Sodium in PDB 6hjz: Xray Structure of Glic in Complex with Succinate

The structure of Xray Structure of Glic in Complex with Succinate, PDB code: 6hjz 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)	12.00 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.713, 132.489, 320.565, 90.00, 102.23, 90.00
R / Rfree (%)	21.7 / 22.7

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

Chlorine

(Cl)

14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Xray Structure of Glic in Complex with Succinate (pdb code 6hjz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Xray Structure of Glic in Complex with Succinate, PDB code: 6hjz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in the Xray Structure of Glic in Complex with Succinate


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 Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:90.7 occ:1.00 O A:ILE71 3.1 92.7 1.0 N A:ILE73 3.1 83.3 1.0 CA A:TRP72 3.6 86.7 1.0 C A:TRP72 3.8 88.8 1.0 O A:ILE73 3.9 82.9 1.0 CB A:ILE73 4.0 84.6 1.0 CA A:ILE73 4.0 81.8 1.0 C A:ILE71 4.0 93.5 1.0 O A:PRO68 4.2 0.2 1.0 N A:TRP72 4.3 88.2 1.0 CG1 A:ILE73 4.4 85.6 1.0 C A:ILE73 4.4 83.8 1.0 CD1 A:ILE73 4.7 93.2 1.0 CD1 A:TRP72 4.7 88.7 1.0 CB A:TRP72 4.8 85.7 1.0 CG A:TRP72 4.9 85.8 1.0 O A:TRP72 4.9 88.9 1.0

Sodium binding site 2 out of 12 in the Xray Structure of Glic in Complex with Succinate


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 Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:0.3 occ:1.00 OG1 B:THR226 3.8 73.1 1.0 OG1 A:THR226 4.0 71.2 1.0 OG1 C:THR226 4.1 72.2 1.0 OG1 E:THR226 4.5 73.8 1.0 OG1 D:THR226 4.6 72.7 1.0 CG2 A:THR226 4.8 69.3 1.0 CG2 B:THR226 4.9 70.3 1.0 CB B:THR226 5.0 72.4 1.0

Sodium binding site 3 out of 12 in the Xray Structure of Glic in Complex with Succinate


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 Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:96.7 occ:1.00 O B:ILE71 2.4 79.1 1.0 O B:PRO68 3.1 88.8 1.0 C B:ILE71 3.5 79.6 1.0 N B:ILE73 3.6 73.3 1.0 CA B:TRP72 3.9 73.9 1.0 C B:TRP72 4.1 77.8 1.0 N B:TRP72 4.1 74.8 1.0 C B:PRO68 4.1 89.5 1.0 CB B:ILE73 4.2 74.6 1.0 CD1 B:ILE73 4.2 84.0 1.0 CG1 B:ILE73 4.3 75.4 1.0 CA B:ILE73 4.5 71.9 1.0 O B:GLU69 4.7 90.0 1.0 CA B:GLU69 4.7 87.0 1.0 CA B:ILE71 4.7 77.6 1.0 N B:ILE71 4.8 78.9 1.0 O B:ILE73 4.8 74.5 1.0 N B:GLU69 4.8 86.6 1.0 C B:GLU69 4.8 89.7 1.0 CG1 B:VAL5 4.8 0.8 1.0

Sodium binding site 4 out of 12 in the Xray Structure of Glic in Complex with Succinate


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 Succinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na406 b:86.4 occ:1.00 O C:ILE71 2.5 84.7 1.0 O C:PRO68 3.0 93.0 1.0 C C:ILE71 3.6 86.0 1.0 N C:ILE73 3.7 78.0 1.0 CA C:TRP72 4.0 80.5 1.0 C C:PRO68 4.0 93.8 1.0 CD1 C:ILE73 4.1 85.7 1.0 CB C:ILE73 4.1 79.1 1.0 CG1 C:ILE73 4.2 79.7 1.0 C C:TRP72 4.2 82.8 1.0 N C:TRP72 4.3 81.6 1.0 CA C:ILE73 4.5 76.6 1.0 CA C:GLU69 4.7 91.1 1.0 N C:GLU69 4.7 90.8 1.0 O C:GLU69 4.8 94.5 1.0 CA C:ILE71 4.8 84.5 1.0 N C:ILE71 4.8 85.8 1.0 C C:GLU69 4.9 94.5 1.0 O C:ILE73 4.9 79.3 1.0

Sodium binding site 5 out of 12 in the Xray Structure of Glic in Complex with Succinate


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 Succinate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:0.7 occ:1.00 N D:ILE73 3.1 83.4 1.0 O1 D:SIN407 3.3 79.0 0.5 O D:ILE73 3.5 83.0 1.0 O D:ILE71 3.6 92.1 1.0 CA D:TRP72 3.8 86.3 1.0 C D:TRP72 3.9 88.3 1.0 CA D:ILE73 3.9 82.0 1.0 CB D:ILE73 4.0 84.7 1.0 C1 D:SIN407 4.2 78.9 0.5 C D:ILE73 4.2 84.0 1.0 CD1 D:TRP72 4.4 88.4 1.0 C D:ILE71 4.5 93.0 1.0 N D:TRP72 4.6 87.8 1.0 CG1 D:ILE73 4.7 85.5 1.0 CG D:TRP72 4.7 85.5 1.0 CB D:TRP72 4.8 85.2 1.0 O D:PRO68 4.8 0.5 1.0 C2 D:SIN407 4.9 78.7 0.5 O2 D:SIN407 4.9 78.9 0.5

Sodium binding site 6 out of 12 in the Xray Structure of Glic in Complex with Succinate


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 Succinate within 5.0Å range: probe atom residue distance (Å) B Occ E:Na405 b:95.6 occ:1.00 O E:ILE71 2.5 91.0 1.0 O E:PRO68 3.1 0.9 1.0 N E:ILE73 3.6 81.8 1.0 C E:ILE71 3.6 91.6 1.0 CA E:TRP72 4.0 84.9 1.0 CB E:ILE73 4.0 83.0 1.0 CD1 E:ILE73 4.0 91.9 1.0 CG1 E:ILE73 4.1 83.9 1.0 C E:TRP72 4.1 86.9 1.0 C E:PRO68 4.1 0.5 1.0 N E:TRP72 4.2 86.3 1.0 CA E:ILE73 4.4 80.3 1.0 O E:ILE73 4.8 82.9 1.0 CA E:GLU69 4.8 0.6 1.0 CA E:ILE71 4.9 90.5 1.0 N E:GLU69 4.9 0.6 1.0 O E:GLU69 4.9 0.8 1.0 N E:ILE71 4.9 92.1 1.0 C E:GLU69 5.0 0.8 1.0

Sodium binding site 7 out of 12 in the Xray Structure of Glic in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Xray Structure of Glic in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ F:Na405 b:83.8 occ:1.00 O F:ILE71 2.5 66.6 1.0 O F:PRO68 2.7 77.4 1.0 C F:ILE71 3.7 67.4 1.0 C F:PRO68 3.8 78.1 1.0 N F:ILE73 3.9 59.5 1.0 O1 F:SIN409 3.9 61.1 0.5 CD1 F:ILE73 4.0 71.2 1.0 CG1 F:ILE73 4.1 62.4 1.0 CA F:TRP72 4.2 60.8 1.0 CB F:ILE73 4.2 61.5 1.0 C F:TRP72 4.3 63.5 1.0 N F:TRP72 4.4 62.4 1.0 CA F:GLU69 4.4 74.4 1.0 N F:GLU69 4.5 74.5 1.0 O F:GLU69 4.6 77.1 1.0 C F:GLU69 4.6 77.1 1.0 CA F:ILE73 4.7 58.6 1.0 O2 F:SIN409 4.7 60.0 0.5 C1 F:SIN409 4.7 60.3 0.5 N F:ILE71 4.7 68.1 1.0 CA F:ILE71 4.8 66.5 1.0 CA F:PRO68 4.9 75.0 1.0

Sodium binding site 8 out of 12 in the Xray Structure of Glic in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Xray Structure of Glic in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ G:Na406 b:86.4 occ:1.00 O G:ILE71 2.3 66.7 1.0 O G:PRO68 2.9 76.2 1.0 C G:ILE71 3.5 66.7 1.0 N G:ILE73 3.8 58.2 1.0 C G:PRO68 4.0 76.4 1.0 CA G:TRP72 4.0 60.2 1.0 CD1 G:ILE73 4.2 68.8 1.0 N G:TRP72 4.2 61.6 1.0 C G:TRP72 4.2 62.4 1.0 CG1 G:ILE73 4.3 59.4 1.0 CB G:ILE73 4.3 58.3 1.0 CA G:GLU69 4.5 75.0 1.0 O G:GLU69 4.5 78.8 1.0 N G:GLU69 4.6 73.7 1.0 N G:ILE71 4.6 66.2 1.0 CA G:ILE73 4.6 55.9 1.0 C G:GLU69 4.6 78.1 1.0 CA G:ILE71 4.6 64.5 1.0 CG1 G:VAL5 4.9 1.0 1.0

Sodium binding site 9 out of 12 in the Xray Structure of Glic in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Xray Structure of Glic in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ G:Na409 b:0.6 occ:1.00 OG1 G:THR226 3.8 63.4 1.0 OG1 F:THR226 4.0 71.2 1.0 OG1 H:THR226 4.2 73.6 1.0 OG1 J:THR226 4.5 66.8 1.0 OG1 I:THR226 4.6 66.0 1.0 CG2 G:THR226 4.9 64.6 1.0 CG2 F:THR226 4.9 67.7 1.0 CB G:THR226 5.0 65.4 1.0

Sodium binding site 10 out of 12 in the Xray Structure of Glic in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Xray Structure of Glic in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ H:Na407 b:84.2 occ:1.00 O H:ILE71 2.4 72.1 1.0 O H:PRO68 3.0 76.8 1.0 N H:ILE73 3.6 67.8 1.0 C H:ILE71 3.6 73.2 1.0 CA H:TRP72 3.9 68.4 1.0 O4 H:SIN409 4.0 67.9 0.5 CD1 H:ILE73 4.1 78.6 1.0 CB H:ILE73 4.1 69.4 1.0 C H:TRP72 4.1 72.1 1.0 CG1 H:ILE73 4.1 70.4 1.0 C H:PRO68 4.1 77.6 1.0 N H:TRP72 4.2 69.3 1.0 O3 H:SIN409 4.3 67.2 0.5 CA H:ILE73 4.4 66.8 1.0 C4 H:SIN409 4.6 67.3 0.5 CA H:GLU69 4.8 74.2 1.0 CA H:ILE71 4.8 71.2 1.0 O H:ILE73 4.8 69.5 1.0 N H:GLU69 4.8 74.0 1.0 O H:GLU69 4.8 77.5 1.0 N H:ILE71 4.9 71.8 1.0 C H:GLU69 5.0 77.6 1.0

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