Magnesium in PDB 8av0: Small Molecule Stabilizer (Compound 1) For C-Raf PS259 and 14-3-3

All present enzymatic activity of Small Molecule Stabilizer (Compound 1) For C-Raf PS259 and 14-3-3:
2.7.11.1;

The structure of Small Molecule Stabilizer (Compound 1) For C-Raf PS259 and 14-3-3, PDB code: 8av0 was solved by E.J.Visser, E.Sijbesma, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.31 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.879, 112.286, 62.865, 90, 90, 90
R / Rfree (%)	14.6 / 18

The structure of Small Molecule Stabilizer (Compound 1) For C-Raf PS259 and 14-3-3 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Small Molecule Stabilizer (Compound 1) For C-Raf PS259 and 14-3-3 (pdb code 8av0). 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 1) For C-Raf PS259 and 14-3-3, PDB code: 8av0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Small Molecule Stabilizer (Compound 1) 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 1) For C-Raf PS259 and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:19.7 occ:1.00 O A:HOH610 2.1 45.6 1.0 OE2 A:GLU89 2.4 18.6 1.0 O A:HOH554 2.4 30.1 1.0 CD A:GLU89 3.5 15.5 1.0 HG2 A:GLU86 3.7 23.9 1.0 HG2 A:GLU89 3.8 16.1 1.0 HH12 A:ARG85 3.8 21.4 1.0 HE22 A:GLN93 4.0 18.6 1.0 O A:HOH523 4.1 28.3 1.0 CG A:GLU89 4.2 13.5 1.0 HB3 A:GLU89 4.2 15.0 1.0 HH11 A:ARG85 4.2 21.4 1.0 OE1 A:GLU89 4.3 15.5 1.0 NH1 A:ARG85 4.4 17.9 1.0 HA A:GLU86 4.4 15.1 1.0 HG1 A:THR90 4.4 22.1 1.0 OE1 A:GLN93 4.5 15.9 1.0 O A:HOH568 4.5 32.8 1.0 HB3 A:GLU86 4.5 17.0 1.0 CG A:GLU86 4.7 20.0 1.0 NE2 A:GLN93 4.7 15.6 1.0 CB A:GLU89 4.8 12.5 1.0 OG1 A:THR90 4.8 18.4 1.0 O A:HOH404 5.0 37.0 1.0 CB A:GLU86 5.0 14.2 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Stabilizer (Compound 1) 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 1) For C-Raf PS259 and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:49.9 occ:1.00 OE2 A:GLU75 2.4 57.6 1.0 HG2 A:GLU75 3.1 75.3 1.0 CD A:GLU75 3.4 60.9 1.0 CG A:GLU75 3.7 62.8 1.0 HG3 A:GLU75 4.0 75.3 1.0 OE1 A:GLU75 4.5 61.3 1.0 HA A:GLU75 4.9 84.1 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Stabilizer (Compound 1) 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 1) For C-Raf PS259 and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:14.2 occ:0.54 OE1 A:GLU2 2.4 17.1 1.0 O A:HOH441 2.5 19.1 1.0 CD A:GLU2 3.4 15.4 1.0 OE2 A:GLU2 3.8 17.1 1.0 HA A:GLU2 4.0 13.3 1.0 H A:ARG3 4.2 13.6 1.0 O A:HOH545 4.4 16.7 1.0 O A:HOH613 4.5 19.0 1.0 HB3 A:GLU2 4.7 14.8 1.0 CG A:GLU2 4.7 13.8 1.0 CA A:GLU2 4.9 11.2 1.0 HG2 A:GLU2 5.0 16.5 1.0 CB A:GLU2 5.0 12.4 1.0 N A:ARG3 5.0 11.4 1.0 O A:HOH440 5.0 25.9 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