Magnesium in PDB 6rwi: Fragment Az-002 Binding at the P53PT387/14-3-3 Sigma Interface

The structure of Fragment Az-002 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rwi 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)	20.94 / 1.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.019, 112.193, 62.898, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.4

The structure of Fragment Az-002 Binding at the P53PT387/14-3-3 Sigma Interface also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Fragment Az-002 Binding at the P53PT387/14-3-3 Sigma Interface (pdb code 6rwi). 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-002 Binding at the P53PT387/14-3-3 Sigma Interface, PDB code: 6rwi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Fragment Az-002 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-002 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:30.0 occ:1.00 O A:HOH431 2.3 23.8 1.0 O A:HOH586 2.4 30.0 1.0 OE2 A:GLU86 2.4 35.8 0.5 OE1 A:GLU86 2.4 30.4 0.5 OE2 A:GLU89 2.5 14.5 1.0 O A:HOH606 2.5 33.1 1.0 CD A:GLU86 2.7 26.9 0.5 CD A:GLU89 3.5 11.8 1.0 CG A:GLU89 4.1 12.1 1.0 O A:HOH528 4.2 27.9 1.0 CG A:GLU86 4.2 18.2 0.5 NH1 A:ARG85 4.4 16.0 1.0 O A:HOH583 4.4 31.4 1.0 OE1 A:GLU89 4.4 13.4 1.0 O A:HOH598 4.5 27.8 1.0 OE1 A:GLN93 4.6 13.6 1.0 CG A:GLU86 4.6 18.2 0.5 OG1 A:THR90 4.8 13.1 1.0 NE2 A:GLN93 4.8 12.8 1.0 CB A:GLU89 4.8 11.3 1.0 O A:HOH408 4.9 33.4 1.0 CB A:GLU86 5.0 14.8 0.5 CB A:GLU86 5.0 14.8 0.5

Magnesium binding site 2 out of 2 in the Fragment Az-002 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-002 Binding at the P53PT387/14-3-3 Sigma Interface within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg401 b:30.0 occ:1.00 O P:HOH511 2.2 26.1 1.0 OD1 P:ASP393 2.2 32.9 1.0 OD1 P:ASP391 2.3 39.6 1.0 O P:HOH502 2.3 25.3 1.0 O P:HOH512 2.5 38.3 1.0 O P:HOH516 2.5 26.1 1.0 CG P:ASP393 3.2 34.1 1.0 CG P:ASP391 3.5 38.2 1.0 OD2 P:ASP393 3.6 28.5 1.0 O P:HOH517 4.0 24.5 1.0 OXT P:ASP393 4.2 41.4 1.0 CB P:MET384 4.2 26.3 1.0 OD2 P:ASP391 4.3 39.8 1.0 O1P P:TPO387 4.4 20.0 1.0 O P:HOH508 4.4 16.0 1.0 CA P:ASP391 4.4 32.1 1.0 O P:HOH505 4.4 38.3 1.0 CB P:ASP391 4.5 36.6 1.0 C P:ASP393 4.5 38.2 1.0 CB P:ASP393 4.5 30.2 1.0 O P:HOH519 4.5 45.5 1.0 O P:HOH513 4.5 30.8 1.0 N P:ASP393 4.6 34.9 1.0 CG P:MET384 4.7 26.6 1.0 CA P:ASP393 4.7 33.4 1.0 C P:ASP391 4.8 35.5 1.0 O P:PHE385 4.8 18.2 1.0 N P:SER392 5.0 32.8 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