Magnesium in PDB 4dhm: Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening

The structure of Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening, PDB code: 4dhm was solved by P.Thiel, L.Roeglin, O.Kohlbacher, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.52 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.200, 112.280, 62.440, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.7

The structure of Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening (pdb code 4dhm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening, PDB code: 4dhm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:7.8 occ:0.50 O A:HOH485 2.2 18.0 0.5 OE1 A:GLU2 2.3 17.0 1.0 O A:HOH443 2.5 18.6 1.0 O A:HOH485 2.8 23.4 0.5 CD A:GLU2 3.3 14.3 1.0 OE2 A:GLU2 3.7 14.2 1.0 O A:HOH428 4.3 12.6 1.0 O A:HOH427 4.5 16.1 1.0 CG A:GLU2 4.6 10.3 1.0 CA A:GLU2 4.8 8.3 1.0 O A:HOH472 4.9 24.4 1.0 N A:ARG3 4.9 8.1 1.0 CB A:GLU2 5.0 8.5 1.0

Magnesium binding site 2 out of 3 in the Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:8.2 occ:1.00 O A:GLU110 2.2 13.1 1.0 O A:HOH530 2.3 23.4 1.0 OE1 A:GLU35 2.3 19.2 1.0 O A:HOH610 2.3 35.8 1.0 OE2 A:GLU35 2.8 25.8 1.0 CD A:GLU35 2.9 21.1 1.0 C A:GLU110 3.5 10.8 1.0 N A:GLY112 4.0 14.6 1.0 CA A:GLU110 4.4 9.7 0.5 CA A:GLU110 4.4 10.4 0.5 CG A:GLU35 4.4 12.8 1.0 CB A:GLU110 4.4 9.4 0.5 N A:ALA111 4.5 9.0 1.0 CA A:ALA111 4.5 11.5 1.0 O A:HOH523 4.5 26.0 1.0 OE1 A:GLU110 4.6 9.9 0.5 CB A:GLU110 4.6 10.7 0.5 CL A:CL304 4.7 55.4 1.0 C A:ALA111 4.7 12.7 1.0 O A:HOH616 4.7 41.8 1.0 O A:HOH567 4.7 25.2 1.0 CA A:GLY112 4.7 15.8 1.0

Magnesium binding site 3 out of 3 in the Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:24.5 occ:1.00 O A:HOH684 2.2 31.8 1.0 OE1 A:GLU86 2.2 10.8 0.4 O A:HOH733 2.4 50.0 1.0 OE2 A:GLU89 2.5 17.6 1.0 O A:HOH764 2.5 40.0 1.0 OE2 A:GLU86 2.7 16.3 0.4 CD A:GLU86 2.8 12.6 0.4 CD A:GLU89 3.5 12.8 1.0 O A:HOH550 4.1 29.1 1.0 CG A:GLU89 4.2 11.6 1.0 CG A:GLU86 4.2 13.0 0.4 O A:HOH576 4.4 30.9 1.0 OE1 A:GLU89 4.4 13.7 1.0 OE1 A:GLN93 4.5 13.4 1.0 NH1 A:ARG85 4.5 17.1 1.0 NE2 A:GLN93 4.7 13.9 1.0 CG A:GLU86 4.7 10.1 0.6 CB A:GLU89 4.8 10.9 1.0 O A:HOH605 4.8 35.1 1.0 OG1 A:THR90 4.8 12.1 0.8 CG2 A:THR90 4.9 8.8 0.2

P.Thiel, L.Roglin, N.Meissner, S.Hennig, O.Kohlbacher, C.Ottmann. Virtual Screening and Experimental Validation Reveal Novel Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions. Chem.Commun.(Camb.) V. 49 8468 2013.
ISSN: ISSN 1359-7345
PubMed: 23939230
DOI: 10.1039/C3CC44612C