Magnesium in PDB 6r5l: Fragment Az-006 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-006 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6r5l 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)	26.42 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.550, 111.980, 62.400, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.8

The structure of Fragment Az-006 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-006 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6r5l). 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-006 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6r5l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Fragment Az-006 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-006 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:25.2 occ:1.00 O A:HOH470 2.2 27.3 1.0 O A:HOH526 2.4 30.8 1.0 OE2 A:GLU89 2.4 16.4 1.0 CD A:GLU89 3.5 13.1 1.0 O A:HOH502 4.1 25.2 1.0 CG A:GLU89 4.2 10.9 1.0 OE1 A:GLU89 4.4 9.5 1.0 NH1 A:ARG85 4.4 16.6 1.0 CG A:GLU86 4.6 17.6 1.0 OE1 A:GLN93 4.7 13.5 1.0 NE2 A:GLN93 4.8 11.9 1.0 CB A:GLU89 4.9 11.6 1.0 OG1 A:THR90 5.0 17.3 1.0

Magnesium binding site 2 out of 2 in the Fragment Az-006 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-006 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:6.8 occ:0.50 OE1 A:GLU2 2.4 16.8 1.0 O A:HOH487 2.5 14.2 1.0 O A:HOH527 2.7 32.9 1.0 CD A:GLU2 3.4 17.4 1.0 OE2 A:GLU2 3.8 14.0 1.0 O A:HOH507 4.3 11.7 1.0 O A:HOH544 4.4 13.7 1.0 CG A:GLU2 4.7 12.3 1.0 CA A:GLU2 4.9 12.0 1.0 N A:ARG3 4.9 10.8 1.0 CB A:GLU2 5.0 9.0 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