Magnesium in PDB 8anf: Small Molecule Stabilizer For Eralpha and 14-3-3 (1074359)

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1074359), PDB code: 8anf 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)	45.46 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.115, 112.503, 62.425, 90, 90, 90
R / Rfree (%)	13.6 / 16.2

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1074359) 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 (1074359) (pdb code 8anf). 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 (1074359), PDB code: 8anf:
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 (1074359)


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 (1074359) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:41.7 occ:1.00 O A:HOH421 3.3 14.8 1.0 O A:HOH625 3.5 35.9 1.0 O A:HOH676 4.4 30.5 1.0 O A:HOH482 4.4 30.2 1.0 NZ A:LYS159 4.5 36.5 1.0 O A:HOH592 4.7 35.7 1.0 OE2 A:GLU189 4.9 19.3 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1074359)


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 (1074359) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:11.1 occ:0.50 OE1 A:GLU2 2.4 16.0 1.0 O A:HOH425 2.5 16.3 1.0 CD A:GLU2 3.4 14.3 1.0 OE2 A:GLU2 3.8 15.2 1.0 O A:HOH576 4.3 15.3 1.0 O A:HOH687 4.4 15.9 1.0 CG A:GLU2 4.7 12.3 1.0 CA A:GLU2 4.9 10.3 1.0 O A:HOH449 5.0 22.3 1.0 N A:ARG3 5.0 10.5 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1074359)


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 (1074359) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:24.8 occ:1.00 O A:HOH462 2.0 28.2 1.0 O A:HOH492 2.2 45.2 1.0 OE2 A:GLU89 2.3 17.5 1.0 O A:HOH624 2.4 34.9 1.0 CD A:GLU89 3.4 13.7 1.0 O A:HOH472 4.0 34.3 1.0 CG A:GLU89 4.1 12.5 1.0 OE1 A:GLU89 4.3 13.7 1.0 O A:HOH442 4.3 35.4 1.0 NH1 A:ARG85 4.4 17.1 1.0 OE1 A:GLN93 4.5 14.2 1.0 NE2 A:GLN93 4.7 15.3 1.0 O A:HOH618 4.7 38.7 1.0 CG A:GLU86 4.7 15.9 1.0 CB A:GLU89 4.8 11.2 1.0 OG1 A:THR90 4.9 17.4 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