Magnesium in PDB 8afn: Small Molecule Stabilizer (Compound 1) For Eralpha and 14-3-3

The structure of Small Molecule Stabilizer (Compound 1) For Eralpha and 14-3-3, PDB code: 8afn 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)	45.40 / 1.36
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.742, 111.898, 62.555, 90, 90, 90
R / Rfree (%)	17.3 / 18.5

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

Chlorine

(Cl)

1 atom

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

Magnesium binding site 1 out of 2 in the Small Molecule Stabilizer (Compound 1) For Eralpha 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 Eralpha and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:34.3 occ:1.00 O A:HOH663 2.9 32.3 1.0 O A:HOH434 3.1 17.7 1.0 O A:HOH644 4.2 30.6 1.0 O A:HOH438 4.2 22.4 1.0 O A:HOH559 4.3 30.6 1.0 HZ2 A:LYS159 4.3 54.0 1.0 HZ1 A:LYS159 4.4 54.0 1.0 O A:HOH480 4.4 28.6 1.0 OE2 A:GLU189 4.6 16.4 1.0 NZ A:LYS159 4.8 45.0 1.0 O A:HOH584 4.9 29.7 1.0 HZ3 A:LYS159 5.0 54.0 1.0

Magnesium binding site 2 out of 2 in the Small Molecule Stabilizer (Compound 1) For Eralpha 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 Eralpha and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:25.1 occ:1.00 O A:HOH431 2.2 29.3 1.0 O A:HOH627 2.2 36.4 1.0 OE2 A:GLU89 2.4 21.8 1.0 O A:HOH609 2.6 33.4 1.0 CD A:GLU89 3.5 16.1 1.0 HG2 A:GLU86 3.6 22.7 1.0 HG2 A:GLU89 3.7 18.3 1.0 HH12 A:ARG85 3.9 22.1 1.0 O A:HOH473 4.0 31.7 1.0 HE22 A:GLN93 4.1 21.0 1.0 CG A:GLU89 4.1 15.2 1.0 HB3 A:GLU89 4.2 19.1 1.0 HH11 A:ARG85 4.3 22.1 1.0 OE1 A:GLU89 4.4 16.5 1.0 O A:HOH573 4.4 34.5 1.0 NH1 A:ARG85 4.4 18.4 1.0 HA A:GLU86 4.5 17.2 1.0 HG1 A:THR90 4.5 24.1 1.0 OE1 A:GLN93 4.5 17.6 1.0 CG A:GLU86 4.5 18.9 1.0 O A:HOH619 4.6 33.3 1.0 NE2 A:GLN93 4.7 17.4 1.0 CB A:GLU89 4.7 15.9 1.0 HB3 A:GLU86 4.8 19.5 1.0 OG1 A:THR90 4.9 20.1 1.0 HG3 A:GLU89 5.0 18.3 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