7 0.7 1.0 CB D:TRP72 4.8 0.6 1.0 C D:ILE73 4.8 0.1 1.0 CB D:VAL5 4.8 0.1 1.0 C D:PRO68 4.9 0.1 1.0 CD1 D:TRP72 4.9 0.7 1.0 CG D:TRP72 5.0 0.3 1.0

Sodium binding site 6 out of 6 in the X-Ray Structure of Glic in Complex with Propionate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of Glic in Complex with Propionate within 5.0Å range: probe atom residue distance (Å) B Occ E:Na402 b:0.3 occ:1.00 O E:ILE71 2.8 0.1 1.0 O E:PRO68 3.4 1.0 1.0 N E:ILE73 3.6 0.5 1.0 CA E:TRP72 3.8 1.0 1.0 C E:ILE71 3.8 0.5 1.0 C E:TRP72 4.1 0.9 1.0 N E:TRP72 4.2 0.3 1.0 CG2 E:VAL5 4.2 0.8 1.0 CB E:ILE73 4.5 0.6 1.0 C E:PRO68 4.5 0.7 1.0 CA E:ILE73 4.6 1.0 1.0 CD1 E:ILE73 4.6 0.1 1.0 CG1 E:ILE73 4.8 0.1 1.0 O E:ILE73 4.8 0.7 1.0 CB E:VAL5 4.8 0.6 1.0 O E:GLU69 4.8 0.1 1.0 CA E:GLU69 4.8 0.4 1.0 C E:GLU69 5.0 0.8 1.0 CG1 E:VAL5 5.0 0.2 1.0 CB E:TRP72 5.0 0.4 1.0

Z.Fourati, M.Delarue. Xray Structure of Glic in Complex with Propionate To Be Published.