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Ruthenium in PDB 4xuj: Nucleosome Core Particle Containing Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound

Protein crystallography data

The structure of Nucleosome Core Particle Containing Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound, PDB code: 4xuj 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) 93.89 / 3.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.426, 109.754, 181.277, 90.00, 90.00, 90.00
R / Rfree (%) 26.3 / 29.9

Other elements in 4xuj:

The structure of Nucleosome Core Particle Containing Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound 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 Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound (pdb code 4xuj). 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 Containing Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound, PDB code: 4xuj:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in 4xuj

Go back to Ruthenium Binding Sites List in 4xuj
Ruthenium binding site 1 out of 3 in the Nucleosome Core Particle Containing Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound


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 From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ru201

b:0.0
occ:1.00
RU D:4A6201 0.0 0.0 1.0
C10 D:4A6201 2.2 0.4 1.0
C9 D:4A6201 2.2 0.4 1.0
C2 D:4A6201 2.2 0.5 1.0
C5 D:4A6201 2.2 0.4 1.0
C3 D:4A6201 2.3 0.5 1.0
C4 D:4A6201 2.3 0.5 1.0
C1 D:4A6201 3.3 0.3 1.0
C6 D:4A6201 3.4 0.2 1.0
ND1 D:HIS79 3.4 89.5 1.0
C7 D:4A6201 3.6 0.8 1.0
CE1 D:HIS79 4.0 90.0 1.0
CG D:HIS79 4.4 88.8 1.0
C8 D:4A6201 4.7 0.1 1.0
CB D:HIS79 4.8 87.5 1.0

Ruthenium binding site 2 out of 3 in 4xuj

Go back to Ruthenium Binding Sites List in 4xuj
Ruthenium binding site 2 out of 3 in the Nucleosome Core Particle Containing Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound


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 From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ru202

b:0.8
occ:1.00
RU H:4A6202 0.0 0.8 1.0
NE2 H:HIS106 2.2 91.0 1.0
C10 H:4A6202 2.2 0.9 1.0
C9 H:4A6202 2.2 1.0 1.0
C5 H:4A6202 2.2 0.0 1.0
C2 H:4A6202 2.2 0.1 1.0
C3 H:4A6202 2.3 0.1 1.0
C4 H:4A6202 2.3 0.1 1.0
O H:HOH301 2.3 66.8 1.0
CE1 H:HIS106 3.0 90.8 1.0
CD2 H:HIS106 3.3 90.1 1.0
C1 H:4A6202 3.3 0.1 1.0
C6 H:4A6202 3.4 0.8 1.0
OE1 H:GLU102 3.5 86.6 1.0
C8 H:4A6202 3.9 0.3 1.0
ND1 H:HIS106 4.2 90.4 1.0
CG H:HIS106 4.4 89.2 1.0
CD H:GLU102 4.7 86.0 1.0
C7 H:4A6202 4.7 0.4 1.0

Ruthenium binding site 3 out of 3 in 4xuj

Go back to Ruthenium Binding Sites List in 4xuj
Ruthenium binding site 3 out of 3 in the Nucleosome Core Particle Containing Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound


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 Adducts From Treatment with A Thiomorpholine-Substituted [(Eta-6-P-Cymene)Ru(3-Hydroxy-2-Pyridone) Cl] Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ru203

b:0.6
occ:1.00
RU H:4A6203 0.0 0.6 1.0
C10 H:4A6203 2.2 0.2 1.0
C9 H:4A6203 2.2 0.3 1.0
C5 H:4A6203 2.2 0.2 1.0
C2 H:4A6203 2.2 0.2 1.0
C3 H:4A6203 2.3 0.2 1.0
C4 H:4A6203 2.3 0.2 1.0
C1 H:4A6203 3.3 1.0 1.0
ND1 H:HIS79 3.4 90.8 1.0
C6 H:4A6203 3.4 0.2 1.0
C7 H:4A6203 3.5 0.2 1.0
CG H:HIS79 4.1 89.7 1.0
CE1 H:HIS79 4.2 91.4 1.0
CB H:HIS79 4.3 88.2 1.0
C8 H:4A6203 4.6 0.1 1.0
O H:HIS79 4.7 88.3 1.0
C H:HIS79 4.9 88.2 1.0

Reference:

M.Hanif, S.M.Meier, Z.Adhireksan, H.Henke, S.Martic, M.Labib, W.Kandioller, M.A.Jakupec, H.B.Kraatz, C.A.Davey, B.K.Keppler, C.G.Hartinger. Contrasting Cytotoxicity and Reactivity of Ruii-Arene Complexes of Morpholine Vs Thiomorpholine Substituted 3-Hydroxy-2-Pyridone Ligands To Be Published.
Page generated: Wed Dec 16 02:08:26 2020

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