Sodium in PDB 6hjb: Xray Structure of Glic in Complex with Malonate

The structure of Xray Structure of Glic in Complex with Malonate, PDB code: 6hjb 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)	49.00 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.099, 133.366, 158.987, 90.00, 101.35, 90.00
R / Rfree (%)	18.2 / 19.9

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

Chlorine

(Cl)

11 atoms

The binding sites of Sodium atom in the Xray Structure of Glic in Complex with Malonate (pdb code 6hjb). 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 Malonate, PDB code: 6hjb:
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 Malonate


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 Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:82.5 occ:1.00 O A:ILE71 2.5 83.1 1.0 O A:PRO68 2.8 91.0 1.0 C A:ILE71 3.7 83.9 1.0 C A:PRO68 3.8 91.5 1.0 N A:ILE73 3.8 77.8 1.0 CA A:TRP72 4.2 77.7 1.0 CB A:ILE73 4.2 78.1 1.0 CD1 A:ILE73 4.3 89.8 1.0 CG2 A:VAL5 4.3 0.4 1.0 C A:TRP72 4.4 82.9 1.0 CA A:GLU69 4.4 87.3 1.0 N A:TRP72 4.4 79.1 1.0 O A:GLU69 4.4 89.8 1.0 CG1 A:ILE73 4.5 79.8 1.0 N A:GLU69 4.5 88.0 1.0 C A:GLU69 4.6 89.4 1.0 CA A:ILE73 4.6 75.6 1.0 N A:ILE71 4.8 84.1 1.0 CA A:ILE71 4.8 82.4 1.0 CA A:PRO68 4.9 87.2 1.0

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


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 Malonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:92.8 occ:1.00 O B:ILE71 2.3 73.5 1.0 O B:PRO68 2.7 84.9 1.0 C B:ILE71 3.4 72.4 1.0 N B:ILE73 3.6 64.5 1.0 C B:PRO68 3.8 83.9 1.0 CA B:TRP72 4.0 66.8 1.0 C B:TRP72 4.1 69.5 1.0 CB B:ILE73 4.1 64.4 1.0 CG1 B:ILE73 4.2 65.5 1.0 N B:TRP72 4.2 67.7 1.0 CD1 B:ILE73 4.2 74.3 1.0 O B:GLU69 4.3 87.5 1.0 CA B:GLU69 4.4 80.6 1.0 C B:GLU69 4.4 85.0 1.0 CA B:ILE73 4.5 62.7 1.0 N B:GLU69 4.5 80.2 1.0 N B:ILE71 4.5 70.9 1.0 CA B:ILE71 4.6 68.7 1.0 CA B:PRO68 4.9 78.2 1.0

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


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 Malonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:94.8 occ:1.00 O C:PRO68 2.4 93.2 1.0 O C:ILE71 2.6 80.7 1.0 C C:PRO68 3.4 92.5 1.0 C C:ILE71 3.8 82.9 1.0 CA C:GLU69 4.0 88.9 1.0 CD1 C:ILE73 4.0 73.9 1.0 N C:GLU69 4.1 89.1 1.0 O C:GLU69 4.2 94.7 1.0 C C:GLU69 4.2 93.2 1.0 N C:ILE73 4.3 73.2 1.0 CG1 C:ILE73 4.3 72.7 1.0 CB C:ILE73 4.4 72.1 1.0 CA C:PRO68 4.5 85.6 1.0 CG2 C:VAL5 4.5 0.9 1.0 CA C:TRP72 4.6 76.3 1.0 N C:ILE71 4.6 86.4 1.0 N C:TRP72 4.6 77.5 1.0 C C:TRP72 4.7 80.5 1.0 CA C:ILE71 4.8 84.1 1.0 CB C:PRO68 4.9 85.5 1.0

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


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 Malonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:97.7 occ:1.00 O D:ILE71 2.2 90.2 1.0 O D:PRO68 2.8 96.1 1.0 C D:ILE71 3.4 90.6 1.0 N D:ILE73 3.7 79.4 1.0 C D:PRO68 3.9 97.2 1.0 CA D:TRP72 4.0 85.7 1.0 CG2 D:VAL5 4.1 0.1 1.0 N D:TRP72 4.1 86.7 1.0 C D:TRP72 4.2 87.5 1.0 CD1 D:ILE73 4.2 80.1 1.0 CB D:ILE73 4.3 78.4 1.0 CG1 D:ILE73 4.3 78.5 1.0 O D:GLU69 4.3 96.4 1.0 CA D:GLU69 4.4 94.0 1.0 C D:GLU69 4.5 95.7 1.0 N D:GLU69 4.5 93.9 1.0 N D:ILE71 4.5 88.8 1.0 CA D:ILE71 4.6 87.2 1.0 CA D:ILE73 4.6 76.5 1.0 CB D:VAL5 4.9 0.1 1.0 CA D:PRO68 5.0 93.2 1.0

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


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 Malonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na408 b:85.6 occ:1.00 CG D:GLU177 3.6 88.7 1.0 N D:GLU177 3.7 82.3 1.0 CD1 D:LEU176 3.9 77.7 1.0 CD1 C:TYR23 3.9 73.3 1.0 O C:GLU147 4.0 83.4 1.0 CE1 C:TYR23 4.1 74.7 1.0 CA D:GLU177 4.1 82.8 1.0 CB D:GLU177 4.5 83.0 1.0 OE1 D:GLU177 4.6 94.8 1.0 CD D:GLU177 4.7 0.8 1.0 CG C:TYR23 4.7 70.1 1.0 C D:LEU176 4.8 83.0 1.0 CA C:LYS148 4.9 72.0 1.0 CA D:LEU176 5.0 74.9 1.0

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


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 Malonate within 5.0Å range: probe atom residue distance (Å) B Occ E:Na404 b:0.6 occ:1.00 O E:ILE71 2.7 82.5 1.0 O E:PRO68 2.8 93.9 1.0 C E:PRO68 3.8 93.9 1.0 C E:ILE71 3.9 84.4 1.0 N E:ILE73 4.1 74.5 1.0 CD1 E:ILE73 4.2 75.7 1.0 CA E:GLU69 4.3 93.6 1.0 N E:GLU69 4.4 92.9 1.0 CG1 E:ILE73 4.4 73.7 1.0 CB E:ILE73 4.4 73.2 1.0 CG2 E:VAL5 4.4 0.6 1.0 O E:GLU69 4.4 96.9 1.0 CA E:TRP72 4.5 79.3 1.0 C E:GLU69 4.5 95.4 1.0 C E:TRP72 4.6 81.6 1.0 N E:TRP72 4.6 80.1 1.0 CA E:ILE73 4.8 72.3 1.0 CA E:PRO68 4.8 85.4 1.0 N E:ILE71 4.9 85.5 1.0

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