Magnesium in PDB 8arz: Small Molecule Stabilizer For Eralpha and 14-3-3 (1076406)

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1076406), PDB code: 8arz 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)	45.52 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.049, 112.494, 62.499, 90, 90, 90
R / Rfree (%)	13.8 / 17

The structure of Small Molecule Stabilizer For Eralpha and 14-3-3 (1076406) 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 (1076406) (pdb code 8arz). 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 (1076406), PDB code: 8arz:
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 (1076406)


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 (1076406) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:42.7 occ:1.00 O A:HOH425 2.7 14.5 1.0 O A:HOH604 3.1 25.8 1.0 O A:HOH573 3.3 29.6 1.0 NZ A:LYS159 4.0 34.4 1.0 O A:HOH419 4.1 35.0 1.0 O A:HOH515 4.3 19.2 1.0 OE2 A:GLU189 4.4 16.1 1.0 O A:HOH636 4.4 32.4 1.0 O A:HOH599 4.7 27.5 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1076406)


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 (1076406) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:12.6 occ:0.50 OE1 A:GLU2 2.4 17.1 1.0 O A:HOH428 2.5 18.0 1.0 CD A:GLU2 3.4 15.4 1.0 OE2 A:GLU2 3.8 16.6 1.0 O A:HOH571 4.3 15.0 1.0 O A:HOH675 4.4 16.6 1.0 CG A:GLU2 4.7 14.0 1.0 CA A:GLU2 4.9 12.0 1.0 N A:ARG3 5.0 11.1 1.0 O A:HOH467 5.0 23.7 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Stabilizer For Eralpha and 14-3-3 (1076406)


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 (1076406) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:26.0 occ:1.00 O A:HOH447 2.0 30.1 1.0 O A:HOH540 2.1 47.3 1.0 OE2 A:GLU89 2.3 17.9 1.0 O A:HOH614 2.3 37.5 1.0 CD A:GLU89 3.4 14.0 1.0 O A:HOH519 3.9 37.5 1.0 CG A:GLU89 4.1 12.9 1.0 OE1 A:GLU89 4.3 14.5 1.0 NH1 A:ARG85 4.4 17.3 1.0 OE1 A:GLN93 4.5 15.0 1.0 O A:HOH612 4.6 36.8 1.0 CG A:GLU86 4.6 16.8 1.0 NE2 A:GLN93 4.7 16.3 1.0 CB A:GLU89 4.8 12.9 1.0 OG1 A:THR90 4.9 18.5 1.0 CD A:GLN93 5.0 14.2 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