Magnesium in PDB 6rki: Fragment Az-023 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-023 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rki was solved by S.Genet, M.Wolter, X.Guillory, B.Somsen, S.Leysen, P.Castaldi, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.62 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.189, 112.530, 62.650, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 20.6

The structure of Fragment Az-023 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-023 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6rki). 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-023 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rki:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Fragment Az-023 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-023 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:4.1 occ:1.00 O A:HOH475 2.2 20.1 1.0 OE2 A:GLU188 2.3 14.1 1.0 CD A:GLU188 3.4 11.8 1.0 CG A:GLU188 3.9 10.7 1.0 OE1 A:GLU188 4.4 12.4 1.0 O A:HOH708 4.5 21.6 1.0

Magnesium binding site 2 out of 2 in the Fragment Az-023 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-023 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:12.9 occ:1.00 O A:HOH437 1.9 30.5 1.0 O A:HOH466 2.1 19.3 1.0 OE1 A:GLU86 2.3 8.5 0.5 OE2 A:GLU86 2.3 8.2 0.5 OE2 A:GLU89 2.4 9.5 1.0 O A:HOH629 2.5 23.4 1.0 CD A:GLU86 2.6 8.7 0.5 CD A:GLU89 3.4 8.3 1.0 CG A:GLU89 4.1 8.2 1.0 CG A:GLU86 4.1 8.8 0.5 O A:HOH555 4.1 23.9 1.0 O A:HOH617 4.2 23.8 1.0 OE1 A:GLU89 4.3 8.5 1.0 NH1 A:ARG85 4.4 11.3 1.0 OE1 A:GLN93 4.5 7.7 1.0 O A:HOH698 4.5 48.8 1.0 O A:HOH546 4.6 20.9 1.0 NE2 A:GLN93 4.7 7.5 1.0 CB A:GLU89 4.8 7.7 1.0 OG1 A:THR90 4.8 8.8 1.0 O A:HOH403 4.8 37.5 1.0 CG A:GLU86 4.9 10.5 0.5 CD A:GLN93 5.0 7.6 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