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Ruthenium in PDB 4kgc: Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium

Protein crystallography data

The structure of Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium, PDB code: 4kgc was solved by Z.Adhireksan, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.60 / 2.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.620, 109.710, 181.940, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 28.2

Other elements in 4kgc:

The structure of Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium (pdb code 4kgc). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 4 binding sites of Ruthenium where determined in the Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium, PDB code: 4kgc:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 4kgc

Go back to Ruthenium Binding Sites List in 4kgc
Ruthenium binding site 1 out of 4 in the Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium


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 (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ru201

b:0.2
occ:1.00
RU1 C:HRU201 0.0 0.2 1.0
N1B C:HRU201 2.1 0.4 1.0
N4B C:HRU201 2.2 0.3 1.0
C6A C:HRU201 2.2 0.4 1.0
C7A C:HRU201 2.2 0.4 1.0
C4A C:HRU201 2.2 0.3 1.0
C3A C:HRU201 2.2 0.4 1.0
C5A C:HRU201 2.2 0.2 1.0
C2A C:HRU201 2.2 0.4 1.0
C2B C:HRU201 3.0 0.3 1.0
C3B C:HRU201 3.1 0.4 1.0
C8A C:HRU201 3.4 1.0 1.0
C1A C:HRU201 3.5 0.4 1.0
OE2 G:GLU41 3.5 82.6 1.0
OE2 C:GLU41 3.6 75.4 1.0
C9A C:HRU201 4.1 1.0 1.0
OE1 C:GLU41 4.2 75.9 1.0
CD G:GLU41 4.2 80.9 1.0
CD C:GLU41 4.2 74.4 1.0
OE1 G:GLU41 4.3 83.9 1.0
C10A C:HRU201 4.8 0.8 1.0

Ruthenium binding site 2 out of 4 in 4kgc

Go back to Ruthenium Binding Sites List in 4kgc
Ruthenium binding site 2 out of 4 in the Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium


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 (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ru201

b:0.6
occ:1.00
RU1 G:HRU201 0.0 0.6 1.0
N1B G:HRU201 2.1 0.5 1.0
N4B G:HRU201 2.1 0.4 1.0
C6A G:HRU201 2.2 1.0 1.0
C7A G:HRU201 2.2 0.1 1.0
C4A G:HRU201 2.2 0.8 1.0
C3A G:HRU201 2.2 0.8 1.0
C2A G:HRU201 2.2 0.9 1.0
C5A G:HRU201 2.2 0.8 1.0
OE2 G:GLU64 2.6 69.8 1.0
C3B G:HRU201 3.1 0.3 1.0
C2B G:HRU201 3.1 0.3 1.0
C1A G:HRU201 3.4 0.6 1.0
C8A G:HRU201 3.4 0.8 1.0
CD G:GLU64 3.8 68.3 1.0
C9A G:HRU201 4.4 0.5 1.0
C10A G:HRU201 4.5 0.8 1.0
OE1 G:GLU64 4.5 70.1 1.0
CG G:GLU64 4.7 63.8 1.0

Ruthenium binding site 3 out of 4 in 4kgc

Go back to Ruthenium Binding Sites List in 4kgc
Ruthenium binding site 3 out of 4 in the Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium


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 Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ru101

b:0.6
occ:1.00
RU1 I:HRU101 0.0 0.6 1.0
N4B I:HRU101 2.1 0.0 1.0
N1B I:HRU101 2.1 0.5 1.0
C7A I:HRU101 2.2 0.7 1.0
C6A I:HRU101 2.2 0.4 1.0
C4A I:HRU101 2.2 0.4 1.0
C3A I:HRU101 2.2 0.7 1.0
C2A I:HRU101 2.2 0.7 1.0
C5A I:HRU101 2.2 0.3 1.0
N7 I:DG-15 2.8 97.0 1.0
C3B I:HRU101 3.0 0.8 1.0
C2B I:HRU101 3.1 0.9 1.0
C1A I:HRU101 3.4 0.9 1.0
C8A I:HRU101 3.5 0.9 1.0
O6 I:DG-15 3.7 97.6 1.0
C5 I:DG-15 3.8 97.1 1.0
C8 I:DG-15 3.8 96.4 1.0
C6 I:DG-15 4.1 97.5 1.0
C10A I:HRU101 4.4 0.7 1.0
C9A I:HRU101 4.6 0.6 1.0
O6 I:DG-14 4.6 88.8 1.0
N9 I:DG-15 5.0 95.8 1.0
C4 I:DG-15 5.0 96.1 1.0

Ruthenium binding site 4 out of 4 in 4kgc

Go back to Ruthenium Binding Sites List in 4kgc
Ruthenium binding site 4 out of 4 in the Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Nucleosome Core Particle Containing (ETA6-P-Cymene)-(1, 2- Ethylenediamine)-Ruthenium within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ru101

b:0.5
occ:1.00
RU1 J:HRU101 0.0 0.5 1.0
N4B J:HRU101 2.1 0.9 1.0
N1B J:HRU101 2.1 0.1 1.0
C6A J:HRU101 2.2 0.9 1.0
C7A J:HRU101 2.2 1.0 1.0
C4A J:HRU101 2.2 0.8 1.0
C3A J:HRU101 2.2 0.8 1.0
C2A J:HRU101 2.2 0.9 1.0
C5A J:HRU101 2.2 0.7 1.0
N7 J:DG-15 2.6 88.2 1.0
C2B J:HRU101 3.0 0.2 1.0
C3B J:HRU101 3.0 1.0 1.0
C1A J:HRU101 3.4 0.8 1.0
C8A J:HRU101 3.4 0.4 1.0
C8 J:DG-15 3.5 87.2 1.0
C5 J:DG-15 3.6 88.2 1.0
O6 J:DG-15 3.7 88.2 1.0
C6 J:DG-15 4.1 88.5 1.0
C10A J:HRU101 4.3 0.8 1.0
C9A J:HRU101 4.6 0.4 1.0
N9 J:DG-15 4.8 86.7 1.0
C4 J:DG-15 4.8 88.1 1.0
O6 J:DG-14 4.9 78.8 1.0

Reference:

Z.Adhireksan, G.E.Davey, P.Campomanes, M.Groessl, C.M.Clavel, H.Yu, A.A.Nazarov, C.H.Yeo, W.H.Ang, P.Droge, U.Rothlisberger, P.J.Dyson, C.A.Davey. Ligand Substitutions Between Ruthenium-Cymene Compounds Can Control Protein Versus Dna Targeting and Anticancer Activity Nat Commun V. 5 3462 2014.
ISSN: ESSN 2041-1723
PubMed: 24637564
DOI: 10.1038/NCOMMS4462
Page generated: Wed Dec 16 02:08:15 2020

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