Magnesium in PDB 6y3w: Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1

The structure of Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1, PDB code: 6y3w 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)	45.65 / 1.34
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.532, 112.487, 62.731, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 18.7

The structure of Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1 (pdb code 6y3w). 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 Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1, PDB code: 6y3w:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:24.0 occ:1.00 O A:GLU161 2.3 19.7 1.0 O A:HOH624 2.3 39.2 1.0 O A:HOH609 2.4 27.2 1.0 C A:GLU161 3.5 14.9 1.0 HA A:MET162 3.6 15.9 0.4 HA A:MET162 3.6 15.8 0.6 HB3 A:GLU161 4.0 19.6 1.0 HG3 A:MET162 4.1 22.9 0.4 HA A:GLU161 4.1 15.5 1.0 HD3 A:PRO163 4.1 20.8 1.0 N A:MET162 4.3 13.2 1.0 CA A:GLU161 4.3 12.9 1.0 CA A:MET162 4.4 13.3 0.4 CA A:MET162 4.4 13.2 0.6 CB A:GLU161 4.7 16.4 1.0 OE1 A:GLU161 4.8 30.6 1.0 HG2 A:MET162 4.9 17.1 0.6 CD A:PRO163 4.9 17.3 1.0 CG A:MET162 5.0 19.0 0.4 HD2 A:PRO163 5.0 20.8 1.0

Magnesium binding site 2 out of 3 in the Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:13.8 occ:0.68 O A:HOH594 2.5 27.2 1.0 OE2 A:GLU2 2.6 14.7 1.0 O A:HOH437 2.7 15.3 1.0 CD A:GLU2 3.6 14.2 1.0 OE1 A:GLU2 4.0 14.5 1.0 HA A:GLU2 4.1 12.2 1.0 H A:ARG3 4.2 13.2 1.0 O A:HOH590 4.5 16.3 1.0 O A:HOH718 4.6 16.0 1.0 CG A:GLU2 4.8 12.5 1.0 HB3 A:GLU2 4.9 14.0 1.0 CA A:GLU2 4.9 10.2 1.0

Magnesium binding site 3 out of 3 in the Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of 14-3-3 Sigma (C38N), Estrogen Related Receptor Gamma (Dbd) Phosphopeptide, and Disulfide Ppi Stabilizer 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:30.8 occ:1.00 O A:GLU110 2.3 15.8 1.0 O A:HOH579 2.3 21.9 1.0 O A:HOH622 2.3 20.1 1.0 OE2 A:GLU35 2.3 17.3 1.0 OE1 A:GLU35 2.7 22.8 1.0 CD A:GLU35 2.8 21.9 1.0 H A:GLY112 3.5 18.3 1.0 C A:GLU110 3.5 13.8 1.0 HB3 A:GLU110 3.7 17.4 0.5 HB3 A:GLU110 3.9 16.3 0.5 HA A:ALA111 3.9 17.3 1.0 N A:GLY112 4.1 15.3 1.0 O A:HOH651 4.2 33.0 1.0 HA A:GLU110 4.3 17.1 0.5 HA A:GLU110 4.3 17.1 0.5 CG A:GLU35 4.3 15.1 1.0 CA A:GLU110 4.4 14.2 0.5 CA A:GLU110 4.4 14.2 0.5 HA3 A:GLY112 4.4 19.4 1.0 N A:ALA111 4.5 13.8 1.0 CB A:GLU110 4.5 14.4 0.5 O A:HOH636 4.5 29.8 1.0 HG2 A:GLU35 4.5 18.1 1.0 CA A:ALA111 4.5 14.4 1.0 CB A:GLU110 4.6 13.5 0.5 O A:HOH475 4.6 23.9 1.0 OE1 A:GLU110 4.7 17.2 0.5 HG3 A:GLU35 4.7 18.1 1.0 C A:ALA111 4.8 15.6 1.0 CA A:GLY112 4.9 16.2 1.0 O A:HOH554 4.9 22.7 1.0 HB2 A:GLU110 5.0 17.4 0.5

E.Sijbesma, B.A.Somsen, G.P.Miley, I.A.Leijten-Van De Gevel, L.Brunsveld, M.R.Arkin, C.Ottmann. Fluorescence Anisotropy-Based Tethering For Discovery of Protein-Protein Interaction Stabilizers. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 33196173
DOI: 10.1021/ACSCHEMBIO.0C00646