Magnesium in PDB 6rl4: Fragment Az-025 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-025 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rl4 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)	66.10 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.888, 111.996, 62.647, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.1

The structure of Fragment Az-025 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-025 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6rl4). 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-025 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rl4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Fragment Az-025 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-025 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:24.2 occ:1.00 HG2 A:GLU188 2.8 14.9 1.0 O A:HOH669 3.0 27.4 1.0 O A:HOH551 3.2 17.0 1.0 CG A:GLU188 3.7 12.4 1.0 OE2 A:GLU188 3.7 15.5 1.0 O A:HOH633 3.9 40.1 1.0 HD12 A:ILE191 3.9 15.8 1.0 HG3 A:GLU188 3.9 14.9 1.0 HD13 A:ILE191 3.9 15.8 1.0 CD A:GLU188 4.2 15.1 1.0 HA A:GLU188 4.2 13.1 1.0 O A:HOH704 4.3 41.0 1.0 CD1 A:ILE191 4.4 13.2 1.0 O A:HOH466 4.4 34.6 1.0 O A:HOH473 4.6 20.8 1.0 CB A:GLU188 4.7 13.8 1.0 HD11 A:ILE191 4.8 15.8 1.0 HB3 A:GLU188 4.8 16.5 1.0 HG21 A:ILE191 4.9 15.2 1.0 CA A:GLU188 4.9 10.9 1.0

Magnesium binding site 2 out of 2 in the Fragment Az-025 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-025 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:16.4 occ:1.00 O A:HOH621 2.3 40.9 1.0 O A:HOH417 2.3 23.8 1.0 OE1 A:GLU86 2.4 17.2 0.5 O A:HOH615 2.4 25.4 1.0 OE2 A:GLU86 2.4 19.6 0.5 OE2 A:GLU89 2.4 15.4 1.0 CD A:GLU86 2.7 15.2 0.5 CD A:GLU89 3.5 9.0 1.0 HG2 A:GLU89 3.7 11.0 1.0 HH12 A:ARG85 3.8 18.9 1.0 HG2 A:GLU86 4.0 12.0 0.5 HE22 A:GLN93 4.0 15.9 1.0 O A:HOH518 4.1 26.8 1.0 CG A:GLU89 4.1 9.1 1.0 HH11 A:ARG85 4.2 18.9 1.0 CG A:GLU86 4.3 15.4 0.5 HB3 A:GLU89 4.3 12.3 1.0 NH1 A:ARG85 4.4 15.8 1.0 OE1 A:GLU89 4.4 11.3 1.0 HA A:GLU86 4.4 12.5 0.5 HA A:GLU86 4.4 12.4 0.5 O A:HOH521 4.5 26.2 1.0 HG1 A:THR90 4.5 16.6 1.0 OE1 A:GLN93 4.5 13.7 1.0 O A:HOH565 4.6 27.3 1.0 HG2 A:GLU86 4.6 18.5 0.5 HG3 A:GLU86 4.7 18.5 0.5 HB3 A:GLU86 4.7 14.4 0.5 NE2 A:GLN93 4.7 13.2 1.0 CB A:GLU89 4.8 10.3 1.0 CG A:GLU86 4.8 10.0 0.5 OG1 A:THR90 4.8 13.8 1.0 O A:HOH406 4.9 35.1 1.0 HG3 A:GLU89 4.9 11.0 1.0 HB3 A:GLU86 5.0 14.5 0.5 CD A:GLN93 5.0 14.8 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