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Magnesium in PDB 4dhn: 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: 4dhn 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) 45.41 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.180, 111.800, 62.400, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 18.5

Other elements in 4dhn:

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

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 4dhn). 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: 4dhn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4dhn

Go back to Magnesium Binding Sites List in 4dhn
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:10.2
occ:0.50
O A:HOH489 2.3 43.9 1.0
OE1 A:GLU2 2.4 18.4 1.0
O A:HOH425 2.6 16.6 1.0
CD A:GLU2 3.4 15.9 1.0
OE2 A:GLU2 3.8 14.7 1.0
O A:HOH435 4.3 13.5 1.0
O A:HOH427 4.5 15.4 1.0
O A:HOH729 4.6 39.7 1.0
CG A:GLU2 4.7 11.9 1.0
CA A:GLU2 4.8 10.6 1.0
O A:HOH475 4.9 28.2 1.0
N A:ARG3 4.9 10.0 1.0
CB A:GLU2 5.0 11.4 1.0

Magnesium binding site 2 out of 3 in 4dhn

Go back to Magnesium Binding Sites List in 4dhn
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:9.1
occ:1.00
O A:HOH561 2.1 25.2 1.0
O A:HOH586 2.2 31.2 1.0
O A:GLU110 2.2 14.5 1.0
OE1 A:GLU35 2.3 18.8 1.0
O A:HOH597 2.3 21.7 1.0
OE2 A:GLU35 2.7 25.0 1.0
CD A:GLU35 2.9 23.0 1.0
C A:GLU110 3.5 13.6 1.0
N A:GLY112 3.9 18.0 1.0
CG A:GLU35 4.4 15.5 1.0
CA A:GLU110 4.4 12.6 0.5
CA A:GLU110 4.4 12.8 0.5
CB A:GLU110 4.4 13.5 0.5
N A:ALA111 4.5 11.7 1.0
CA A:ALA111 4.5 12.3 1.0
O A:HOH503 4.5 23.7 1.0
O A:HOH593 4.6 39.7 1.0
O A:HOH598 4.6 33.2 1.0
OE1 A:GLU110 4.6 14.2 0.5
CB A:GLU110 4.7 13.7 0.5
C A:ALA111 4.7 15.6 1.0
CA A:GLY112 4.7 18.3 1.0
O A:HOH573 4.8 34.0 1.0
CL A:CL305 4.8 54.7 1.0
O A:HOH466 5.0 28.9 1.0

Magnesium binding site 3 out of 3 in 4dhn

Go back to Magnesium Binding Sites List in 4dhn
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:28.8
occ:1.00
O A:HOH705 1.9 27.1 0.5
O A:HOH644 2.1 28.0 1.0
OE2 A:GLU86 2.4 14.9 0.4
O A:HOH705 2.4 25.5 0.5
OE1 A:GLU86 2.5 15.0 0.4
OE2 A:GLU89 2.5 17.6 1.0
CD A:GLU86 2.8 12.9 0.4
CD A:GLU89 3.5 11.1 1.0
O A:HOH619 4.0 30.0 1.0
CG A:GLU89 4.1 12.9 1.0
CG A:GLU86 4.3 14.5 0.4
O A:HOH544 4.4 31.8 1.0
OE1 A:GLU89 4.4 12.4 1.0
OE1 A:GLN93 4.5 14.7 1.0
NH1 A:ARG85 4.5 17.5 1.0
NE2 A:GLN93 4.7 15.3 1.0
CB A:GLU89 4.8 12.7 1.0
O A:HOH643 4.8 33.1 1.0
OG1 A:THR90 4.9 16.8 1.0
CG A:GLU86 4.9 13.3 0.6
CD A:GLN93 5.0 17.9 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: Mon Dec 14 12:22:19 2020

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