Ruthenium 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:

Magnesium

(Mg)

1 atom

The binding sites of Ruthenium 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 Ruthenium atom.
In total 2 binding sites of Ruthenium where 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:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 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 Ruthenium with other atoms in the Ru 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 G:Ru201 b:1.0 occ:1.00 RU G:RUD201 0.0 1.0 1.0 OE1 G:GLU64 2.1 0.8 1.0 OE2 G:GLU61 2.1 1.0 1.0 C22 G:RUD201 2.2 0.6 1.0 C21 G:RUD201 2.2 0.1 1.0 C23 G:RUD201 2.2 1.0 1.0 C18 G:RUD201 2.2 0.6 1.0 C20 G:RUD201 2.3 0.2 1.0 C19 G:RUD201 2.3 0.0 1.0 P1 G:RUD201 2.3 0.8 1.0 CD G:GLU64 3.2 1.0 1.0 CD G:GLU61 3.3 0.9 1.0 C24 G:RUD201 3.3 0.9 1.0 C17 G:RUD201 3.4 0.4 1.0 C4 G:RUD201 3.5 0.5 1.0 C5 G:RUD201 3.5 0.1 1.0 C3 G:RUD201 3.5 0.5 1.0 OE2 G:GLU64 3.9 0.8 1.0 OE1 G:GLU61 3.9 1.0 1.0 CG G:GLU64 4.3 98.8 1.0 CG G:GLU61 4.4 99.6 1.0 C25 G:RUD201 4.5 0.0 1.0 CB G:GLU64 4.7 84.3 1.0 N2 G:RUD201 4.8 0.1 1.0 N3 G:RUD201 4.8 0.6 1.0 N1 G:RUD201 4.8 0.7 1.0 CA G:GLU61 4.9 77.8 1.0

Ruthenium binding site 2 out of 2 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 Ruthenium with other atoms in the Ru binding site number 2 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 H:Ru201 b:0.4 occ:1.00 RU H:RUD201 0.0 0.4 1.0 OE1 H:GLU102 2.1 0.8 1.0 NE2 H:HIS106 2.2 0.2 1.0 C20 H:RUD201 2.2 0.4 1.0 C21 H:RUD201 2.2 0.3 1.0 C18 H:RUD201 2.2 0.4 1.0 C19 H:RUD201 2.3 0.7 1.0 C22 H:RUD201 2.3 0.5 1.0 C23 H:RUD201 2.3 0.0 1.0 P1 H:RUD201 2.4 0.4 1.0 CE1 H:HIS106 2.7 0.3 1.0 CD H:GLU102 3.4 1.0 1.0 C24 H:RUD201 3.4 0.8 1.0 C17 H:RUD201 3.4 0.5 1.0 CD2 H:HIS106 3.5 0.9 1.0 C3 H:RUD201 3.6 0.9 1.0 C5 H:RUD201 3.6 0.9 1.0 C4 H:RUD201 3.6 0.2 1.0 ND1 H:HIS106 4.0 97.9 1.0 CG H:GLU102 4.2 0.5 1.0 OE2 H:GLU102 4.3 0.1 1.0 CG H:HIS106 4.4 94.0 1.0 C25 H:RUD201 4.4 0.5 1.0 CB H:GLU102 4.5 94.5 1.0 C12 G:RRK202 4.6 0.9 1.0 C11 G:RRK202 4.7 0.5 1.0 N1 H:RUD201 4.8 0.1 1.0 C13 G:RRK202 4.8 0.1 1.0 N3 H:RUD201 4.9 0.1 1.0 N2 H:RUD201 4.9 0.9 1.0 C26 H:RUD201 4.9 0.4 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