Magnesium in PDB 6rwh: Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex

The structure of Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex, PDB code: 6rwh 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)	21.71 / 1.68
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.642, 112.176, 63.089, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.7

The structure of Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex (pdb code 6rwh). 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-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex, PDB code: 6rwh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:30.0 occ:1.00 OE2 A:GLU35 1.9 22.3 1.0 O A:HOH545 2.2 25.4 1.0 O A:HOH524 2.4 26.1 1.0 OE1 A:GLU35 2.5 27.4 1.0 CD A:GLU35 2.5 21.9 1.0 O A:GLU110 2.5 19.5 1.0 C A:GLU110 3.8 18.3 1.0 CG A:GLU35 4.0 18.6 1.0 N A:GLY112 4.5 19.9 1.0 O A:HOH419 4.5 28.2 1.0 CA A:GLU110 4.6 15.9 0.6 CA A:GLU110 4.6 16.6 0.4 CB A:GLU110 4.6 16.0 0.6 CB A:GLU110 4.7 17.3 0.4 N A:ALA111 4.8 17.6 1.0 OE1 A:GLU110 4.8 17.7 0.6 CA A:ALA111 4.9 18.4 1.0 O A:HOH530 5.0 25.6 1.0

Magnesium binding site 2 out of 2 in the Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fragment Az-007 Binding at A Primary and Secondary Binding Site of the the P53PT387/14-3-3 Sigma Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg401 b:30.0 occ:1.00 O P:HOH504 2.1 34.4 1.0 OD1 P:ASP391 2.2 52.7 1.0 O P:HOH502 2.3 30.4 1.0 OD1 P:ASP393 2.3 36.2 1.0 O P:HOH505 2.6 31.5 1.0 CG P:ASP393 3.3 37.4 1.0 CG P:ASP391 3.4 48.0 1.0 OD2 P:ASP393 3.7 31.1 1.0 OD2 P:ASP391 4.2 52.9 1.0 O1P P:TPO387 4.3 20.0 1.0 CB P:MET384 4.3 33.3 1.0 CA P:ASP391 4.4 42.1 1.0 OXT P:ASP393 4.4 43.7 1.0 CB P:ASP391 4.4 45.8 1.0 O P:HOH506 4.5 32.4 1.0 O P:HOH503 4.5 22.7 1.0 C P:ASP393 4.6 42.5 1.0 N P:ASP393 4.6 38.5 1.0 CB P:ASP393 4.6 33.5 1.0 CG P:MET384 4.8 33.8 1.0 O P:PHE385 4.8 22.8 1.0 C P:ASP391 4.8 43.8 1.0 CA P:ASP393 4.8 39.2 1.0 N P:SER392 5.0 39.1 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