5OBD

X-ray structure of the adduct formed upon reaction of ribonuclease A with the compound fac-[RuII(CO)3Cl2(N3-MIM), MIM=methyl-imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ru-Based CO releasing molecules with azole ligands: interaction with proteins and the CO release mechanism disclosed by X-ray crystallography.

Pontillo, N.Ferraro, G.Messori, L.Tamasi, G.Merlino, A.

(2017) Dalton Trans 46: 9621-9629

  • DOI: 10.1039/c7dt01991b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • fac-[Ru <sup>II </sup>(CO) <sub>3 </sub>Cl <sub>2 </sub>(N <sup>3 </sup>-Imidazole)] (Ru <sup>II </sup>IM), fac-[Ru <sup>II </sup>(CO) <sub>3 </sub>Cl <sub>2 </sub>(N <sup>3 </sup>-methyl-imidazole)] (Ru <sup>II </sup>MIM) and fac-[Ru <sup>II </sup>( ...

    fac-[Ru II (CO) 3 Cl 2 (N 3 -Imidazole)] (Ru II IM), fac-[Ru II (CO) 3 Cl 2 (N 3 -methyl-imidazole)] (Ru II MIM) and fac-[Ru II (CO) 3 Cl 2 (N 3 -methyl-benzimidazole)] (Ru II MBI) are three ruthenium based CO releasing molecules (Ru-CORMs) that are cytotoxic towards ovarian and colon carcinoma cell lines. Detailed structural information on the adducts formed upon reaction of Ru II IM and Ru II MIM with hen egg white lysozyme and of the three Ru-CORMs with bovine pancreatic ribonuclease is provided here by X-ray crystallography. Comparative analysis of seven crystal structures of these adducts allows one to delineate some general trends in the reactivity of these Ru-CORMs with proteins. Indeed, in all cases Ru-CORMs bind these model systems upon detachment of the azole ligand and concomitant coordination to a protein His or Asp residue. Apparently the three Ru-CORMs progressively dissociate losing azoles, chlorides, and one or two CO molecules. Data were compared with those reported in the literature for adducts of the same proteins with other Ru-CORMs and with in-solution data previously obtained on the same systems. These results are potentially useful for a better understanding of the chemistry, potential toxicity and mechanism of actions of these interesting Ru-CORMs and are helpful in defining the molecular mechanisms of CO release.


    Organizational Affiliation

    Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.,Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cinthia, I-80126, Napoli, Italy. antonello.merlino@unina.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
Gene Names: RNASE1 (RNS1)
EC: 4.6.1.18
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
9Q8
Query on 9Q8

Download SDF File 
Download CCD File 
A, B
tris(oxidaniumylidynemethyl)-tris(oxidanyl)ruthenium
C3 H3 O6 Ru
CSTVJYAZRLCYQF-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.628α = 90.00
b = 32.773β = 90.00
c = 72.246γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references