Magnesium in PDB 5xf3: Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration)

The structure of Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration), PDB code: 5xf3 was solved by Z.Ma, Z.Adhireksan, B.S.Murray, P.J.Dyson, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.75 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.190, 109.400, 174.820, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27

The structure of Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration) also contains other interesting chemical elements:

Ruthenium

(Ru)

2 atoms

The binding sites of Magnesium atom in the Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration) (pdb code 5xf3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration), PDB code: 5xf3:

Magnesium binding site 1 out of 1 in the Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:67.1 occ:1.00 OD1 E:ASP77 2.3 69.6 1.0 CG E:ASP77 3.2 63.5 1.0 OD2 E:ASP77 3.4 66.9 1.0 O F:LEU22 3.9 63.2 1.0 OE1 E:GLN76 4.1 77.4 1.0 CG E:GLU73 4.5 53.2 1.0 O E:GLU73 4.6 68.8 1.0 CB E:ASP77 4.7 56.2 1.0 N E:ASP77 4.9 60.9 1.0 CD E:GLN76 5.0 69.2 1.0

G.E.Davey, Z.Adhireksan, Z.Ma, T.Riedel, D.Sharma, S.Padavattan, D.Rhodes, A.Ludwig, S.Sandin, B.S.Murray, P.J.Dyson, C.A.Davey. Nucleosome Acidic Patch-Targeting Binuclear Ruthenium Compounds Induce Aberrant Chromatin Condensation Nat Commun V. 8 1575 2017.
ISSN: ESSN 2041-1723
PubMed: 29146919
DOI: 10.1038/S41467-017-01680-4