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Chlorine 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:

Ruthenium (Ru) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6bo2

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Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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:Cl203

b:46.0
occ:0.90
 CL1 A:E3D203 0.0 46.0 0.9
RU1 A:E3D203 2.4 32.6 0.9
NE2 A:HIS15 3.0 29.2 1.0
C2 A:E3D203 3.0 35.2 0.9
NE A:ARG14 3.1 51.5 1.0
C1 A:E3D203 3.2 33.4 0.9
CD2 A:HIS15 3.3 30.7 1.0
CL2 A:E3D203 3.4 47.9 0.9
N2 A:E3D203 3.4 33.5 0.9
CA A:ALA11 3.7 27.2 1.0
CB A:ALA11 3.7 29.0 1.0
NH2 A:ARG14 3.8 40.8 1.0
CZ A:ARG14 3.8 49.9 1.0
CD A:ARG14 3.9 52.0 1.0
CB A:ARG14 4.0 40.3 1.0
CG A:ARG14 4.0 47.4 1.0
CE1 A:HIS15 4.2 33.9 1.0
O A:ALA11 4.2 27.5 1.0
O A:HOH341 4.4 41.6 1.0
N1 A:E3D203 4.5 31.0 0.9
C A:ALA11 4.5 26.3 1.0
CG A:HIS15 4.6 32.8 1.0
C5 A:E3D203 4.7 33.2 0.9
N A:ALA11 4.8 28.3 1.0

Chlorine binding site 2 out of 5 in 6bo2

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Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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:Cl203

b:47.9
occ:0.90
 CL2 A:E3D203 0.0 47.9 0.9
RU1 A:E3D203 2.4 32.6 0.9
O A:HOH341 3.1 41.6 1.0
NE2 A:HIS15 3.1 29.2 1.0
C1 A:E3D203 3.2 33.4 0.9
CL1 A:E3D203 3.4 46.0 0.9
C3 A:E3D203 3.5 32.0 0.9
CG1 A:ILE88 3.5 26.1 1.0
N1 A:E3D203 3.6 31.0 0.9
CD2 A:HIS15 3.7 30.7 1.0
N A:ILE88 3.7 22.5 1.0
CE1 A:HIS15 4.0 33.9 1.0
OD1 A:ASP87 4.1 34.4 1.0
CA A:ASP87 4.3 26.8 1.0
CB A:ALA11 4.3 29.0 1.0
N2 A:E3D203 4.4 33.5 0.9
CD1 A:ILE88 4.4 26.3 1.0
CB A:ILE88 4.5 26.2 1.0
C A:ASP87 4.5 25.3 1.0
O A:SER86 4.5 26.9 1.0
CA A:ILE88 4.5 23.6 1.0
CG A:HIS15 4.7 32.8 1.0
CG A:ASP87 4.7 33.0 1.0
CG2 A:ILE88 4.7 26.4 1.0
ND1 A:HIS15 4.8 40.7 1.0
C4 A:E3D203 4.8 32.5 0.9
NH2 A:ARG14 4.9 40.8 1.0
CZ A:PHE3 4.9 24.4 1.0
N A:THR89 4.9 24.6 1.0

Chlorine binding site 3 out of 5 in 6bo2

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Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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:Cl204

b:43.7
occ:0.80
 CL1 A:E3D204 0.0 43.7 0.8
RU1 A:E3D204 2.4 33.5 0.8
CE A:LYS33 3.2 27.3 1.0
C1 A:E3D204 3.2 31.4 0.8
C3 A:E3D204 3.4 34.5 0.8
CL2 A:E3D204 3.5 49.9 0.8
O A:HOH339 3.5 51.1 1.0
NZ A:LYS33 3.5 26.7 1.0
N1 A:E3D204 3.6 33.8 0.8
N2 A:E3D204 4.4 34.3 0.8
O A:HOH330 4.6 46.0 1.0
CD A:LYS33 4.7 23.2 1.0
CH2 A:TRP123 4.8 36.3 1.0
C4 A:E3D204 4.8 33.9 0.8
CZ3 A:TRP123 4.9 34.5 1.0

Chlorine binding site 4 out of 5 in 6bo2

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Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl204

b:49.9
occ:0.80
 CL2 A:E3D204 0.0 49.9 0.8
RU1 A:E3D204 2.4 33.5 0.8
NZ A:LYS33 3.1 26.7 1.0
O A:HOH330 3.2 46.0 1.0
C1 A:E3D204 3.4 31.4 0.8
C2 A:E3D204 3.4 38.1 0.8
O A:HOH347 3.5 46.5 1.0
CL1 A:E3D204 3.5 43.7 0.8
CE A:LYS33 3.6 27.3 1.0
N2 A:E3D204 3.7 34.3 0.8
CE2 A:PHE38 3.7 22.9 1.0
CD2 A:PHE38 4.3 21.4 1.0
CB A:ARG5 4.5 35.8 1.0
CD A:LYS33 4.6 23.2 1.0
O A:HOH339 4.6 51.1 1.0
N1 A:E3D204 4.7 33.8 0.8
CZ A:PHE38 4.7 21.6 1.0
O A:HOH334 4.8 28.3 1.0

Chlorine binding site 5 out of 5 in 6bo2

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Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl205

b:40.2
occ:1.00
 RU A:RU202 2.5 23.0 0.5
O A:HOH363 3.1 30.7 1.0
N A:ASN59 3.1 18.0 1.0
O A:HOH372 3.2 46.4 1.0
O A:HOH302 3.3 23.2 1.0
CB A:ASN59 3.5 18.6 1.0
O A:HOH376 3.6 46.6 1.0
O A:HOH362 3.7 36.5 1.0
CA A:ILE58 3.7 16.2 1.0
O A:GLN57 3.8 18.6 1.0
C A:ILE58 3.9 16.4 1.0
CA A:ASN59 3.9 17.4 1.0
CD1 A:TRP63 3.9 20.9 1.0
NE1 A:TRP63 4.1 24.3 1.0
O A:HOH361 4.5 48.8 1.0
CD1 A:ILE98 4.5 23.6 1.0
C A:GLN57 4.6 16.2 1.0
CB A:ILE58 4.7 16.7 1.0
N A:ILE58 4.7 15.3 1.0
CG2 A:ILE58 4.7 17.3 1.0
OD1 A:ASP52 4.7 22.2 1.0
CG A:ASN59 4.8 21.2 1.0
CG1 A:ILE58 4.9 19.0 1.0
C A:ASN59 5.0 17.2 1.0
O A:ASN59 5.0 21.9 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 22:57:09 2024

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