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

Protein crystallography data

The structure of Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening, PDB code: 4dhp 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) 19.53 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.250, 112.230, 62.420, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19.6

Other elements in 4dhp:

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

Fluorine (F) 6 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening (pdb code 4dhp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Small-Molecule Inhibitors of 14-3-3 Protein-Protein Interactions From Virtual Screening, PDB code: 4dhp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4dhp

Go back to Magnesium Binding Sites List in 4dhp
Magnesium binding site 1 out of 5 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:7.5
occ:0.50
O A:HOH514 2.3 14.8 0.5
OE1 A:GLU2 2.4 13.3 1.0
O A:HOH427 2.6 15.7 1.0
O A:HOH514 2.9 26.8 0.5
CD A:GLU2 3.4 10.8 1.0
OE2 A:GLU2 3.7 11.7 1.0
O A:HOH422 4.3 10.7 1.0
O A:HOH430 4.5 13.7 1.0
O A:HOH751 4.5 49.2 1.0
CG A:GLU2 4.7 8.7 1.0
O A:HOH667 4.7 36.3 1.0
CA A:GLU2 4.8 6.9 1.0
O A:HOH457 4.9 19.4 1.0
N A:ARG3 4.9 7.0 1.0
CB A:GLU2 5.0 7.5 1.0

Magnesium binding site 2 out of 5 in 4dhp

Go back to Magnesium Binding Sites List in 4dhp
Magnesium binding site 2 out of 5 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:6.6
occ:1.00
OE2 A:GLU188 2.3 16.8 1.0
O A:HOH501 2.4 20.3 1.0
CD A:GLU188 3.4 13.0 1.0
CG A:GLU188 3.8 10.1 1.0
OE1 A:GLU188 4.4 16.5 1.0
O A:HOH503 4.6 28.3 1.0

Magnesium binding site 3 out of 5 in 4dhp

Go back to Magnesium Binding Sites List in 4dhp
Magnesium binding site 3 out of 5 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:24.1
occ:1.00
O A:HOH643 2.1 26.5 1.0
O A:HOH762 2.1 41.9 1.0
O A:HOH763 2.1 55.8 1.0
OE1 A:GLU86 2.4 12.5 0.4
OE2 A:GLU89 2.4 14.2 1.0
OE2 A:GLU86 2.5 13.9 0.4
O A:HOH600 2.8 36.8 1.0
CD A:GLU86 2.8 11.7 0.4
CD A:GLU89 3.5 9.2 1.0
O A:HOH526 4.1 24.9 1.0
CG A:GLU89 4.1 9.9 1.0
CG A:GLU86 4.3 10.8 0.4
OE1 A:GLU89 4.4 10.8 1.0
O A:HOH640 4.4 28.8 1.0
OE1 A:GLN93 4.5 12.4 1.0
NH1 A:ARG85 4.5 14.4 1.0
NE2 A:GLN93 4.6 13.4 1.0
CB A:GLU89 4.8 9.7 1.0
OG1 A:THR90 4.8 13.5 1.0
CG A:GLU86 4.8 10.1 0.6
O A:HOH596 4.9 40.8 1.0
CD A:GLN93 4.9 14.9 1.0

Magnesium binding site 4 out of 5 in 4dhp

Go back to Magnesium Binding Sites List in 4dhp
Magnesium binding site 4 out of 5 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:65.8
occ:1.00
OE1 A:GLU80 2.6 11.9 1.0
CA A:GLY78 3.3 17.1 1.0
N A:GLY78 3.3 19.9 1.0
CD A:GLU80 3.5 14.8 1.0
O A:HOH552 3.6 36.7 1.0
OE2 A:GLU80 3.9 13.8 1.0
O A:HOH574 4.0 29.5 1.0
C A:GLY78 4.1 15.1 1.0
O A:GLY78 4.6 16.6 1.0
CG A:GLU80 4.6 11.6 1.0
CB A:GLU80 4.8 11.0 1.0
N A:PRO79 4.8 13.9 1.0
N A:GLU80 5.0 10.8 1.0

Magnesium binding site 5 out of 5 in 4dhp

Go back to Magnesium Binding Sites List in 4dhp
Magnesium binding site 5 out of 5 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 5 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:Mg305

b:40.0
occ:1.00
O A:HOH402 2.1 33.3 1.0
O A:GLU161 2.3 14.1 1.0
O A:HOH550 2.6 29.6 1.0
C A:GLU161 3.5 12.9 1.0
CA A:MET162 4.4 11.0 1.0
N A:MET162 4.4 11.6 1.0
CA A:GLU161 4.4 12.8 0.3
CA A:GLU161 4.4 12.4 0.7
O A:HOH777 4.6 38.8 1.0
CD A:PRO163 4.8 13.4 1.0
CB A:GLU161 4.8 13.2 0.3
CB A:GLU161 4.8 12.7 0.7
OE1 A:GLU161 4.9 19.2 0.7
O A:HOH720 5.0 32.9 1.0

Reference:

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
Page generated: Thu Aug 15 17:09:57 2024

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