Atomistry » Ruthenium » PDB 4l55-5ira » 5dnn
Atomistry »
  Ruthenium »
    PDB 4l55-5ira »
      5dnn »

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

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy