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Ruthenium in PDB 6bo2: Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl

Enzymatic activity of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl

All present enzymatic activity of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl:
3.2.1.17;

Protein crystallography data

The structure of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl, PDB code: 6bo2 was solved by M.P.Sullivan, C.G.Hartinger, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.69 / 1.48
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.762, 78.762, 36.928, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.3

Other elements in 6bo2:

The structure of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl (pdb code 6bo2). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl, PDB code: 6bo2:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in 6bo2

Go back to Ruthenium Binding Sites List in 6bo2
Ruthenium binding site 1 out of 3 in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru202

b:23.0
occ:0.50
 O A:HOH363 1.8 30.7 1.0
O A:HOH372 2.2 46.4 1.0
CL A:CL205 2.5 40.2 1.0
O A:HOH376 2.6 46.6 1.0
O A:ALA107 2.8 38.2 1.0
O A:HOH301 2.8 33.1 1.0
O A:HOH362 3.0 36.5 1.0
O A:HOH302 3.5 23.2 1.0
C A:ALA107 3.7 34.8 1.0
CB A:ALA107 4.2 32.3 1.0
CA A:ALA107 4.4 33.0 1.0
O A:HOH375 4.5 73.6 1.0
N A:TRP108 4.6 32.0 1.0
CA A:TRP108 4.8 27.3 1.0
CB A:ASN59 4.9 18.6 1.0
O A:GLN57 4.9 18.6 1.0

Ruthenium binding site 2 out of 3 in 6bo2

Go back to Ruthenium Binding Sites List in 6bo2
Ruthenium binding site 2 out of 3 in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:32.6
occ:0.90
 RU1 A:E3D203 0.0 32.6 0.9
O A:HOH341 2.0 41.6 1.0
C1 A:E3D203 2.1 33.4 0.9
NE2 A:HIS15 2.1 29.2 1.0
CL2 A:E3D203 2.4 47.9 0.9
CL1 A:E3D203 2.4 46.0 0.9
NH2 A:ARG14 2.4 40.8 1.0
CE1 A:HIS15 2.8 33.9 1.0
CZ A:ARG14 3.0 49.9 1.0
N1 A:E3D203 3.1 31.0 0.9
N2 A:E3D203 3.1 33.5 0.9
NE A:ARG14 3.3 51.5 1.0
CD2 A:HIS15 3.3 30.7 1.0
C3 A:E3D203 3.6 32.0 0.9
C2 A:E3D203 3.6 35.2 0.9
ND1 A:HIS15 4.1 40.7 1.0
NH1 A:ARG14 4.1 58.4 1.0
CG A:HIS15 4.3 32.8 1.0
C5 A:E3D203 4.3 33.2 0.9
C4 A:E3D203 4.3 32.5 0.9
CD A:ARG14 4.5 52.0 1.0
OD1 A:ASP87 4.8 34.4 1.0

Ruthenium binding site 3 out of 3 in 6bo2

Go back to Ruthenium Binding Sites List in 6bo2
Ruthenium binding site 3 out of 3 in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:33.5
occ:0.80
 RU1 A:E3D204 0.0 33.5 0.8
C1 A:E3D204 2.1 31.4 0.8
O A:HOH330 2.1 46.0 1.0
NZ A:LYS33 2.2 26.7 1.0
O A:HOH339 2.2 51.1 1.0
CL1 A:E3D204 2.4 43.7 0.8
CL2 A:E3D204 2.4 49.9 0.8
CE A:LYS33 3.0 27.3 1.0
N2 A:E3D204 3.1 34.3 0.8
N1 A:E3D204 3.1 33.8 0.8
C3 A:E3D204 3.6 34.5 0.8
C2 A:E3D204 3.6 38.1 0.8
C5 A:E3D204 4.3 33.8 0.8
C4 A:E3D204 4.3 33.9 0.8
OD1 A:ASN37 4.4 28.8 1.0
O A:HOH334 4.4 28.3 1.0
CD A:LYS33 4.4 23.2 1.0

Reference:

M.P.Sullivan, M.K.Nieuwoudt, G.A.Bowmaker, N.Y.S.Lam, D.Truong, D.C.Goldstone, C.G.Hartinger. Unexpected Arene Ligand Exchange Results in the Oxidation of An Organoruthenium Anticancer Agent: the First X-Ray Structure of A Protein-Ru(Carbene) Adduct. Chem. Commun. (Camb.) V. 54 6120 2018.
ISSN: ESSN 1364-548X
PubMed: 29713703
DOI: 10.1039/C8CC02433B
Page generated: Thu Oct 10 13:06:17 2024

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