Magnesium in PDB 8ary: Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273)

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273), PDB code: 8ary 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)	45.58 / 1.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.135, 112.296, 62.651, 90, 90, 90
R / Rfree (%)	13.6 / 16.5

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273) (pdb code 8ary). 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 Molecular Stabilizer For Eralpha and 14-3-3 (1080273), PDB code: 8ary:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:42.2 occ:1.00 O A:HOH422 2.7 14.8 1.0 O A:HOH622 3.1 31.7 1.0 O A:HOH507 3.3 29.1 1.0 O A:HOH434 3.9 35.9 1.0 NZ A:LYS159 3.9 33.9 1.0 O A:HOH533 4.3 18.7 1.0 OE2 A:GLU189 4.4 15.7 1.0 O A:HOH632 4.6 33.3 1.0 O A:HOH615 4.7 29.5 1.0

Magnesium binding site 2 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:11.6 occ:0.50 OE1 A:GLU2 2.4 16.4 1.0 O A:HOH418 2.5 16.3 1.0 CD A:GLU2 3.4 13.4 1.0 OE2 A:GLU2 3.8 14.8 1.0 O A:HOH573 4.3 16.0 1.0 O A:HOH693 4.4 15.9 1.0 CG A:GLU2 4.7 12.1 1.0 CA A:GLU2 4.9 10.6 1.0 N A:ARG3 5.0 11.4 1.0 CB A:GLU2 5.0 11.4 1.0

Magnesium binding site 3 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080273) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:22.8 occ:1.00 O A:HOH406 1.9 34.3 1.0 O A:HOH451 2.0 28.8 1.0 O A:HOH514 2.2 42.4 1.0 O A:HOH625 2.4 36.2 1.0 OE2 A:GLU89 2.4 17.1 1.0 O A:HOH603 2.5 35.5 1.0 CD A:GLU89 3.4 14.1 1.0 O A:HOH494 3.9 33.2 1.0 CG A:GLU89 4.2 12.8 1.0 O A:HOH543 4.3 34.4 1.0 OE1 A:GLU89 4.3 14.3 1.0 NH1 A:ARG85 4.4 17.2 1.0 NE2 A:GLN93 4.5 13.3 1.0 O A:HOH616 4.5 35.5 1.0 CG A:GLU86 4.6 15.9 1.0 OE1 A:GLN93 4.6 18.6 1.0 CB A:GLU89 4.8 12.3 1.0 OG1 A:THR90 4.9 18.3 1.0 CD A:GLN93 5.0 13.7 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