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Sodium 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
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 6bo1

Go back to Sodium Binding Sites List in 6bo1
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na201

b:26.9
occ:1.00
 O A:SER60 2.2 20.8 1.0
O A:HOH381 2.3 29.8 1.0
O A:HOH355 2.4 20.8 1.0
O A:ARG73 2.4 32.0 1.0
OG A:SER72 2.4 28.1 1.0
O A:CYS64 2.6 18.1 1.0
CB A:SER72 3.2 28.9 1.0
C A:SER60 3.4 17.0 1.0
C A:ARG73 3.5 25.3 1.0
C A:CYS64 3.6 17.0 1.0
N A:ARG73 3.9 26.5 1.0
CA A:ASN65 4.0 15.3 1.0
O A:ARG61 4.1 26.6 1.0
C A:SER72 4.1 29.9 1.0
CA A:SER60 4.1 14.4 1.0
N A:ASN65 4.2 15.4 1.0
C A:ARG61 4.2 19.6 1.0
CA A:SER72 4.3 29.3 1.0
N A:ARG61 4.3 17.9 1.0
N A:ASN74 4.3 26.3 1.0
CA A:ARG61 4.4 19.4 1.0
CA A:ARG73 4.4 25.8 1.0
N A:CYS64 4.4 17.1 1.0
CB A:SER60 4.4 14.8 1.0
CA A:ASN74 4.6 23.4 1.0
O A:HOH369 4.6 25.6 1.0
O A:SER72 4.6 33.6 1.0
CA A:CYS64 4.6 15.6 1.0
OD1 A:ASN65 4.7 22.0 1.0
CB A:ASN74 4.7 21.5 1.0
CB A:THR69 4.7 14.7 1.0
N A:ASP66 4.7 13.0 1.0
N A:TRP62 4.8 20.6 1.0
CB A:ASN65 4.8 18.0 1.0
C A:ASN65 4.9 14.4 1.0
O A:THR69 4.9 18.7 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: Tue Oct 8 02:12:39 2024

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