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

Protein crystallography data

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

Other elements in 5cp6:

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

Ruthenium Binding Sites:

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 5cp6

Go back to Ruthenium Binding Sites List in 5cp6
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 5cp6

Go back to Ruthenium Binding Sites List in 5cp6
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 5cp6

Go back to Ruthenium Binding Sites List in 5cp6
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

Reference:

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
Page generated: Wed Dec 16 02:08:26 2020

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