Magnesium in PDB 8a68: Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3

All present enzymatic activity of Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3:
2.7.11.1;

The structure of Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3, PDB code: 8a68 was solved by D.N.Kenanova, E.J.Visser, J.Virta, E.Sijbesma, F.Centorrino, M.Zhong, H.Vickery, J.Neitz, L.Brunsveld, C.Ottmann, M.R.Arkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.402, 112.257, 62.751, 90, 90, 90
R / Rfree (%)	15.9 / 17.9

The binding sites of Magnesium atom in the Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3 (pdb code 8a68). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3, PDB code: 8a68:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:27.5 occ:1.00 O A:HOH693 2.9 21.1 1.0 O A:HOH421 3.0 14.0 1.0 O A:HOH455 4.2 15.5 1.0 O A:HOH662 4.4 19.6 1.0 OE2 A:GLU189 4.6 15.6 1.0 O A:HOH667 4.8 31.4 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:12.4 occ:0.50 OE1 A:GLU2 2.4 13.2 1.0 O A:HOH475 2.5 14.7 1.0 CD A:GLU2 3.4 15.6 1.0 OE2 A:GLU2 3.8 15.4 1.0 HA A:GLU2 4.0 13.2 1.0 H A:ARG3 4.2 11.1 1.0 O A:HOH580 4.3 12.9 1.0 O A:HOH706 4.4 15.4 1.0 CG A:GLU2 4.7 11.2 1.0 HB3 A:GLU2 4.7 12.5 1.0 CA A:GLU2 4.9 11.0 1.0 O A:HOH423 5.0 23.3 1.0 N A:ARG3 5.0 9.3 1.0 HG2 A:GLU2 5.0 13.5 1.0 CB A:GLU2 5.0 10.4 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Small Molecule Stabilizer (Compound 5) For C-Raf(PS259) and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:21.5 occ:1.00 O A:HOH404 1.9 26.9 1.0 O A:HOH648 2.2 31.8 1.0 O A:HOH549 2.2 36.4 1.0 O A:HOH440 2.3 25.7 1.0 OE2 A:GLU89 2.5 17.8 1.0 CD A:GLU89 3.5 11.4 1.0 HH12 A:ARG85 3.7 18.9 1.0 HG2 A:GLU86 3.9 19.1 1.0 HG2 A:GLU89 3.9 13.1 1.0 O A:HOH541 4.1 24.9 1.0 HH11 A:ARG85 4.2 18.9 1.0 HE22 A:GLN93 4.2 19.8 1.0 CG A:GLU89 4.2 10.9 1.0 HB3 A:GLU89 4.2 13.0 1.0 NH1 A:ARG85 4.3 15.8 1.0 OE1 A:GLU89 4.3 12.3 1.0 HA A:GLU86 4.4 12.4 1.0 O A:HOH557 4.4 31.3 1.0 O A:HOH647 4.5 34.2 1.0 HG1 A:THR90 4.6 18.0 1.0 HB3 A:GLU86 4.6 15.6 1.0 OE1 A:GLN93 4.6 13.5 1.0 O A:HOH408 4.7 33.1 1.0 CG A:GLU86 4.7 15.9 1.0 CB A:GLU89 4.8 10.8 1.0 NE2 A:GLN93 4.8 16.5 1.0 OG1 A:THR90 4.9 15.0 1.0

D.N.Kenanova, E.J.Visser, J.M.Virta, E.Sijbesma, F.Centorrino, H.R.Vickery, M.Zhong, R.J.Neitz, L.Brunsveld, C.Ottmann, M.R.Arkin. A Systematic Approach to the Discovery of Protein–Protein Interaction Stabilizers Acs Cent.Sci. 2023.
ISSN: ESSN 2374-7951
DOI: 10.1021/ACSCENTSCI.2C01449