Magnesium in PDB 8bfc: Binary Structure of 14-3-3S and RND3 Phosphopeptide

The structure of Binary Structure of 14-3-3S and RND3 Phosphopeptide, PDB code: 8bfc 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)	45.59 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.366, 112.395, 62.68, 90, 90, 90
R / Rfree (%)	16.4 / 17.2

The structure of Binary Structure of 14-3-3S and RND3 Phosphopeptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Binary Structure of 14-3-3S and RND3 Phosphopeptide (pdb code 8bfc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Binary Structure of 14-3-3S and RND3 Phosphopeptide, PDB code: 8bfc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Binary Structure of 14-3-3S and RND3 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Structure of 14-3-3S and RND3 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:17.8 occ:1.00 O A:GLU161 2.3 16.9 1.0 O A:HOH564 2.6 32.8 1.0 O A:HOH542 2.6 24.3 1.0 C A:GLU161 3.5 13.6 1.0 CA A:GLU161 4.3 11.4 1.0 N A:MET162 4.3 11.7 0.4 N A:MET162 4.4 11.5 0.6 CA A:MET162 4.4 12.3 0.4 CA A:MET162 4.4 12.3 0.6 OE2 A:GLU115 4.5 36.5 1.0 CB A:GLU161 4.7 14.1 1.0 OE1 A:GLU161 4.7 31.3 1.0 CG A:MET162 4.9 16.5 0.4 CD A:PRO163 4.9 14.7 1.0

Magnesium binding site 2 out of 4 in the Binary Structure of 14-3-3S and RND3 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Structure of 14-3-3S and RND3 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:4.9 occ:0.63 O A:GLU110 2.3 14.0 1.0 O A:HOH601 2.4 21.1 1.0 OE2 A:GLU35 2.4 15.4 1.0 O A:HOH608 2.4 18.6 1.0 OE1 A:GLU35 2.7 21.0 1.0 CD A:GLU35 2.9 20.6 1.0 C A:GLU110 3.5 13.5 1.0 N A:GLY112 4.1 14.3 1.0 CG A:GLU35 4.3 13.3 1.0 CA A:GLU110 4.4 12.1 1.0 N A:ALA111 4.5 11.8 1.0 CA A:ALA111 4.5 12.3 1.0 O A:HOH462 4.5 24.3 1.0 CB A:GLU110 4.6 13.3 1.0 C A:ALA111 4.7 13.2 1.0 CA A:GLY112 4.8 15.0 1.0 O A:HOH458 4.8 22.8 1.0

Magnesium binding site 3 out of 4 in the Binary Structure of 14-3-3S and RND3 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Binary Structure of 14-3-3S and RND3 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:8.4 occ:0.55 O A:HOH596 2.5 28.4 1.0 OE1 A:GLU2 2.6 14.8 1.0 O A:HOH415 2.7 14.5 1.0 O A:HOH616 2.8 29.3 1.0 CD A:GLU2 3.6 14.4 1.0 OE2 A:GLU2 4.0 13.5 1.0 O A:HOH573 4.5 13.8 1.0 O A:HOH669 4.6 15.2 1.0 CG A:GLU2 4.8 10.2 1.0 CA A:GLU2 4.9 7.7 1.0 N A:ARG3 5.0 8.6 1.0

Magnesium binding site 4 out of 4 in the Binary Structure of 14-3-3S and RND3 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Binary Structure of 14-3-3S and RND3 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:27.1 occ:1.00 OE1 A:GLU80 2.4 14.8 1.0 O A:HOH583 2.4 31.4 1.0 O A:LYS77 2.4 30.4 1.0 O A:HOH632 2.6 31.4 1.0 OE2 A:GLU80 2.8 20.5 1.0 CD A:GLU80 2.8 15.2 1.0 O A:HOH456 2.9 23.2 1.0 C A:LYS77 3.5 30.1 1.0 CA A:GLY78 4.1 16.3 1.0 CG A:GLU80 4.1 12.8 1.0 N A:GLY78 4.2 25.0 1.0 CA A:LYS77 4.6 33.2 1.0 CB A:GLU80 4.8 9.8 1.0 C A:GLY78 4.8 13.1 1.0 CD A:PRO79 5.0 14.2 1.0 CB A:LYS77 5.0 27.9 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