Atomistry » Sodium » PDB 6bfo-6c02 » 6bo1
Atomistry »
  Sodium »
    PDB 6bfo-6c02 »
      6bo1 »

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 Dec 15 11:59:24 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy