Potassium in PDB 6e8y: Unliganded Human Glycerol 3-Phosphate Dehydrogenase

All present enzymatic activity of Unliganded Human Glycerol 3-Phosphate Dehydrogenase:
1.1.1.8;

The structure of Unliganded Human Glycerol 3-Phosphate Dehydrogenase, PDB code: 6e8y was solved by L.S.Mydy, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.370, 76.160, 64.390, 90.00, 96.03, 90.00
R / Rfree (%)	17 / 21

The binding sites of Potassium atom in the Unliganded Human Glycerol 3-Phosphate Dehydrogenase (pdb code 6e8y). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Unliganded Human Glycerol 3-Phosphate Dehydrogenase, PDB code: 6e8y:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Unliganded Human Glycerol 3-Phosphate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Unliganded Human Glycerol 3-Phosphate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:K403 b:29.6 occ:1.00 O A:ALA26 2.4 24.0 1.0 O A:PHE32 2.7 35.0 1.0 HD3 A:PRO34 2.7 39.1 1.0 O A:LEU29 2.8 31.4 1.0 O A:ALA27 2.9 34.6 1.0 HA A:ALA27 3.4 38.9 1.0 C A:ALA27 3.5 28.1 1.0 HB3 A:PRO34 3.6 43.3 1.0 CD A:PRO34 3.6 32.6 1.0 C A:ALA26 3.6 29.5 1.0 C A:LEU29 3.7 29.2 1.0 HA A:ALA30 3.9 39.4 1.0 C A:PHE32 3.9 39.8 1.0 CA A:ALA27 3.9 32.4 1.0 N A:PRO34 4.0 29.3 1.0 HA A:PRO34 4.0 31.5 1.0 HG3 A:PRO34 4.0 38.1 1.0 H A:LEU29 4.1 32.9 1.0 H A:PHE32 4.1 43.2 1.0 N A:LEU29 4.1 27.4 1.0 CB A:PRO34 4.2 36.1 1.0 CG A:PRO34 4.2 31.8 1.0 HB2 A:PHE32 4.2 35.8 1.0 N A:ALA27 4.3 29.4 1.0 C A:GLN28 4.3 26.8 1.0 CA A:PRO34 4.3 26.3 1.0 HD2 A:PRO34 4.3 39.1 1.0 N A:GLN28 4.4 28.0 1.0 O A:ALA30 4.4 46.2 1.0 C A:ASP33 4.5 39.2 1.0 CA A:ALA30 4.5 32.9 1.0 HA A:ASP33 4.5 31.5 1.0 N A:ALA30 4.5 36.1 1.0 CA A:LEU29 4.5 21.8 1.0 C A:ALA30 4.6 40.0 1.0 O A:GLN28 4.6 24.1 1.0 HA A:ALA26 4.7 36.2 1.0 N A:PHE32 4.7 36.0 1.0 CA A:PHE32 4.7 32.5 1.0 CA A:ALA26 4.8 30.2 1.0 N A:ASP33 4.8 33.5 1.0 CA A:ASP33 4.8 26.3 1.0 CB A:PHE32 4.9 29.9 1.0 CA A:GLN28 4.9 26.7 1.0 H A:GLN28 5.0 33.5 1.0

Potassium binding site 2 out of 2 in the Unliganded Human Glycerol 3-Phosphate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Unliganded Human Glycerol 3-Phosphate Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:K401 b:25.2 occ:1.00 O B:PHE32 2.6 26.6 1.0 O B:HOH613 2.6 31.2 1.0 O B:LEU29 2.7 25.1 1.0 O B:ALA26 2.8 21.5 1.0 O B:ALA27 3.1 24.5 1.0 O B:HOH651 3.1 35.7 1.0 HD3 B:PRO34 3.3 28.9 1.0 HA B:ALA30 3.4 39.2 1.0 C B:LEU29 3.5 29.7 1.0 C B:ALA27 3.7 23.9 1.0 HA B:ALA27 3.7 25.1 1.0 H B:PHE32 3.8 33.9 1.0 C B:PHE32 3.8 26.7 1.0 C B:ALA26 3.9 17.4 1.0 HB3 B:PRO34 4.0 33.1 1.0 CA B:ALA30 4.1 32.7 1.0 H B:LEU29 4.1 31.0 1.0 CA B:ALA27 4.1 20.9 1.0 CD B:PRO34 4.1 24.1 1.0 N B:LEU29 4.1 25.9 1.0 N B:ALA30 4.1 32.1 1.0 HB2 B:PHE32 4.1 27.0 1.0 O B:ALA30 4.3 32.2 1.0 C B:ALA30 4.3 31.7 1.0 N B:PRO34 4.3 21.7 1.0 C B:GLN28 4.4 31.2 1.0 N B:PHE32 4.4 28.2 1.0 HA B:PRO34 4.4 25.3 1.0 CA B:LEU29 4.5 26.8 1.0 N B:ALA27 4.5 20.4 1.0 HA B:ASP33 4.5 30.5 1.0 N B:GLN28 4.5 24.5 1.0 CA B:PHE32 4.6 24.5 1.0 HG3 B:PRO34 4.6 32.7 1.0 CB B:PRO34 4.6 27.6 1.0 C B:ASP33 4.7 23.6 1.0 CG B:PRO34 4.7 27.3 1.0 CA B:PRO34 4.8 21.1 1.0 O B:GLN28 4.8 26.3 1.0 N B:ASP33 4.8 27.5 1.0 CB B:PHE32 4.8 22.5 1.0 HD2 B:PRO34 4.8 28.9 1.0 H B:ALA30 4.9 38.5 1.0 CA B:ASP33 4.9 25.4 1.0 HA B:ALA26 5.0 23.6 1.0 O B:HOH605 5.0 30.1 1.0

L.S.Mydy, J.R.Cristobal, R.D.Katigbak, P.Bauer, A.C.Reyes, S.C.L.Kamerlin, J.P.Richard, A.M.Gulick. Human Glycerol 3-Phosphate Dehydrogenase: X-Ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry V. 58 1061 2019.
ISSN: ISSN 1520-4995
PubMed: 30640445
DOI: 10.1021/ACS.BIOCHEM.8B01103