Sodium in PDB 7s49: 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: 7s49 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)	30.00 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.407, 129.407, 240.548, 90, 90, 120
R / Rfree (%)	15.8 / 22.6

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

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Inhibitor-Bound Galactokinase (pdb code 7s49). 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: 7s49:
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:Na406 b:54.4 occ:1.00 O A:GLN369 2.6 73.2 1.0 O A:GLY374 2.7 80.6 1.0 O A:TYR372 2.8 77.4 1.0 OE1 A:GLN369 2.9 73.4 1.0 HG3 A:GLN369 3.2 77.0 1.0 HB3 A:TYR372 3.7 71.8 1.0 CD A:GLN369 3.7 73.3 1.0 HA A:THR375 3.7 72.8 1.0 C A:GLN369 3.8 75.9 1.0 CG A:GLN369 3.9 74.8 1.0 C A:GLY374 3.9 79.5 1.0 C A:TYR372 4.0 78.7 1.0 HD2 A:TYR372 4.1 69.3 1.0 H A:TYR372 4.1 79.0 1.0 HA A:GLN369 4.1 72.0 1.0 H A:ALA376 4.3 66.8 1.0 CA A:GLN369 4.4 73.5 1.0 CB A:TYR372 4.5 70.8 1.0 HG2 A:GLN369 4.6 75.5 1.0 CA A:THR375 4.6 70.8 1.0 CA A:TYR372 4.6 74.6 1.0 N A:THR375 4.7 74.3 1.0 CD2 A:TYR372 4.7 67.8 1.0 N A:TYR372 4.7 78.0 1.0 CB A:GLN369 4.8 72.8 1.0 N A:GLY374 4.8 76.0 1.0 HA A:GLU370 4.8 85.8 1.0 N A:GLU370 4.8 78.7 1.0 C A:GLY373 4.9 79.8 1.0 NE2 A:GLN369 4.9 74.4 1.0 CA A:GLY374 5.0 79.8 1.0 CG A:TYR372 5.0 69.9 1.0 O A:GLY373 5.0 86.9 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:Na404 b:65.4 occ:1.00 O B:GLN369 2.5 103.1 1.0 OE1 B:GLN369 2.5 105.8 1.0 O B:GLY374 2.7 94.3 1.0 O B:TYR372 2.9 100.7 1.0 HB3 B:TYR372 3.4 94.7 1.0 CD B:GLN369 3.4 101.3 1.0 HG3 B:GLN369 3.4 109.3 1.0 HA B:THR375 3.6 93.4 1.0 C B:GLN369 3.6 105.5 1.0 HD2 B:TYR372 3.8 89.5 1.0 H B:TYR372 3.9 100.1 1.0 C B:GLY374 3.9 90.5 1.0 HA B:GLN369 3.9 99.2 1.0 CG B:GLN369 3.9 106.0 1.0 C B:TYR372 4.0 100.0 1.0 H B:ALA376 4.1 89.6 1.0 CB B:TYR372 4.2 92.8 1.0 CA B:GLN369 4.3 102.1 1.0 CA B:THR375 4.4 91.3 1.0 CA B:TYR372 4.5 95.7 1.0 NE2 B:GLN369 4.5 94.4 1.0 HA B:GLU370 4.5 114.2 1.0 N B:TYR372 4.6 99.0 1.0 N B:THR375 4.6 89.9 1.0 CD2 B:TYR372 4.6 86.9 1.0 HE21 B:GLN369 4.6 20.0 0.0 N B:GLU370 4.6 108.0 1.0 CB B:GLN369 4.7 105.5 1.0 HG2 B:GLN369 4.7 107.6 1.0 O B:GLY373 4.8 100.7 1.0 C B:GLY373 4.8 95.5 1.0 N B:GLY374 4.9 89.8 1.0 OG1 B:THR375 4.9 95.1 1.0 CG B:TYR372 4.9 87.1 1.0 HB2 B:TYR372 4.9 91.2 1.0 N B:ALA376 4.9 86.3 1.0 CA B:GLU370 4.9 112.6 1.0 CA B:GLY374 5.0 89.0 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