Magnesium in PDB 8aps: Small Molecular Stabilizer For Eralpha and 14-3-3 (1083744)

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1083744), PDB code: 8aps 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)	41.94 / 1.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.565, 112.833, 62.582, 90, 90, 90
R / Rfree (%)	13.3 / 15.1

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1083744) 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 (1083744) (pdb code 8aps). 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 (1083744), PDB code: 8aps:
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 (1083744)


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 (1083744) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:32.2 occ:1.00 O A:HOH643 3.3 28.1 1.0 O A:HOH439 3.5 10.3 1.0 O A:HOH413 4.2 19.9 1.0 O A:HOH586 4.3 25.6 1.0 NZ A:LYS159 4.5 30.5 1.0 O A:HOH711 4.5 20.9 1.0 OE2 A:GLU189 4.9 9.9 1.0

Magnesium binding site 2 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1083744)


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 (1083744) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:8.0 occ:0.50 O A:HOH609 2.4 21.4 1.0 OE1 A:GLU2 2.4 11.4 1.0 O A:HOH432 2.5 10.9 1.0 CD A:GLU2 3.4 9.5 1.0 OE2 A:GLU2 3.8 10.8 1.0 O A:HOH577 4.3 12.0 1.0 O A:HOH718 4.4 11.3 1.0 CG A:GLU2 4.7 8.4 1.0 CA A:GLU2 4.9 6.9 1.0 N A:ARG3 5.0 6.8 1.0

Magnesium binding site 3 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1083744)


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 (1083744) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:16.7 occ:1.00 O A:HOH408 1.9 31.5 1.0 O A:HOH443 2.0 26.2 1.0 O A:HOH539 2.2 33.7 1.0 O A:HOH710 2.3 35.6 1.0 OE2 A:GLU89 2.3 13.4 1.0 O A:HOH603 2.5 28.9 1.0 O A:HOH619 2.5 29.4 1.0 CD A:GLU89 3.4 10.0 1.0 O A:HOH568 4.1 35.1 1.0 CG A:GLU89 4.2 8.8 1.0 OE1 A:GLU89 4.3 10.0 1.0 NH1 A:ARG85 4.4 12.7 1.0 OE1 A:GLN93 4.5 10.9 1.0 O A:HOH425 4.5 25.7 1.0 O A:HOH624 4.6 28.8 1.0 CG A:GLU86 4.6 12.4 1.0 NE2 A:GLN93 4.7 11.6 1.0 CB A:GLU89 4.8 8.2 1.0 OG1 A:THR90 4.9 13.4 1.0 CD A:GLN93 5.0 9.1 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