Magnesium in PDB 8aze: Small Molecule Stabilizer For Eralpha and 14-3-3 (1075306)

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1075306), PDB code: 8aze was solved by M.Konstantinidou, E.J.Visser, E.M.F.Vandenboorn, C.Sheng, P.Jaishankar, M.J.A.M.Overmans, S.Dutta, J.Neitz, A.Renslo, C.Ottmann, L.Brunsveld, M.Arkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.32 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.846, 111.849, 62.305, 90, 90, 90
R / Rfree (%)	16.7 / 20.1

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1075306) 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 (1075306) (pdb code 8aze). 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 (1075306), PDB code: 8aze:
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 (1075306)


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 (1075306) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:40.0 occ:1.00 O A:HOH432 2.7 14.1 1.0 O A:HOH599 3.0 31.5 1.0 O A:HOH662 3.2 30.9 1.0 O A:HOH428 4.2 28.1 1.0 NZ A:LYS159 4.2 49.9 1.0 O A:HOH526 4.3 15.2 1.0 OE2 A:GLU189 4.4 14.7 1.0 O A:HOH554 4.9 26.5 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1075306)


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 (1075306) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:9.2 occ:0.50 O A:HOH529 2.2 33.6 1.0 OE1 A:GLU2 2.4 13.5 1.0 O A:HOH436 2.5 14.6 1.0 O A:HOH635 2.7 32.4 1.0 CD A:GLU2 3.4 15.6 1.0 OE2 A:GLU2 3.8 14.2 1.0 O A:HOH552 4.3 11.2 1.0 O A:HOH665 4.4 14.5 1.0 CG A:GLU2 4.7 10.5 1.0 CA A:GLU2 4.9 8.8 1.0 O A:HOH453 5.0 20.6 1.0 N A:ARG3 5.0 7.5 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1075306)


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 (1075306) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:17.1 occ:1.00 O A:HOH481 2.1 24.1 1.0 O A:HOH588 2.2 34.7 1.0 O A:HOH589 2.4 28.9 1.0 OE2 A:GLU89 2.4 16.5 1.0 CD A:GLU89 3.5 11.1 1.0 O A:HOH492 4.1 25.1 1.0 CG A:GLU89 4.2 11.1 1.0 OE1 A:GLU89 4.4 12.0 1.0 O A:HOH616 4.5 28.2 1.0 OE1 A:GLN93 4.5 13.3 1.0 NH1 A:ARG85 4.5 16.2 1.0 NE2 A:GLN93 4.7 13.3 1.0 O A:HOH606 4.7 33.0 1.0 CG A:GLU86 4.8 17.8 1.0 CB A:GLU89 4.8 9.7 1.0 OG1 A:THR90 4.8 13.5 1.0 CD A:GLN93 5.0 13.4 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