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Sodium 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
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 6bo2

Go back to Sodium Binding Sites List in 6bo2
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na201

b:22.8
occ:1.00
 O A:CYS64 2.3 20.2 1.0
O A:SER60 2.4 23.5 1.0
O A:HOH351 2.4 26.1 1.0
O A:ARG73 2.4 27.5 1.0
O A:HOH365 2.5 35.8 1.0
OG A:SER72 2.6 34.0 1.0
CB A:SER72 3.3 28.6 1.0
C A:CYS64 3.4 18.2 1.0
C A:SER60 3.5 20.1 1.0
C A:ARG73 3.5 23.3 1.0
N A:ARG73 3.8 29.6 1.0
CA A:ASN65 3.9 18.3 1.0
N A:ASN65 4.1 18.6 1.0
C A:SER72 4.1 29.8 1.0
CA A:SER60 4.1 18.6 1.0
O A:HOH364 4.2 39.5 1.0
CB A:SER60 4.3 19.9 1.0
CA A:ARG73 4.3 28.9 1.0
CA A:SER72 4.3 29.8 1.0
N A:CYS64 4.4 17.8 1.0
C A:ARG61 4.4 21.5 1.0
N A:ASN74 4.5 27.3 1.0
O A:ARG61 4.5 26.4 1.0
CA A:CYS64 4.5 18.8 1.0
N A:ARG61 4.6 19.4 1.0
CA A:ASN74 4.6 25.4 1.0
O A:SER72 4.7 38.0 1.0
N A:ASP66 4.7 16.6 1.0
CB A:THR69 4.7 19.2 1.0
N A:TRP62 4.7 22.6 1.0
CA A:ARG61 4.8 20.9 1.0
CB A:ASN74 4.8 24.9 1.0
CB A:ASN65 4.8 21.4 1.0
C A:ASN65 4.8 16.8 1.0
OD1 A:ASN65 4.9 28.2 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: Mon Aug 18 03:54:49 2025

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