Magnesium in PDB 8atp: Small Molecule Stabilizer (1075481) For Eralpha and 14-3-3

The structure of Small Molecule Stabilizer (1075481) For Eralpha and 14-3-3, PDB code: 8atp was solved by E.M.F.Vandenboorn, E.J.Visser, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.113, 112.517, 62.496, 90, 90, 90
R / Rfree (%)	12.8 / 15.5

The structure of Small Molecule Stabilizer (1075481) For Eralpha and 14-3-3 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Small Molecule Stabilizer (1075481) For Eralpha and 14-3-3 (pdb code 8atp). 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 (1075481) For Eralpha and 14-3-3, PDB code: 8atp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Small Molecule Stabilizer (1075481) For Eralpha and 14-3-3


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 (1075481) For Eralpha and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:38.1 occ:1.00 O A:HOH437 2.7 11.1 1.0 O A:HOH646 3.1 23.6 1.0 O A:HOH617 3.3 25.6 1.0 NZ A:LYS159 4.1 29.6 1.0 O A:HOH427 4.1 33.3 1.0 O A:HOH546 4.3 15.8 1.0 OE2 A:GLU189 4.4 12.0 1.0 O A:HOH669 4.6 33.5 1.0 O A:HOH612 4.7 25.9 1.0 O A:HOH542 5.0 29.0 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Stabilizer (1075481) For Eralpha and 14-3-3


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 (1075481) For Eralpha and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:8.8 occ:0.50 O A:HOH624 2.3 25.8 1.0 OE1 A:GLU2 2.4 13.3 1.0 O A:HOH429 2.5 13.9 1.0 CD A:GLU2 3.4 11.2 1.0 OE2 A:GLU2 3.8 12.5 1.0 O A:HOH599 4.3 13.2 1.0 O A:HOH730 4.4 13.8 1.0 CG A:GLU2 4.6 9.5 1.0 CA A:GLU2 4.9 7.7 1.0 N A:ARG3 5.0 7.9 1.0 O A:HOH497 5.0 20.8 1.0 CB A:GLU2 5.0 8.9 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Stabilizer (1075481) For Eralpha and 14-3-3


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 (1075481) For Eralpha and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:21.3 occ:1.00 O A:HOH411 1.8 30.8 1.0 O A:HOH456 2.0 26.8 1.0 O A:HOH539 2.2 40.3 1.0 OE2 A:GLU89 2.3 14.3 1.0 O A:HOH651 2.4 32.1 1.0 O A:HOH639 2.6 34.4 1.0 CD A:GLU89 3.4 10.1 1.0 O A:HOH507 4.0 36.1 1.0 CG A:GLU89 4.2 9.4 1.0 O A:HOH474 4.3 31.2 1.0 OE1 A:GLU89 4.3 10.6 1.0 NH1 A:ARG85 4.4 13.0 1.0 OE1 A:GLN93 4.5 11.9 1.0 O A:HOH649 4.5 30.7 1.0 CG A:GLU86 4.7 12.8 1.0 NE2 A:GLN93 4.7 12.6 1.0 CB A:GLU89 4.8 8.9 1.0 OG1 A:THR90 4.9 15.3 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