Sodium in PDB 7s4c: Crystal Structure of Inhibitor-Bound Galactokinase

All present enzymatic activity of Crystal Structure of Inhibitor-Bound Galactokinase:
2.7.1.6;

The structure of Crystal Structure of Inhibitor-Bound Galactokinase, PDB code: 7s4c was solved by F.G.Whitby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.61 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.216, 129.216, 240.789, 90, 90, 120
R / Rfree (%)	17.6 / 21.5

The structure of Crystal Structure of Inhibitor-Bound Galactokinase also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Fluorine	(F)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Inhibitor-Bound Galactokinase (pdb code 7s4c). 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 Inhibitor-Bound Galactokinase, PDB code: 7s4c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Inhibitor-Bound Galactokinase


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 Inhibitor-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:35.2 occ:1.00 O A:GLY374 2.5 53.6 1.0 O A:GLN369 2.6 60.0 1.0 O A:TYR372 2.7 56.4 1.0 OE1 A:GLN369 2.9 50.9 1.0 HG3 A:GLN369 3.1 55.7 1.0 HB3 A:TYR372 3.4 51.0 1.0 HA A:THR375 3.6 52.3 1.0 CD A:GLN369 3.6 51.8 1.0 C A:GLN369 3.7 58.1 1.0 C A:GLY374 3.7 52.6 1.0 CG A:GLN369 3.8 54.2 1.0 H A:TYR372 3.9 55.7 1.0 C A:TYR372 3.9 55.1 1.0 HD2 A:TYR372 3.9 48.7 1.0 HA A:GLN369 3.9 53.2 1.0 H A:ALA376 4.1 48.8 1.0 CB A:TYR372 4.2 50.3 1.0 CA A:GLN369 4.3 54.3 1.0 CA A:TYR372 4.5 52.7 1.0 CA A:THR375 4.5 51.5 1.0 HG2 A:GLN369 4.5 55.1 1.0 N A:THR375 4.5 51.6 1.0 N A:TYR372 4.5 54.9 1.0 CD2 A:TYR372 4.5 48.0 1.0 CB A:GLN369 4.7 53.8 1.0 N A:GLY374 4.7 52.9 1.0 HA A:GLU370 4.8 65.8 1.0 C A:GLY373 4.8 56.0 1.0 N A:GLU370 4.8 60.5 1.0 NE2 A:GLN369 4.8 50.3 1.0 CG A:TYR372 4.8 48.7 1.0 CA A:GLY374 4.8 52.5 1.0 H A:GLY374 5.0 51.6 1.0 HB2 A:TYR372 5.0 49.2 1.0 N A:GLY373 5.0 55.2 1.0 O A:GLY373 5.0 57.9 1.0 HE22 A:GLN369 5.0 50.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Inhibitor-Bound Galactokinase


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 Inhibitor-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:77.5 occ:1.00 OE1 B:GLN369 2.1 95.7 1.0 O B:TYR372 2.4 95.0 1.0 O B:GLY374 2.6 94.7 1.0 O B:HOH551 2.8 73.2 1.0 O B:GLN369 2.8 95.7 1.0 CD B:GLN369 3.3 93.1 1.0 O B:GLY373 3.5 99.1 1.0 C B:TYR372 3.5 92.3 1.0 HB3 B:TYR372 3.5 86.5 1.0 HA B:THR375 3.7 91.5 1.0 C B:GLY374 3.8 91.7 1.0 H B:TYR372 3.9 92.2 1.0 C B:GLY373 3.9 95.3 1.0 C B:GLN369 4.0 95.0 1.0 HD2 B:TYR372 4.0 82.5 1.0 NE2 B:GLN369 4.1 86.5 1.0 HG3 B:GLN369 4.1 98.8 1.0 HA B:GLN369 4.2 88.5 1.0 CB B:TYR372 4.3 84.9 1.0 CA B:TYR372 4.3 88.2 1.0 CG B:GLN369 4.3 95.7 1.0 HG23 B:THR375 4.4 99.8 1.0 N B:GLY373 4.4 92.4 1.0 HE22 B:GLN369 4.4 87.3 1.0 HA2 B:GLY373 4.4 98.7 1.0 H B:ALA376 4.5 83.8 1.0 CA B:GLY373 4.5 95.5 1.0 N B:TYR372 4.5 90.4 1.0 N B:GLY374 4.5 92.2 1.0 CA B:THR375 4.6 90.0 1.0 HE21 B:GLN369 4.6 85.0 1.0 CD2 B:TYR372 4.6 80.7 1.0 CA B:GLN369 4.7 90.8 1.0 N B:THR375 4.7 90.0 1.0 CA B:GLY374 4.7 91.6 1.0 O B:GLU370 4.8 103.9 1.0 CG B:TYR372 4.8 81.8 1.0 HA B:GLU370 5.0 105.6 1.0

L.Liu, M.Tang, R.Pragani, F.G.Whitby, Y.Q.Zhang, B.Balakrishnan, Y.Fang, S.Karavadhi, D.Tao, C.A.Leclair, M.D.Hall, J.J.Marugan, M.Boxer, M.Shen, C.P.Hill, K.Lai, S.Patnaik. Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors Journal of Medicinal 2021CHEMISTRY.
DOI: 10.1021/ACS.JMEDCHEM.1C00945