8C3B | pdb_00008c3b

X-ray structure of RNase A upon reaction with a Ruthenium(II)-arene Complexed with Glycosylated Carbene Ligands (5)

• PDB DOI: https://doi.org/10.2210/pdb8C3B/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2022-12-23 Released: 2024-01-10 
• Deposition Author(s): Ferraro, G., Merlino, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Ruthenium(II)–Arene Complexes with Glycosylated NHC-Carbene Co-Ligands: Synthesis, Hydrolytic Behavior, and Binding to Biological Molecules

Annunziata, A., Cucciolito, M.E., Di Ronza, M., Ferraro, G., Hadiji, M., Merlino, A., Ortiz, D., Scopelliti, R., Fadaei Tirani, F., Dyson, P.J., Ruffo, F.

(2023) Organometallics 42: 952-964

• DOI: https://doi.org/10.1021/acs.organomet.3c00128

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.26 kDa 
• Atom Count: 2,369 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A [auth AAA], B [auth BBB]	124	Bos taurus	Mutation(s): 0  EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T9L (Subject of Investigation/LOI)	E [auth BBB]	(1,3-dimethylimidazol-1-ium-2-yl)-tetrakis(oxidanyl)ruthenium C5 H12 N2 O4 Ru GBFAIMOOTSOZCZ-UHFFFAOYSA-J
R6U (Subject of Investigation/LOI)	D [auth AAA]	(1,3-dimethylimidazol-1-ium-2-yl)-tris(oxidanyl)ruthenium C5 H11 N2 O3 Ru NXUITYSMOYFBJL-UHFFFAOYSA-K
T9U (Subject of Investigation/LOI)	F [auth BBB]	(1,3-dimethyl-2~{H}-imidazol-2-yl)-oxidanyl-oxidanylidene-ruthenium C5 H10 N2 O2 Ru DEXKHQIKGXONQU-UHFFFAOYSA-M
SO4	C [auth AAA]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.227 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.74	α = 90
b = 32.92	β = 90.008
c = 72.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Ferraro, G., Merlino, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary