Ruthenium in PDB 5cp6: Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6]

The structure of Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6], PDB code: 5cp6 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)	76.39 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.570, 109.570, 182.610, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.1

The structure of Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6] also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Ruthenium atom in the Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6] (pdb code 5cp6). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6], PDB code: 5cp6:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6]


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 Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6] within 5.0Å range: probe atom residue distance (Å) B Occ I:Ru101 b:0.5 occ:1.00 RU1 I:RUH101 0.0 0.5 1.0 N7 I:DG-15 2.0 0.3 1.0 N1B I:RUH101 2.1 0.3 1.0 N2B I:RUH101 2.2 0.9 1.0 C2A I:RUH101 2.2 0.6 1.0 C4A I:RUH101 2.2 0.6 1.0 C3A I:RUH101 2.2 0.2 1.0 C1A I:RUH101 2.2 0.5 1.0 C6A I:RUH101 2.2 0.7 1.0 C5A I:RUH101 2.2 0.6 1.0 C5 I:DG-15 3.0 0.2 1.0 C1B I:RUH101 3.0 1.0 1.0 C8 I:DG-15 3.0 0.6 1.0 C2B I:RUH101 3.1 0.3 1.0 O6 I:DG-15 3.2 0.9 1.0 C10 I:RUH101 3.4 0.5 1.0 C7A I:RUH101 3.4 0.8 1.0 C6 I:DG-15 3.4 0.2 1.0 C8A I:RUH101 3.9 0.1 1.0 C9A I:RUH101 3.9 0.1 1.0 C4 I:DG-15 4.1 0.7 1.0 N9 I:DG-15 4.2 0.3 1.0 N1 I:DG-15 4.8 0.4 1.0 O6 I:DG-14 4.9 0.2 1.0 C11 I:RUH101 5.0 0.8 1.0

Ruthenium binding site 2 out of 3 in the Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6]


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 Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6] within 5.0Å range: probe atom residue distance (Å) B Occ J:Ru101 b:0.5 occ:1.00 RU1 J:RUH101 0.0 0.5 1.0 N7 J:DG-15 2.0 0.9 1.0 N1B J:RUH101 2.1 0.9 1.0 C2A J:RUH101 2.2 0.2 1.0 N2B J:RUH101 2.2 0.6 1.0 C4A J:RUH101 2.2 0.8 1.0 C3A J:RUH101 2.2 0.2 1.0 C5A J:RUH101 2.2 0.3 1.0 C1A J:RUH101 2.2 0.2 1.0 C6A J:RUH101 2.2 0.0 1.0 C8 J:DG-15 2.9 0.5 1.0 C1B J:RUH101 3.1 0.3 1.0 C5 J:DG-15 3.1 0.4 1.0 C2B J:RUH101 3.1 0.3 1.0 C10 J:RUH101 3.4 0.5 1.0 C7A J:RUH101 3.4 0.4 1.0 O6 J:DG-15 3.5 0.4 1.0 C6 J:DG-15 3.6 0.5 1.0 C8A J:RUH101 3.8 0.8 1.0 C9A J:RUH101 3.8 0.6 1.0 N9 J:DG-15 4.1 0.9 1.0 C4 J:DG-15 4.2 0.5 1.0 C11 J:RUH101 4.8 0.6 1.0 C14 J:RUH101 4.8 96.2 1.0

Ruthenium binding site 3 out of 3 in the Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6]


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Nucleosome Core Particle with Adducts From the Anticancer Compound, [(ETA6-5,8,9,10-Tetrahydroanthracene)Ru(Ethylenediamine)Cl][PF6] within 5.0Å range: probe atom residue distance (Å) B Occ J:Ru102 b:0.6 occ:1.00 RU1 J:RUH102 0.0 0.6 1.0 N2B J:RUH102 2.1 0.1 1.0 N1B J:RUH102 2.1 0.1 1.0 C1B J:RUH102 3.0 0.1 1.0 C2B J:RUH102 3.0 0.8 1.0 C4' I:DG13 4.0 0.1 1.0 C5' I:DG13 4.1 0.6 1.0 O4' I:DG13 4.1 0.1 1.0

Z.Ma, G.Palermo, Z.Adhireksan, B.S.Murray, T.Von Erlach, P.J.Dyson, U.Rothlisberger, C.A.Davey. An Organometallic Compound Which Exhibits A Dna Topology-Dependent One-Stranded Intercalation Mode. Angew.Chem.Int.Ed.Engl. V. 55 7441 2016.
ISSN: ESSN 1521-3773
PubMed: 27184539
DOI: 10.1002/ANIE.201602145