Magnesium in PDB 6s40: Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40 was solved by S.Leysen, X.Guillory, M.Wolter, S.Genet, B.Somsen, 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)	41.04 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.090, 112.115, 62.604, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.7

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	6 atoms

The binding sites of Magnesium atom in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites (pdb code 6s40). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:10.3 occ:1.00 OE2 A:GLU188 2.2 22.7 1.0 CD A:GLU188 3.3 23.6 1.0 CG A:GLU188 3.8 21.8 1.0 OE1 A:GLU188 4.4 22.8 1.0 O A:HOH594 4.5 31.1 1.0

Magnesium binding site 2 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:26.4 occ:0.98 O A:HOH430 2.1 35.5 1.0 OE2 A:GLU89 2.3 16.5 1.0 O A:HOH479 2.4 36.4 1.0 CD A:GLU89 3.3 15.2 1.0 O A:HOH455 4.0 29.6 1.0 CG A:GLU89 4.1 14.6 1.0 O A:HOH552 4.1 38.3 1.0 OE1 A:GLU89 4.3 13.9 1.0 NH1 A:ARG85 4.3 17.8 1.0 OE1 A:GLN93 4.5 13.8 1.0 CG A:GLU86 4.6 20.4 1.0 CB A:GLU89 4.7 14.0 1.0 NE2 A:GLN93 4.8 14.0 1.0 O A:HOH570 4.9 32.5 1.0 OG1 A:THR90 4.9 13.2 0.7

Magnesium binding site 3 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:7.8 occ:0.50 OE1 A:GLU2 2.4 13.2 1.0 O A:HOH429 2.5 13.3 1.0 CD A:GLU2 3.4 13.8 1.0 OE2 A:GLU2 3.7 14.2 1.0 O A:HOH530 4.3 10.2 1.0 O A:HOH606 4.5 16.3 1.0 CG A:GLU2 4.6 12.7 1.0 CA A:GLU2 4.8 11.2 1.0 N A:ARG3 4.9 10.5 1.0 CB A:GLU2 5.0 12.1 1.0

Magnesium binding site 4 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:44.2 occ:1.00 O A:HOH476 2.1 28.3 1.0 O A:HOH420 2.5 21.0 1.0 N A:MET-2 3.0 19.2 1.0 N A:ALA-3 3.3 26.2 1.0 OE1 A:GLU31 3.3 19.8 1.0 CB A:MET-2 3.4 16.0 1.0 CA A:GLY-4 3.4 31.8 1.0 O A:HOH473 3.4 11.8 1.0 C A:GLY-4 3.4 29.3 1.0 CG A:MET-2 3.6 16.9 1.0 CA A:MET-2 3.7 17.3 1.0 O A:HOH529 3.9 33.0 1.0 C A:ALA-3 4.0 21.6 1.0 O A:HOH604 4.0 36.0 1.0 O A:HOH544 4.1 29.6 1.0 CA A:ALA-3 4.1 27.4 1.0 O A:GLY-4 4.2 23.6 1.0 CA A:GLY28 4.2 10.2 1.0 C A:MET-2 4.3 15.1 1.0 N A:GLY-1 4.3 13.9 1.0 CD A:GLU31 4.5 15.5 1.0 CB A:ALA-3 4.6 28.6 1.0 N A:GLY28 4.7 10.1 1.0 NZ A:LYS27 4.7 14.8 1.0 O A:HOH470 4.7 13.4 1.0 N A:GLY-4 4.8 35.6 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