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 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy