Sodium in PDB 6hj3: Xray Structure of Glic in Complex with Fumarate

The structure of Xray Structure of Glic in Complex with Fumarate, PDB code: 6hj3 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 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.510, 132.650, 159.860, 90.00, 102.08, 90.00
R / Rfree (%)	19.7 / 21.6

The structure of Xray Structure of Glic in Complex with Fumarate also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Sodium atom in the Xray Structure of Glic in Complex with Fumarate (pdb code 6hj3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Xray Structure of Glic in Complex with Fumarate, PDB code: 6hj3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Xray Structure of Glic in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xray Structure of Glic in Complex with Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:0.4 occ:1.00 O A:ILE71 2.6 0.4 1.0 O A:PRO68 3.2 0.9 1.0 N A:ILE73 3.5 0.3 1.0 C A:ILE71 3.8 1.0 1.0 CA A:TRP72 4.0 1.0 1.0 CB A:ILE73 4.0 0.1 1.0 C A:TRP72 4.1 0.6 1.0 C A:PRO68 4.2 0.2 1.0 CD1 A:ILE73 4.3 0.7 1.0 CA A:ILE73 4.3 97.9 1.0 CG1 A:ILE73 4.3 0.5 1.0 N A:TRP72 4.3 0.3 1.0 O A:GLU69 4.6 0.1 1.0 O A:ILE73 4.6 95.0 1.0 CA A:GLU69 4.7 0.0 1.0 CG2 A:VAL5 4.8 0.1 1.0 N A:GLU69 4.8 0.2 1.0 C A:GLU69 4.9 0.0 1.0 CB A:VAL5 5.0 0.5 1.0

Sodium binding site 2 out of 6 in the Xray Structure of Glic in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xray Structure of Glic in Complex with Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:0.8 occ:1.00 O A:HOH501 2.3 0.7 1.0 O D:HOH509 3.4 0.0 1.0 OG1 C:THR226 3.5 81.1 1.0 OG1 B:THR226 3.9 80.0 1.0 O E:HOH503 4.0 86.2 1.0 OG1 D:THR226 4.0 80.0 1.0 OG1 A:THR226 4.4 78.5 1.0 OG1 E:THR226 4.5 78.9 1.0 CG2 C:THR226 4.5 80.5 1.0 CB C:THR226 4.6 79.2 1.0 CG2 B:THR226 4.7 69.0 1.0 CB B:THR226 4.9 72.8 1.0

Sodium binding site 3 out of 6 in the Xray Structure of Glic in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Xray Structure of Glic in Complex with Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:0.3 occ:1.00 O B:ILE71 2.4 98.7 1.0 O B:PRO68 2.9 0.2 1.0 N B:ILE73 3.3 92.8 1.0 C B:ILE71 3.6 0.4 1.0 CB B:ILE73 3.7 90.4 1.0 CD1 B:ILE73 3.9 0.9 1.0 C B:TRP72 3.9 99.6 1.0 CA B:TRP72 3.9 97.2 1.0 CG1 B:ILE73 4.0 92.2 1.0 C B:PRO68 4.0 0.5 1.0 CA B:ILE73 4.0 88.7 1.0 N B:TRP72 4.2 97.7 1.0 O B:ILE73 4.6 89.9 1.0 O B:GLU69 4.7 0.3 1.0 CA B:GLU69 4.7 0.1 1.0 N B:GLU69 4.7 0.9 1.0 CA B:ILE71 4.8 98.3 1.0 C B:ILE73 4.8 90.3 1.0 C B:GLU69 4.9 0.8 1.0 N B:ILE71 4.9 0.6 1.0 O B:TRP72 4.9 0.2 1.0 CG2 B:ILE73 4.9 88.4 1.0 CA B:PRO68 5.0 0.9 1.0

Sodium binding site 4 out of 6 in the Xray Structure of Glic in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Xray Structure of Glic in Complex with Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na405 b:97.6 occ:1.00 O C:ILE71 2.6 0.0 1.0 O C:PRO68 3.1 0.8 1.0 N C:ILE73 3.5 0.0 1.0 C C:ILE71 3.8 0.3 1.0 CB C:ILE73 3.8 0.0 1.0 CA C:TRP72 4.1 0.6 1.0 CD1 C:ILE73 4.1 0.5 1.0 C C:PRO68 4.1 1.0 1.0 C C:TRP72 4.1 0.2 1.0 CG1 C:ILE73 4.2 0.7 1.0 CA C:ILE73 4.2 98.3 1.0 N C:TRP72 4.4 0.6 1.0 O C:ILE73 4.7 0.1 1.0 CA C:GLU69 4.7 0.9 1.0 O C:GLU69 4.7 0.9 1.0 N C:GLU69 4.8 0.9 1.0 C C:GLU69 5.0 0.6 1.0

Sodium binding site 5 out of 6 in the Xray Structure of Glic in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Xray Structure of Glic in Complex with Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:0.1 occ:1.00 O D:ILE71 2.5 0.0 1.0 O D:PRO68 3.1 0.9 1.0 N D:ILE73 3.5 0.6 1.0 C D:ILE71 3.7 0.3 1.0 CA D:TRP72 3.9 0.0 1.0 CB D:ILE73 4.1 99.6 1.0 C D:TRP72 4.1 0.7 1.0 C D:PRO68 4.2 0.3 1.0 N D:TRP72 4.3 0.4 1.0 CD1 D:ILE73 4.4 0.1 1.0 CA D:ILE73 4.4 97.2 1.0 CG1 D:ILE73 4.4 0.1 1.0 O D:GLU69 4.5 0.6 1.0 CA D:GLU69 4.6 0.6 1.0 CG2 D:VAL5 4.8 0.7 1.0 O D:ILE73 4.8 98.0 1.0 C D:GLU69 4.8 0.3 1.0 N D:GLU69 4.8 0.9 1.0 CB D:VAL5 4.9 0.6 1.0 CA D:ILE71 4.9 0.7 1.0 N D:ILE71 5.0 0.6 1.0

Sodium binding site 6 out of 6 in the Xray Structure of Glic in Complex with Fumarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Xray Structure of Glic in Complex with Fumarate within 5.0Å range: probe atom residue distance (Å) B Occ E:Na405 b:0.0 occ:1.00 O E:ILE71 2.5 0.3 1.0 O E:PRO68 2.6 0.2 1.0 C E:PRO68 3.6 0.5 1.0 C E:ILE71 3.7 0.2 1.0 N E:ILE73 3.9 98.7 1.0 CD1 E:ILE73 4.1 0.7 1.0 CA E:GLU69 4.2 0.4 1.0 CB E:ILE73 4.2 97.5 1.0 N E:GLU69 4.2 0.9 1.0 O E:GLU69 4.3 0.1 1.0 CG1 E:ILE73 4.3 98.7 1.0 CA E:TRP72 4.3 0.8 1.0 C E:GLU69 4.4 0.8 1.0 C E:TRP72 4.4 0.3 1.0 N E:TRP72 4.5 0.4 1.0 CA E:PRO68 4.7 0.8 1.0 CA E:ILE73 4.7 95.0 1.0 N E:ILE71 4.7 0.9 1.0 CA E:ILE71 4.8 0.5 1.0

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