Magnesium in PDB 8aq1: Small Molecule Stabilizer For Eralpha and 14-3-3 (1083743)

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1083743), PDB code: 8aq1 was solved by E.J.Visser, E.M.F.Vandenboorn, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.16 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.249, 112.428, 62.645, 90, 90, 90
R / Rfree (%)	16.1 / 18.1

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1083743) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1083743) (pdb code 8aq1). 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 For Eralpha and 14-3-3 (1083743), PDB code: 8aq1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1083743)


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 For Eralpha and 14-3-3 (1083743) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:29.1 occ:1.00 O A:HOH682 3.2 24.9 1.0 O A:HOH437 3.5 10.5 1.0 O A:HOH468 4.2 18.5 1.0 O A:HOH644 4.4 22.6 1.0 O A:HOH653 4.4 20.6 1.0 O A:HOH578 4.5 23.2 1.0 OE2 A:GLU189 4.9 10.3 1.0 NZ A:LYS159 5.0 30.0 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1083743)


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 For Eralpha and 14-3-3 (1083743) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:6.8 occ:0.50 O A:HOH625 2.3 25.2 1.0 OE1 A:GLU2 2.4 11.4 1.0 O A:HOH421 2.5 11.0 1.0 CD A:GLU2 3.4 11.1 1.0 OE2 A:GLU2 3.8 10.5 1.0 O A:HOH582 4.3 10.3 1.0 O A:HOH721 4.5 12.0 1.0 CG A:GLU2 4.7 7.9 1.0 CA A:GLU2 4.8 6.2 1.0 N A:ARG3 4.9 6.4 1.0 CB A:GLU2 5.0 7.5 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1083743)


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 For Eralpha and 14-3-3 (1083743) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:17.9 occ:1.00 O A:HOH450 2.0 22.7 1.0 O A:HOH719 2.2 37.8 1.0 O A:HOH561 2.2 37.6 1.0 O A:HOH655 2.3 29.6 1.0 OE2 A:GLU89 2.3 12.0 1.0 O A:HOH638 2.4 31.7 1.0 CD A:GLU89 3.4 7.9 1.0 O A:HOH474 4.1 25.3 1.0 CG A:GLU89 4.2 8.0 1.0 OE1 A:GLU89 4.3 8.6 1.0 O A:HOH529 4.4 25.2 1.0 NH1 A:ARG85 4.4 12.2 1.0 OE1 A:GLN93 4.5 10.4 1.0 O A:HOH641 4.5 26.6 1.0 CG A:GLU86 4.7 11.5 1.0 NE2 A:GLN93 4.7 11.0 1.0 CB A:GLU89 4.8 8.0 1.0 OG1 A:THR90 4.9 12.6 1.0 CD A:GLN93 5.0 9.9 1.0

M.Konstantinidou, E.J.Visser, E.Vandenboorn, S.Chen, P.Jaishankar, M.Overmans, S.Dutta, R.J.Neitz, A.R.Renslo, C.Ottmann, L.Brunsveld, M.R.Arkin. Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3 Sigma /Er Alpha Protein-Protein Interaction From Nonselective Fragments. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 37676236
DOI: 10.1021/JACS.3C05161