Magnesium in PDB 8b2k: Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10

The structure of Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10, PDB code: 8b2k was solved by B.A.Somsen, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.56 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.431, 112.183, 62.598, 90, 90, 90
R / Rfree (%)	16.7 / 17.9

The structure of Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10 also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10 (pdb code 8b2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10, PDB code: 8b2k:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:18.3 occ:1.00 O A:GLU161 2.3 16.1 1.0 O A:HOH541 2.5 22.8 1.0 O A:HOH601 2.6 30.4 1.0 C A:GLU161 3.4 12.2 1.0 CA A:MET162 4.3 11.7 0.5 N A:MET162 4.3 10.6 0.5 N A:MET162 4.3 10.5 0.5 CA A:GLU161 4.3 11.2 1.0 CA A:MET162 4.4 11.6 0.5 OE2 A:GLU115 4.5 33.9 1.0 CB A:GLU161 4.7 13.7 1.0 CG A:MET162 4.7 16.3 0.5 OE1 A:GLU161 4.8 29.0 1.0 CD A:PRO163 4.9 13.5 1.0

Magnesium binding site 2 out of 3 in the Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:5.7 occ:0.47 O A:HOH608 2.5 28.8 1.0 OE1 A:GLU2 2.6 12.4 1.0 O A:HOH418 2.7 12.7 1.0 O A:HOH649 3.0 30.2 1.0 CD A:GLU2 3.6 11.4 1.0 OE2 A:GLU2 4.0 11.9 1.0 O A:HOH583 4.5 12.9 1.0 O A:HOH692 4.6 13.7 1.0 CG A:GLU2 4.9 9.3 1.0 CA A:GLU2 4.9 7.8 1.0 N A:ARG3 5.0 8.1 1.0

Magnesium binding site 3 out of 3 in the Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Structure of 14-3-3S, RND3 Phosphopeptide and Dual-Reactive Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:14.9 occ:1.00 O A:HOH613 2.3 17.8 1.0 O A:GLU110 2.3 9.9 0.5 O A:HOH510 2.3 19.2 1.0 O A:GLU110 2.3 11.2 0.5 OE2 A:GLU35 2.4 15.1 1.0 OE1 A:GLU35 2.6 19.1 1.0 CD A:GLU35 2.8 17.8 1.0 C A:GLU110 3.5 10.1 0.5 C A:GLU110 3.6 10.0 0.5 N A:GLY112 4.1 12.6 1.0 O A:HOH629 4.1 29.6 1.0 CG A:GLU35 4.3 12.6 1.0 CA A:GLU110 4.4 10.5 0.5 CB A:GLU110 4.4 10.2 0.5 CA A:GLU110 4.4 10.8 0.5 N A:ALA111 4.5 10.4 1.0 OE1 A:GLU110 4.5 16.2 0.5 CA A:ALA111 4.5 11.4 1.0 O A:HOH451 4.6 21.6 1.0 C A:ALA111 4.7 12.4 1.0 CB A:GLU110 4.8 9.9 0.5 CA A:GLY112 4.8 12.7 1.0 O A:HOH556 5.0 20.6 1.0

B.A.Somsen, R.J.C.Schellekens, C.J.A.Verhoef, M.R.Arkin, C.Ottmann, P.J.Cossar, L.Brunsveld. Reversible Dual-Covalent Molecular Locking of the 14-3-3/Err Gamma Protein-Protein Interaction As A Molecular Glue Drug Discovery Approach. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 36926879
DOI: 10.1021/JACS.2C12781