Magnesium in PDB 4dho: 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: 4dho 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)	19.46 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.940, 111.690, 62.290, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.3

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

Chlorine

(Cl)

2 atoms

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

Magnesium binding site 1 out of 4 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:9.0 occ:0.50 O A:HOH528 2.4 38.1 1.0 OE1 A:GLU2 2.4 15.1 1.0 O A:HOH420 2.5 15.4 1.0 CD A:GLU2 3.4 13.4 1.0 O A:HOH595 3.7 45.5 1.0 OE2 A:GLU2 3.7 15.4 1.0 O A:HOH456 4.3 15.1 1.0 O A:HOH713 4.4 41.0 1.0 O A:HOH431 4.5 15.1 1.0 CG A:GLU2 4.7 12.1 1.0 CA A:GLU2 4.9 9.4 1.0 N A:ARG3 4.9 8.8 1.0

Magnesium binding site 2 out of 4 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:8.8 occ:1.00 O A:HOH575 2.2 22.2 1.0 O A:GLU110 2.2 13.2 1.0 O A:HOH585 2.2 29.0 1.0 OE1 A:GLU35 2.3 16.9 1.0 OE2 A:GLU35 2.8 21.1 1.0 CD A:GLU35 2.9 18.4 1.0 C A:GLU110 3.5 11.7 1.0 N A:GLY112 3.9 15.2 1.0 CA A:GLU110 4.4 11.3 0.5 CA A:GLU110 4.4 11.9 0.5 CG A:GLU35 4.4 12.2 1.0 N A:ALA111 4.4 10.9 1.0 CA A:ALA111 4.5 12.7 1.0 CB A:GLU110 4.6 11.2 0.5 O A:HOH651 4.6 38.5 1.0 CA A:GLY112 4.6 15.9 1.0 C A:ALA111 4.6 13.9 1.0 OE1 A:GLU110 4.6 11.3 0.5 CL A:CL305 4.7 53.0 1.0 CB A:GLU110 4.7 12.2 0.5 O A:HOH649 4.8 26.7 1.0 O A:HOH468 5.0 25.3 1.0

Magnesium binding site 3 out of 4 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:25.1 occ:1.00 O A:HOH660 2.2 28.0 1.0 OE1 A:GLU86 2.4 13.7 0.4 OE2 A:GLU86 2.4 14.9 0.4 OE2 A:GLU89 2.4 16.3 1.0 CD A:GLU86 2.7 12.2 0.4 O A:HOH604 3.0 35.0 1.0 CD A:GLU89 3.5 10.3 1.0 O A:HOH605 4.1 27.8 1.0 CG A:GLU89 4.2 11.3 1.0 CG A:GLU86 4.3 13.2 0.4 O A:HOH564 4.3 33.2 1.0 OE1 A:GLU89 4.5 12.7 1.0 NH1 A:ARG85 4.5 16.7 1.0 OE1 A:GLN93 4.5 15.4 1.0 NE2 A:GLN93 4.6 11.5 1.0 CB A:GLU89 4.8 9.6 1.0 OG1 A:THR90 4.8 14.2 1.0 CG A:GLU86 4.9 14.3 0.6 CD A:GLN93 5.0 12.6 1.0

Magnesium binding site 4 out of 4 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 4 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:Mg304 b:33.5 occ:1.00 O A:GLU161 2.3 16.8 1.0 O A:HOH539 2.4 31.4 1.0 O A:HOH573 2.5 44.0 1.0 O A:HOH541 2.6 32.9 1.0 C A:GLU161 3.5 14.7 1.0 CA A:MET162 4.3 14.4 1.0 N A:MET162 4.3 13.6 1.0 CA A:GLU161 4.4 14.4 0.3 CA A:GLU161 4.4 14.1 0.7 CB A:GLU161 4.8 14.6 0.3 CD A:PRO163 4.8 15.8 1.0 CB A:GLU161 4.8 14.8 0.7 O A:HOH501 4.9 19.8 0.5

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