Magnesium in PDB 8ar5: Small Molecular Stabilizer For Eralpha and 14-3-3 (1080265)

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080265), PDB code: 8ar5 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)	41.79 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.14, 112.354, 62.41, 90, 90, 90
R / Rfree (%)	13.6 / 16.2

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080265) 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 (1080265) (pdb code 8ar5). 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 (1080265), PDB code: 8ar5:
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 (1080265)


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 (1080265) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:34.0 occ:1.00 O A:HOH656 3.1 32.6 1.0 O A:HOH434 3.4 13.0 1.0 O A:HOH415 4.2 21.6 1.0 O A:HOH614 4.3 25.7 1.0 O A:HOH631 4.5 26.1 1.0 NZ A:LYS159 4.8 29.9 1.0 OE2 A:GLU189 4.9 11.8 1.0

Magnesium binding site 2 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080265)


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 (1080265) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:8.1 occ:0.50 O A:HOH613 2.3 23.6 1.0 OE1 A:GLU2 2.4 12.6 1.0 O A:HOH421 2.5 12.9 1.0 CD A:GLU2 3.4 9.8 1.0 OE2 A:GLU2 3.8 12.0 1.0 O A:HOH582 4.3 12.2 1.0 O A:HOH712 4.4 12.8 1.0 CG A:GLU2 4.7 8.5 1.0 CA A:GLU2 4.9 7.4 1.0 N A:ARG3 5.0 7.3 1.0 O A:HOH500 5.0 19.4 1.0

Magnesium binding site 3 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080265)


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 (1080265) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:21.1 occ:1.00 O A:HOH452 2.0 25.5 1.0 O A:HOH513 2.1 47.6 1.0 OE2 A:GLU89 2.3 13.2 1.0 O A:HOH635 2.3 32.2 1.0 O A:HOH619 2.6 34.3 1.0 CD A:GLU89 3.4 9.9 1.0 CG A:GLU89 4.2 9.2 1.0 O A:HOH599 4.3 54.2 1.0 OE1 A:GLU89 4.3 10.7 1.0 O A:HOH472 4.3 29.8 1.0 NH1 A:ARG85 4.4 13.2 1.0 OE1 A:GLN93 4.5 11.3 1.0 O A:HOH633 4.6 32.6 1.0 CG A:GLU86 4.7 12.3 1.0 NE2 A:GLN93 4.7 12.9 1.0 CB A:GLU89 4.8 8.6 1.0 OG1 A:THR90 4.9 14.9 1.0 CD A:GLN93 5.0 10.5 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