Magnesium in PDB 6rkk: Fragment Az-021 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-021 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rkk 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)	25.64 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.120, 112.420, 62.620, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 27.2

The structure of Fragment Az-021 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-021 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6rkk). 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-021 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rkk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Fragment Az-021 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-021 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:7.7 occ:1.00 O A:HOH568 2.1 16.5 1.0 OE2 A:GLU188 2.3 16.1 1.0 HG2 A:GLU188 3.3 18.0 1.0 CD A:GLU188 3.4 15.7 1.0 CG A:GLU188 3.8 15.0 1.0 HG3 A:GLU188 4.0 18.0 1.0 OE1 A:GLU188 4.4 10.7 1.0 O A:HOH738 4.5 20.2 1.0

Magnesium binding site 2 out of 2 in the Fragment Az-021 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-021 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:11.8 occ:1.00 O A:HOH495 2.1 19.2 1.0 OE2 A:GLU89 2.3 12.0 1.0 O A:HOH620 2.6 18.8 1.0 CD A:GLU89 3.3 11.2 1.0 HG2 A:GLU89 3.7 10.8 1.0 HH12 A:ARG85 3.7 14.1 1.0 HE22 A:GLN93 3.9 19.2 1.0 HG2 A:GLU86 4.0 20.7 1.0 CG A:GLU89 4.0 9.0 1.0 HH11 A:ARG85 4.1 14.1 1.0 O A:HOH513 4.1 21.3 1.0 OE1 A:GLU89 4.2 10.1 1.0 O A:HOH595 4.2 19.9 1.0 NH1 A:ARG85 4.3 11.7 1.0 HB3 A:GLU89 4.3 8.3 1.0 HA A:GLU86 4.4 11.0 1.0 OE1 A:GLN93 4.5 12.9 1.0 HG1 A:THR90 4.5 17.6 1.0 NE2 A:GLN93 4.6 16.0 1.0 HB3 A:GLU86 4.6 14.6 1.0 O A:HOH752 4.7 29.0 1.0 O A:HOH617 4.8 19.9 1.0 CB A:GLU89 4.8 6.9 1.0 CG A:GLU86 4.8 17.3 1.0 HG3 A:GLU89 4.8 10.8 1.0 OG1 A:THR90 4.9 14.7 1.0 CD A:GLN93 5.0 14.5 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