Magnesium in PDB 6slv: Fragment Az-013 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-013 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6slv was solved by C.Ottmann, M.Wolter, X.Guillory, S.Leysen, S.Genet, B.Somsen, J.Patel, P.Castaldi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.84 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.322, 112.398, 62.672, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.8

The structure of Fragment Az-013 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-013 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6slv). 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-013 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6slv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Fragment Az-013 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-013 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:3.8 occ:1.00 O A:HOH478 2.3 16.6 1.0 OE2 A:GLU188 2.3 18.1 1.0 HG2 A:GLU188 3.3 17.7 1.0 CD A:GLU188 3.4 15.1 1.0 CG A:GLU188 3.8 14.7 1.0 HG3 A:GLU188 4.3 17.7 1.0 OE1 A:GLU188 4.4 12.2 1.0 O A:HOH640 4.7 22.3 1.0 HB3 A:GLU188 5.0 13.6 1.0

Magnesium binding site 2 out of 3 in the Fragment Az-013 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-013 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:15.2 occ:1.00 O A:HOH419 2.0 35.6 1.0 O A:HOH420 2.2 21.6 1.0 OE2 A:GLU89 2.3 8.9 1.0 OE1 A:GLU86 2.3 14.5 0.5 OE2 A:GLU86 2.4 9.7 0.5 O A:HOH584 2.5 34.2 1.0 CD A:GLU86 2.7 10.0 0.5 CD A:GLU89 3.3 7.9 1.0 HG2 A:GLU86 3.7 15.6 0.5 HG2 A:GLU89 3.7 9.6 1.0 HH12 A:ARG85 3.8 14.4 1.0 HE22 A:GLN93 4.0 10.1 1.0 CG A:GLU89 4.1 8.0 1.0 HH11 A:ARG85 4.2 14.4 1.0 OE1 A:GLU89 4.2 8.5 1.0 O A:HOH494 4.2 21.4 1.0 HB3 A:GLU89 4.2 7.0 1.0 CG A:GLU86 4.2 13.9 0.5 HA A:GLU86 4.3 8.5 0.5 HA A:GLU86 4.3 8.5 0.5 NH1 A:ARG85 4.3 12.0 1.0 O A:HOH574 4.4 23.1 1.0 HG1 A:THR90 4.4 15.3 1.0 OE1 A:GLN93 4.5 8.7 1.0 HB3 A:GLU86 4.6 11.2 0.5 HG2 A:GLU86 4.6 16.7 0.5 CG A:GLU86 4.6 13.0 0.5 O A:HOH554 4.7 20.8 1.0 HG3 A:GLU86 4.7 16.7 0.5 NE2 A:GLN93 4.7 8.4 1.0 CB A:GLU89 4.7 5.8 1.0 OG1 A:THR90 4.8 12.8 1.0 HB3 A:GLU86 4.9 11.2 0.5 HG3 A:GLU89 4.9 9.6 1.0 CB A:GLU86 5.0 9.3 0.5 CB A:GLU86 5.0 9.3 0.5

Magnesium binding site 3 out of 3 in the Fragment Az-013 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-013 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:5.1 occ:0.52 OE1 A:GLU2 2.4 10.6 1.0 O A:HOH602 2.5 38.4 1.0 O A:HOH459 2.6 6.2 1.0 CD A:GLU2 3.5 9.1 1.0 OE2 A:GLU2 3.9 10.3 1.0 HA A:GLU2 4.0 6.8 1.0 H A:ARG3 4.1 8.9 1.0 O A:HOH556 4.3 4.7 1.0 O A:HOH649 4.5 9.0 1.0 HB3 A:GLU2 4.6 7.0 1.0 CG A:GLU2 4.7 4.8 1.0 CA A:GLU2 4.9 5.7 1.0 O A:HOH479 4.9 23.5 1.0 N A:ARG3 5.0 7.4 1.0 CB A:GLU2 5.0 5.8 1.0 HG2 A:GLU2 5.0 5.8 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