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Chlorine in PDB 6bo1: Mono-Adduct Formed After 3 Days in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl

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

All present enzymatic activity of Mono-Adduct Formed After 3 Days 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 Mono-Adduct Formed After 3 Days in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl, PDB code: 6bo1 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) 55.21 / 1.24
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.076, 78.076, 37.278, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.9

Other elements in 6bo1:

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

Ruthenium (Ru) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Mono-Adduct Formed After 3 Days in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl (pdb code 6bo1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Mono-Adduct Formed After 3 Days in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Ruthenium(II) with Hewl, PDB code: 6bo1:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6bo1

Go back to Chlorine Binding Sites List in 6bo1
Chlorine binding site 1 out of 2 in the Mono-Adduct Formed After 3 Days 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 Chlorine with other atoms in the Cl binding site number 1 of Mono-Adduct Formed After 3 Days 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:Cl202

b:39.0
occ:0.65
 CL1 A:E3D202 0.0 39.0 0.7
RU1 A:E3D202 2.4 25.5 0.7
C3 A:E3D202 3.1 23.3 0.7
C1 A:E3D202 3.2 24.5 0.7
NH1 A:ARG14 3.4 35.9 1.0
N1 A:E3D202 3.4 23.4 0.7
NE A:ARG14 3.4 33.9 1.0
CL2 A:E3D202 3.4 33.4 0.7
CB A:ALA11 3.6 23.0 1.0
CA A:ALA11 3.6 22.1 1.0
NE2 A:HIS15 3.6 36.2 1.0
CZ A:ARG14 3.9 35.3 1.0
CD2 A:HIS15 3.9 31.3 1.0
N2 A:E3D202 4.4 25.9 0.7
O A:ALA11 4.4 24.5 1.0
C A:ALA11 4.5 22.2 1.0
CD A:ARG14 4.5 32.1 1.0
O A:HOH376 4.6 32.7 1.0
N A:ALA11 4.6 22.1 1.0
CB A:ARG14 4.7 26.6 1.0
C4 A:E3D202 4.7 23.8 0.7
CE1 A:HIS15 4.8 37.0 1.0

Chlorine binding site 2 out of 2 in 6bo1

Go back to Chlorine Binding Sites List in 6bo1
Chlorine binding site 2 out of 2 in the Mono-Adduct Formed After 3 Days 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 Chlorine with other atoms in the Cl binding site number 2 of Mono-Adduct Formed After 3 Days 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:Cl202

b:33.4
occ:0.65
 CL2 A:E3D202 0.0 33.4 0.7
RU1 A:E3D202 2.4 25.5 0.7
O A:HOH376 3.2 32.7 1.0
NE2 A:HIS15 3.3 36.2 1.0
C1 A:E3D202 3.3 24.5 0.7
C2 A:E3D202 3.4 27.7 0.7
CL1 A:E3D202 3.4 39.0 0.7
N A:ILE88 3.6 21.4 1.0
N2 A:E3D202 3.6 25.9 0.7
CG1 A:ILE88 3.7 20.4 1.0
CD2 A:HIS15 3.8 31.3 1.0
OD1 A:ASP87 4.0 28.3 1.0
CA A:ASP87 4.1 22.4 1.0
CB A:ALA11 4.3 23.0 1.0
CE1 A:HIS15 4.3 37.0 1.0
C A:ASP87 4.3 21.5 1.0
O A:SER86 4.4 27.4 1.0
CB A:ILE88 4.5 19.9 1.0
N1 A:E3D202 4.5 23.4 0.7
CA A:ILE88 4.5 19.7 1.0
CD1 A:ILE88 4.5 22.0 1.0
CG A:ASP87 4.6 29.6 1.0
NH1 A:ARG14 4.6 35.9 1.0
CG2 A:ILE88 4.6 19.8 1.0
CZ A:PHE3 4.7 20.4 1.0
C5 A:E3D202 4.9 24.6 0.7
CB A:ASP87 4.9 25.7 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: Fri Jul 26 22:57:08 2024

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