Magnesium in PDB 8c4f: Small Molecule Amidine Soak in 14-3-3/Era (AZ037)

The structure of Small Molecule Amidine Soak in 14-3-3/Era (AZ037), PDB code: 8c4f was solved by E.J.Visser, E.Sijbesma, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.36 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.703, 111.843, 62.472, 90, 90, 90
R / Rfree (%)	18.4 / 20.1

The binding sites of Magnesium atom in the Small Molecule Amidine Soak in 14-3-3/Era (AZ037) (pdb code 8c4f). 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 Amidine Soak in 14-3-3/Era (AZ037), PDB code: 8c4f:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Small Molecule Amidine Soak in 14-3-3/Era (AZ037)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Small Molecule Amidine Soak in 14-3-3/Era (AZ037) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:32.9 occ:1.00 O A:HOH420 3.5 21.6 1.0 O A:HOH666 4.1 37.2 1.0 HZ2 A:LYS159 4.2 49.6 1.0 HZ1 A:LYS159 4.3 49.6 1.0 O A:HOH444 4.3 30.7 1.0 NZ A:LYS159 4.6 41.3 1.0 OE2 A:GLU189 4.7 18.3 1.0 O A:HOH595 4.9 38.3 1.0 HZ3 A:LYS159 5.0 49.6 1.0

Magnesium binding site 2 out of 3 in the Small Molecule Amidine Soak in 14-3-3/Era (AZ037)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Small Molecule Amidine Soak in 14-3-3/Era (AZ037) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:18.1 occ:0.62 O A:HOH423 2.6 20.7 1.0 OE1 A:GLU2 2.7 21.4 1.0 CD A:GLU2 3.7 22.1 1.0 OE2 A:GLU2 4.0 22.4 1.0 HA A:GLU2 4.1 17.9 1.0 H A:ARG3 4.2 17.6 1.0 O A:HOH571 4.5 22.2 1.0 O A:HOH659 4.6 21.1 1.0 CG A:GLU2 4.9 18.9 1.0 HB3 A:GLU2 5.0 19.3 1.0 CA A:GLU2 5.0 14.9 1.0 N A:ARG3 5.0 14.6 1.0

Magnesium binding site 3 out of 3 in the Small Molecule Amidine Soak in 14-3-3/Era (AZ037)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Small Molecule Amidine Soak in 14-3-3/Era (AZ037) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:25.0 occ:1.00 O A:HOH596 2.4 36.8 1.0 OE2 A:GLU89 2.4 21.7 1.0 CD A:GLU89 3.5 16.6 1.0 HG2 A:GLU86 3.7 25.7 1.0 HG2 A:GLU89 3.7 19.5 1.0 HH12 A:ARG85 3.9 27.8 1.0 O A:HOH564 4.0 32.2 1.0 HE22 A:GLN93 4.1 20.5 1.0 CG A:GLU89 4.2 16.2 1.0 HH11 A:ARG85 4.3 27.8 1.0 HB3 A:GLU89 4.4 19.3 1.0 OE1 A:GLU89 4.4 16.7 1.0 O A:HOH486 4.4 33.9 1.0 NH1 A:ARG85 4.5 23.2 1.0 OE1 A:GLN93 4.5 18.4 1.0 HG1 A:THR90 4.5 24.9 1.0 HA A:GLU86 4.5 19.3 1.0 CG A:GLU86 4.6 21.4 1.0 O A:HOH608 4.7 37.1 1.0 HB3 A:GLU86 4.7 22.2 1.0 NE2 A:GLN93 4.7 17.1 1.0 OG1 A:THR90 4.8 20.8 1.0 CB A:GLU89 4.9 16.1 1.0 HG3 A:GLU89 4.9 19.5 1.0

E.J.Visser, P.Jaishankar, E.Sijbesma, M.A.M.Pennings, E.M.F.Vandenboorn, X.Guillory, R.J.Neitz, J.Morrow, S.Dutta, A.R.Renslo, L.Brunsveld, M.R.Arkin, C.Ottmann. From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions Via Fragment Linking. Angew.Chem.Int.Ed.Engl. 08004 2023.
ISSN: ESSN 1521-3773
PubMed: 37455289
DOI: 10.1002/ANIE.202308004