Sodium in PDB 8g2e: PKM2 Bound to Compound 2

All present enzymatic activity of PKM2 Bound to Compound 2:
2.7.1.40;

The structure of PKM2 Bound to Compound 2, PDB code: 8g2e was solved by J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.66 / 1.84
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.81, 115.965, 131.841, 90, 90, 90
R / Rfree (%)	16.3 / 19

The structure of PKM2 Bound to Compound 2 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the PKM2 Bound to Compound 2 (pdb code 8g2e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the PKM2 Bound to Compound 2, PDB code: 8g2e:

Sodium binding site 1 out of 1 in the PKM2 Bound to Compound 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of PKM2 Bound to Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na617 b:59.1 occ:1.00 OE1 A:GLU418 2.2 35.2 1.0 CD A:GLU418 3.0 32.8 1.0 O A:GLU418 3.4 13.6 1.0 CG A:GLU418 3.4 22.4 1.0 CB A:LYS422 3.8 21.5 1.0 OE2 A:GLU418 4.1 34.7 1.0 N A:LYS422 4.2 18.3 1.0 C A:GLU418 4.2 12.9 1.0 CA A:LYS422 4.3 19.8 1.0 CD A:LYS422 4.5 29.7 1.0 CA A:GLU418 4.6 12.2 1.0 CB A:GLU418 4.6 15.5 1.0 CG A:LYS422 4.6 24.9 1.0 CB A:PHE421 4.8 14.7 1.0 C A:PHE421 5.0 17.8 1.0

T.J.Wubben, S.Chaudhury, B.T.Watch, J.A.Stuckey, E.Weh, R.Fernando, M.Goswami, M.Pawar, J.C.Rech, C.G.Besirli. Development of Novel Small-Molecule Activators of Pyruvate Kinase Muscle Isozyme 2, PKM2, to Reduce Photoreceptor Apoptosis Pharmaceuticals V. 16 2023.
ISSN: ESSN 1424-8247
DOI: 10.3390/PH16050705