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Ruthenium in PDB 5xf5: Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration)

Protein crystallography data

The structure of Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration), PDB code: 5xf5 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) 70.65 / 2.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.210, 109.670, 182.040, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.4

Other elements in 5xf5:

The structure of Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration) 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 An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration) (pdb code 5xf5). 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 with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration), PDB code: 5xf5:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5xf5

Go back to Ruthenium Binding Sites List in 5xf5
Ruthenium binding site 1 out of 2 in the Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration)


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 An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ru201

b:0.8
occ:1.00
RU G:RUD201 0.0 0.8 1.0
OE2 G:GLU61 2.1 0.8 1.0
OE1 G:GLU64 2.1 0.8 1.0
C18 G:RUD201 2.2 0.6 1.0
C19 G:RUD201 2.2 0.7 1.0
C21 G:RUD201 2.2 0.0 1.0
C23 G:RUD201 2.2 0.6 1.0
C20 G:RUD201 2.2 0.4 1.0
C22 G:RUD201 2.2 0.1 1.0
P1 G:RUD201 2.3 0.6 1.0
CD G:GLU64 3.3 0.7 1.0
CD G:GLU61 3.3 97.0 1.0
C17 G:RUD201 3.4 0.9 1.0
C24 G:RUD201 3.4 0.9 1.0
C3 G:RUD201 3.5 0.6 1.0
C5 G:RUD201 3.5 0.3 1.0
C4 G:RUD201 3.6 0.7 1.0
OE2 G:GLU64 3.9 0.4 1.0
OE1 G:GLU61 4.0 94.7 1.0
CG G:GLU61 4.5 86.8 1.0
CG G:GLU64 4.5 92.6 1.0
C25 G:RUD201 4.7 0.3 1.0
N3 G:RUD201 4.7 0.2 1.0
N1 G:RUD201 4.7 0.7 1.0
N2 G:RUD201 4.8 1.0 1.0
CB G:GLU64 4.9 81.8 1.0

Ruthenium binding site 2 out of 2 in 5xf5

Go back to Ruthenium Binding Sites List in 5xf5
Ruthenium binding site 2 out of 2 in the Nucleosome Core Particle with An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration)


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 An Adduct of A Binuclear Rapta (Ru- Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,S-Configuration) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ru203

b:0.6
occ:1.00
RU G:RUD203 0.0 0.6 1.0
OE2 G:GLU91 2.1 0.4 1.0
C19 G:RUD203 2.2 0.8 1.0
C18 G:RUD203 2.2 0.6 1.0
C20 G:RUD203 2.2 0.9 1.0
C23 G:RUD203 2.2 0.1 1.0
C21 G:RUD203 2.2 0.0 1.0
C22 G:RUD203 2.3 0.4 1.0
P1 G:RUD203 2.3 0.8 1.0
CD G:GLU91 3.4 0.6 1.0
C17 G:RUD203 3.4 0.7 1.0
C24 G:RUD203 3.4 0.4 1.0
C3 G:RUD203 3.5 0.8 1.0
C5 G:RUD203 3.5 0.1 1.0
C4 G:RUD203 3.5 0.0 1.0
OE1 G:GLU91 4.1 0.1 1.0
C25 G:RUD203 4.1 0.2 1.0
CG G:GLU91 4.5 0.3 1.0
N1 G:RUD203 4.8 0.2 1.0
N3 G:RUD203 4.8 0.1 1.0
N2 G:RUD203 4.8 0.3 1.0
CB G:GLU91 5.0 87.5 1.0

Reference:

G.E.Davey, Z.Adhireksan, Z.Ma, T.Riedel, D.Sharma, S.Padavattan, D.Rhodes, A.Ludwig, S.Sandin, B.S.Murray, P.J.Dyson, C.A.Davey. Nucleosome Acidic Patch-Targeting Binuclear Ruthenium Compounds Induce Aberrant Chromatin Condensation Nat Commun V. 8 1575 2017.
ISSN: ESSN 2041-1723
PubMed: 29146919
DOI: 10.1038/S41467-017-01680-4
Page generated: Wed Dec 16 02:08:45 2020

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