Magnesium in PDB 8alv: Small Molecular Stabilizer For Eralpha and 14-3-3 (1076403)

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1076403), PDB code: 8alv 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)	45.45 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.052, 112.316, 62.468, 90, 90, 90
R / Rfree (%)	15.4 / 18.5

The structure of Small Molecular Stabilizer For Eralpha and 14-3-3 (1076403) 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 (1076403) (pdb code 8alv). 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 (1076403), PDB code: 8alv:
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 (1076403)


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 (1076403) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:30.1 occ:1.00 O A:HOH677 3.2 28.3 1.0 O A:HOH439 3.6 13.1 1.0 O A:HOH413 4.2 23.0 1.0 HZ2 A:LYS159 4.3 47.8 1.0 O A:HOH655 4.4 26.6 1.0 O A:HOH661 4.5 26.0 1.0 O A:HOH593 4.5 28.2 1.0 HZ1 A:LYS159 4.7 47.8 1.0 NZ A:LYS159 4.9 39.8 1.0 OE2 A:GLU189 4.9 14.4 1.0 HG A:SER192 4.9 25.8 1.0

Magnesium binding site 2 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1076403)


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 (1076403) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:12.5 occ:0.61 O A:HOH437 2.3 16.2 1.0 OE1 A:GLU2 2.3 17.4 1.0 O A:HOH670 2.5 35.5 1.0 CD A:GLU2 3.3 17.7 1.0 OE2 A:GLU2 3.6 17.9 1.0 HA A:GLU2 4.1 14.0 1.0 O A:HOH595 4.2 14.9 1.0 H A:ARG3 4.2 12.5 1.0 O A:HOH744 4.6 16.8 1.0 O A:HOH668 4.6 37.2 1.0 CG A:GLU2 4.6 15.2 1.0 HB3 A:GLU2 4.6 16.9 1.0 O A:HOH464 4.7 27.7 1.0 HG2 A:GLU2 4.8 18.2 1.0 CA A:GLU2 4.9 11.7 1.0 CB A:GLU2 4.9 14.1 1.0 N A:ARG3 5.0 10.4 1.0

Magnesium binding site 3 out of 3 in the Small Molecular Stabilizer For Eralpha and 14-3-3 (1076403)


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 (1076403) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:28.5 occ:1.00 O A:HOH456 2.1 26.4 1.0 O A:HOH648 2.3 36.2 1.0 O A:HOH657 2.3 32.5 1.0 OE2 A:GLU89 2.4 17.3 1.0 CD A:GLU89 3.5 12.4 1.0 HG2 A:GLU89 3.8 13.6 1.0 HG2 A:GLU86 3.8 19.4 1.0 HH12 A:ARG85 3.9 19.8 1.0 O A:HOH530 4.1 27.6 1.0 HE22 A:GLN93 4.1 19.4 1.0 CG A:GLU89 4.2 11.3 1.0 HB3 A:GLU89 4.3 14.0 1.0 HH11 A:ARG85 4.3 19.8 1.0 OE1 A:GLU89 4.3 12.7 1.0 NH1 A:ARG85 4.5 16.5 1.0 HA A:GLU86 4.5 13.6 1.0 OE1 A:GLN93 4.5 13.7 1.0 HG1 A:THR90 4.5 19.3 1.0 O A:HOH445 4.6 28.7 1.0 O A:HOH651 4.6 37.4 1.0 NE2 A:GLN93 4.7 16.2 1.0 HB3 A:GLU86 4.7 17.9 1.0 CG A:GLU86 4.7 16.2 1.0 CB A:GLU89 4.8 11.7 1.0 OG1 A:THR90 4.9 16.1 1.0 HG3 A:GLU89 5.0 13.6 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