Magnesium in PDB 8b39: Small Molecular Stabilizer For Eralpha and 14-3-3 (1080299)

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080299), PDB code: 8b39 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 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.11, 112.675, 62.456, 90, 90, 90
R / Rfree (%)	13.2 / 16

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1080299) 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 (1080299) (pdb code 8b39). 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 (1080299), PDB code: 8b39:
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 (1080299)


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 (1080299) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:29.2 occ:1.00 O A:HOH428 2.8 10.6 1.0 O A:HOH675 3.0 22.1 1.0 O A:HOH622 3.3 23.0 1.0 O A:HOH420 3.8 23.9 1.0 NZ A:LYS159 4.2 35.8 1.0 O A:HOH535 4.3 13.8 1.0 OE2 A:GLU189 4.4 10.9 1.0 O A:HOH660 4.5 27.8 1.0 O A:HOH453 4.7 24.9 1.0 O A:HOH528 4.9 25.1 1.0

Magnesium binding site 2 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080299)


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 (1080299) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:8.6 occ:0.50 O A:HOH612 2.3 27.3 1.0 OE1 A:GLU2 2.4 12.2 1.0 O A:HOH424 2.5 12.4 1.0 CD A:GLU2 3.4 10.3 1.0 OE2 A:GLU2 3.8 11.5 1.0 O A:HOH601 4.3 12.4 1.0 O A:HOH717 4.4 12.3 1.0 CG A:GLU2 4.7 9.3 1.0 CA A:GLU2 4.8 8.6 1.0 N A:ARG3 5.0 9.1 1.0 CB A:GLU2 5.0 9.4 1.0

Magnesium binding site 3 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1080299)


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 (1080299) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:18.6 occ:1.00 O A:HOH413 2.0 33.0 1.0 O A:HOH434 2.1 24.9 1.0 OE2 A:GLU89 2.3 14.1 1.0 O A:HOH554 2.4 34.4 1.0 O A:HOH634 2.5 30.7 1.0 CD A:GLU89 3.4 10.2 1.0 O A:HOH445 4.0 29.9 1.0 CG A:GLU89 4.1 9.7 1.0 OE1 A:GLU89 4.3 10.4 1.0 O A:HOH446 4.4 29.3 1.0 NH1 A:ARG85 4.5 12.2 1.0 OE1 A:GLN93 4.5 11.4 1.0 O A:HOH633 4.6 28.4 1.0 CG A:GLU86 4.6 12.7 1.0 NE2 A:GLN93 4.7 12.8 1.0 CB A:GLU89 4.8 9.6 1.0 OG1 A:THR90 4.9 14.5 1.0 CD A:GLN93 5.0 10.8 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