Ruthenium in PDB 5dnm: Nucleosome Core Particle Containing Adducts of Ruthenium(II)-Toluene Pta Complex

The structure of Nucleosome Core Particle Containing Adducts of Ruthenium(II)-Toluene Pta Complex, PDB code: 5dnm was solved by Z.Adhireksan, R.Muhammad, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.61 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.680, 109.820, 182.340, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.1

The structure of Nucleosome Core Particle Containing Adducts of Ruthenium(II)-Toluene Pta Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Ruthenium atom in the Nucleosome Core Particle Containing Adducts of Ruthenium(II)-Toluene Pta Complex (pdb code 5dnm). 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 Containing Adducts of Ruthenium(II)-Toluene Pta Complex, PDB code: 5dnm:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in the Nucleosome Core Particle Containing Adducts of Ruthenium(II)-Toluene Pta Complex


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 Containing Adducts of Ruthenium(II)-Toluene Pta Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Ru202 b:0.4 occ:1.00 RU G:RAX202 0.0 0.4 1.0 C9 G:RAX202 2.2 0.4 1.0 C10 G:RAX202 2.2 0.3 1.0 C5 G:RAX202 2.2 0.6 1.0 C2 G:RAX202 2.2 0.1 1.0 C3 G:RAX202 2.3 0.8 1.0 C4 G:RAX202 2.3 0.9 1.0 P1 G:RAX202 2.3 0.7 1.0 OE1 G:GLU64 2.4 0.0 1.0 OE2 G:GLU61 2.5 0.4 1.0 C1 G:RAX202 3.4 0.3 1.0 C18 G:RAX202 3.4 0.7 1.0 CD G:GLU64 3.5 0.2 1.0 C20 G:RAX202 3.5 0.8 1.0 C16 G:RAX202 3.6 0.8 1.0 CD G:GLU61 3.6 0.6 1.0 OE2 G:GLU64 3.8 0.4 1.0 OE1 G:GLU61 4.1 0.5 1.0 N1 H:RAX202 4.6 0.3 1.0 N3 G:RAX202 4.7 0.4 1.0 N2 G:RAX202 4.8 0.8 1.0 CG G:GLU64 4.8 95.5 1.0 CG G:GLU61 4.8 92.1 1.0 N1 G:RAX202 4.8 0.2 1.0 C19 H:RAX202 4.9 0.7 1.0 CB G:GLU64 5.0 79.2 1.0

Ruthenium binding site 2 out of 2 in the Nucleosome Core Particle Containing Adducts of Ruthenium(II)-Toluene Pta Complex


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 Containing Adducts of Ruthenium(II)-Toluene Pta Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Ru202 b:0.9 occ:1.00 RU H:RAX202 0.0 0.9 1.0 C10 H:RAX202 2.2 0.2 1.0 C9 H:RAX202 2.2 0.0 1.0 C2 H:RAX202 2.2 0.6 1.0 NE2 H:HIS106 2.2 0.5 1.0 C3 H:RAX202 2.2 0.1 1.0 C5 H:RAX202 2.2 0.9 1.0 C4 H:RAX202 2.3 0.3 1.0 P1 H:RAX202 2.4 0.7 1.0 CE1 H:HIS106 3.0 0.6 1.0 OE1 H:GLU102 3.3 0.9 1.0 C1 H:RAX202 3.3 0.3 1.0 CD2 H:HIS106 3.4 0.4 1.0 C20 H:RAX202 3.4 0.0 1.0 C18 H:RAX202 3.6 0.7 1.0 C16 H:RAX202 3.6 0.2 1.0 ND1 H:HIS106 4.2 0.8 1.0 CD H:GLU102 4.3 0.3 1.0 CG H:HIS106 4.4 95.1 1.0 N2 H:RAX202 4.7 0.2 1.0 OE2 H:GLU102 4.8 97.3 1.0 N1 H:RAX202 4.9 0.3 1.0 N3 H:RAX202 4.9 0.1 1.0

Z.Adhireksan, G.Palermo, T.Riedel, Z.Ma, R.Muhammad, U.Rothlisberger, P.J.Dyson, C.A.Davey. Allosteric Cross-Talk in Chromatin Can Mediate Drug-Drug Synergy Nat Commun V. 8 14860 2017.
ISSN: ESSN 2041-1723
PubMed: 28358030
DOI: 10.1038/NCOMMS14860