Sodium in PDB 7rcm: Crystal Structure of Adp-Bound Galactokinase

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

The structure of Crystal Structure of Adp-Bound Galactokinase, PDB code: 7rcm 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)	39.82 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.793, 128.793, 240.652, 90, 90, 120
R / Rfree (%)	19.6 / 23.6

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

Magnesium

(Mg)

2 atoms

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

Sodium binding site 1 out of 2 in the Crystal Structure of Adp-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 Adp-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:48.0 occ:1.00 O A:GLN369 2.5 72.7 1.0 O A:GLY374 2.7 68.0 1.0 O A:TYR372 2.7 71.5 1.0 OE1 A:GLN369 3.0 68.7 1.0 C A:GLN369 3.6 72.3 1.0 CD A:GLN369 3.6 67.8 1.0 CG A:GLN369 3.8 69.8 1.0 C A:TYR372 3.9 69.8 1.0 C A:GLY374 3.9 67.1 1.0 CA A:GLN369 4.2 69.2 1.0 CB A:TYR372 4.4 65.3 1.0 CA A:TYR372 4.5 68.1 1.0 N A:TYR372 4.6 69.3 1.0 CB A:GLN369 4.6 68.9 1.0 CA A:THR375 4.6 65.0 1.0 N A:GLU370 4.7 74.7 1.0 N A:THR375 4.7 65.3 1.0 N A:GLY374 4.7 68.1 1.0 CD2 A:TYR372 4.7 63.7 1.0 NE2 A:GLN369 4.8 65.2 1.0 C A:GLY373 4.8 71.0 1.0 CA A:GLY374 4.9 67.2 1.0 N A:GLY373 5.0 70.3 1.0 CG A:TYR372 5.0 64.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Adp-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 Adp-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:50.7 occ:1.00 O B:GLN369 2.3 90.1 1.0 NE2 B:GLN369 2.4 86.8 1.0 O B:TYR372 2.7 93.2 1.0 O B:GLY374 2.7 86.2 1.0 CD B:GLN369 3.5 85.2 1.0 C B:GLN369 3.5 90.4 1.0 C B:TYR372 3.8 90.4 1.0 C B:GLY374 3.9 83.5 1.0 CG B:GLN369 4.0 89.0 1.0 CA B:GLN369 4.2 86.5 1.0 CB B:TYR372 4.2 84.8 1.0 O B:GLY373 4.4 91.5 1.0 CA B:TYR372 4.4 87.4 1.0 CD2 B:TYR372 4.5 80.8 1.0 OE1 B:GLN369 4.5 82.8 1.0 N B:TYR372 4.5 89.0 1.0 C B:GLY373 4.6 88.7 1.0 CA B:THR375 4.6 81.3 1.0 N B:GLU370 4.6 94.8 1.0 N B:THR375 4.7 81.3 1.0 O B:GLU370 4.7 97.6 1.0 CB B:GLN369 4.7 87.7 1.0 CG B:TYR372 4.7 81.8 1.0 N B:GLY374 4.8 84.8 1.0 N B:GLY373 4.8 90.1 1.0 CA B:GLY374 4.9 83.4 1.0 C B:GLU370 5.0 96.8 1.0 CA B:GLU370 5.0 98.4 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