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Ruthenium in PDB 5dnn: Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes

Protein crystallography data

The structure of Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes, PDB code: 5dnn was solved by Z.Adhireksan, Z.Ma, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.87 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.726, 109.948, 182.041, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.6

Other elements in 5dnn:

The structure of Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes also contains other interesting chemical elements:

Gold (Au) 2 atoms
Magnesium (Mg) 1 atom

Ruthenium Binding Sites:

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

Ruthenium binding site 1 out of 2 in 5dnn

Go back to Ruthenium Binding Sites List in 5dnn
Ruthenium binding site 1 out of 2 in the Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes


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 Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ru202

b:0.2
occ:1.00
RU G:RAX202 0.0 0.2 1.0
C9 G:RAX202 2.2 0.1 1.0
C10 G:RAX202 2.2 0.2 1.0
C5 G:RAX202 2.2 0.7 1.0
C2 G:RAX202 2.2 0.8 1.0
C3 G:RAX202 2.3 0.0 1.0
C4 G:RAX202 2.3 0.5 1.0
P1 G:RAX202 2.4 0.8 1.0
OE1 G:GLU64 2.4 0.8 1.0
OE2 G:GLU61 2.6 0.4 1.0
C1 G:RAX202 3.4 0.6 1.0
CD G:GLU64 3.5 0.0 1.0
C18 G:RAX202 3.5 0.7 1.0
C20 G:RAX202 3.5 0.5 1.0
C16 G:RAX202 3.6 0.3 1.0
CD G:GLU61 3.7 99.6 1.0
OE2 G:GLU64 3.8 0.2 1.0
OE1 G:GLU61 4.1 1.0 1.0
N1 H:RAX202 4.4 0.3 1.0
C19 H:RAX202 4.7 0.2 1.0
CG G:GLU64 4.8 87.0 1.0
N3 G:RAX202 4.8 0.1 1.0
N2 G:RAX202 4.8 0.1 1.0
N1 G:RAX202 4.8 0.7 1.0
CG G:GLU61 4.9 84.4 1.0
CB G:GLU64 5.0 77.9 1.0

Ruthenium binding site 2 out of 2 in 5dnn

Go back to Ruthenium Binding Sites List in 5dnn
Ruthenium binding site 2 out of 2 in the Nucleosome Core Particle Containing Adducts of Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes


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 Gold(I)- Triethylphosphane and Ruthenium(II)-Toluene Pta Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ru202

b:0.6
occ:1.00
RU H:RAX202 0.0 0.6 1.0
C10 H:RAX202 2.2 0.9 1.0
C9 H:RAX202 2.2 0.3 1.0
C2 H:RAX202 2.2 0.3 1.0
C5 H:RAX202 2.2 0.7 1.0
C3 H:RAX202 2.2 0.9 1.0
C4 H:RAX202 2.3 0.8 1.0
NE2 H:HIS106 2.3 0.3 1.0
P1 H:RAX202 2.3 0.2 1.0
CE1 H:HIS106 3.1 0.3 1.0
OE1 H:GLU102 3.1 0.6 1.0
C1 H:RAX202 3.4 0.7 1.0
CD2 H:HIS106 3.5 93.9 1.0
C20 H:RAX202 3.5 0.4 1.0
C16 H:RAX202 3.6 0.9 1.0
C18 H:RAX202 3.6 0.6 1.0
CD H:GLU102 4.3 99.0 1.0
ND1 H:HIS106 4.3 94.1 1.0
CG H:HIS106 4.5 88.5 1.0
N2 H:RAX202 4.8 0.7 1.0
N1 H:RAX202 4.8 0.3 1.0
N3 H:RAX202 4.8 0.3 1.0
OE2 H:GLU102 4.9 85.2 1.0

Reference:

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
Page generated: Wed Dec 16 02:08:28 2020

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