Magnesium in PDB 6rm5: Fragment Az-016 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-016 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rm5 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)	26.47 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.729, 111.890, 62.670, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.7

The structure of Fragment Az-016 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-016 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6rm5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Fragment Az-016 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rm5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Fragment Az-016 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-016 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:24.1 occ:1.00 OE2 A:GLU188 2.2 35.9 1.0 HG2 A:GLU188 3.2 46.0 1.0 CD A:GLU188 3.2 36.6 1.0 CG A:GLU188 3.7 38.3 1.0 HG3 A:GLU188 3.9 46.0 1.0 OE1 A:GLU188 4.3 32.1 1.0

Magnesium binding site 2 out of 3 in the Fragment Az-016 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-016 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:44.4 occ:1.00 OE2 A:GLU89 2.3 30.5 1.0 CD A:GLU89 3.4 27.1 1.0 HG2 A:GLU89 3.5 34.9 1.0 HE22 A:GLN93 3.9 35.3 1.0 CG A:GLU89 4.0 29.1 1.0 HG2 A:GLU86 4.0 40.6 1.0 HB3 A:GLU89 4.2 34.8 1.0 HH12 A:ARG85 4.2 35.4 1.0 OE1 A:GLN93 4.3 28.9 1.0 OE1 A:GLU89 4.4 26.7 1.0 HG1 A:THR90 4.4 38.0 1.0 HA A:GLU86 4.4 30.8 1.0 HH11 A:ARG85 4.5 35.4 1.0 NE2 A:GLN93 4.6 29.4 1.0 CB A:GLU89 4.7 29.0 1.0 NH1 A:ARG85 4.7 29.5 1.0 HG3 A:GLU89 4.8 34.9 1.0 HB3 A:GLU86 4.8 34.0 1.0 OG1 A:THR90 4.8 31.7 1.0 CD A:GLN93 4.8 29.9 1.0 CG A:GLU86 4.9 33.8 1.0

Magnesium binding site 3 out of 3 in the Fragment Az-016 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 3 of Fragment Az-016 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:24.4 occ:0.50 OE1 A:GLU2 2.4 29.2 1.0 O A:HOH409 2.5 26.6 1.0 CD A:GLU2 3.4 27.6 1.0 OE2 A:GLU2 3.7 30.6 1.0 HA A:GLU2 4.0 30.6 1.0 H A:ARG3 4.2 27.1 1.0 O A:HOH465 4.3 23.1 1.0 O A:HOH483 4.5 27.7 1.0 HB3 A:GLU2 4.6 30.9 1.0 CG A:GLU2 4.7 25.1 1.0 CA A:GLU2 4.9 25.5 1.0 CB A:GLU2 4.9 25.7 1.0 N A:ARG3 5.0 22.6 1.0 HG2 A:GLU2 5.0 30.1 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