Magnesium in PDB 6rk8: Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rk8 was solved by S.Genet, M.Wolter, X.Guillory, B.Somsen, S.Leysen, J.Patel, P.Castaldi, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.03 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.264, 112.131, 62.878, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.9

The structure of Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6rk8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rk8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:16.0 occ:1.00 OE2 A:GLU188 2.3 25.7 1.0 HG2 A:GLU188 3.3 22.0 1.0 CD A:GLU188 3.3 27.2 1.0 CG A:GLU188 3.8 18.3 1.0 HG3 A:GLU188 4.2 22.0 1.0 OE1 A:GLU188 4.4 24.3 1.0

Magnesium binding site 2 out of 2 in the Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fragment Az-014 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:34.0 occ:1.00 OE2 A:GLU89 2.3 22.2 1.0 CD A:GLU89 3.3 16.6 1.0 HG2 A:GLU89 3.6 19.2 1.0 HG2 A:GLU86 3.8 20.9 1.0 HH12 A:ARG85 3.9 26.3 1.0 CG A:GLU89 4.0 16.0 1.0 HB3 A:GLU89 4.0 18.3 1.0 HE22 A:GLN93 4.1 25.6 1.0 HH11 A:ARG85 4.2 26.3 1.0 OE1 A:GLU89 4.3 14.2 1.0 HA A:GLU86 4.3 15.1 1.0 HG1 A:THR90 4.4 24.1 1.0 NH1 A:ARG85 4.4 21.9 1.0 OE1 A:GLN93 4.5 21.0 1.0 CB A:GLU89 4.6 15.2 1.0 HB3 A:GLU86 4.6 19.7 1.0 CG A:GLU86 4.7 17.4 1.0 NE2 A:GLN93 4.7 21.4 1.0 HG3 A:GLU89 4.8 19.2 1.0 OG1 A:THR90 4.8 20.0 1.0 CD A:GLN93 5.0 20.1 1.0

X.Guillory, M.Wolter, S.Leysen, J.F.Neves, A.Kuusk, S.Genet, B.Somsen, J.Morrow, E.Rivers, L.Van Beek, J.Patel, R.Goodnow, H.Schoenherr, N.Fuller, Q.Cao, R.G.Doveston, L.Brunsveld, M.R.Arkin, M.P.Castaldi, H.Boyd, I.Landrieu, H.Chen, C.Ottmann. Fragment-Based Differential Targeting of Ppi Stabilizer Interfaces. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32501690
DOI: 10.1021/ACS.JMEDCHEM.9B01942