7QHR | pdb_00007qhr

Unexpected imidazole coordination to dirhodium tetraacetate complex in a protein environment: insights from X-ray crystallography and quantum chemistry

• PDB DOI: https://doi.org/10.2210/pdb7QHR/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2021-12-13 Released: 2022-06-08 
• Deposition Author(s): Loreto, D., Merlino, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Unexpected Imidazole Coordination to the Dirhodium Center in a Protein Environment: Insights from X-ray Crystallography and Quantum Chemistry.

Loreto, D., Fasulo, F., Munoz-Garcia, A.B., Pavone, M., Merlino, A.

(2022) Inorg Chem 61: 8402-8405

• PubMed: 35609175 
• DOI: https://doi.org/10.1021/acs.inorgchem.2c01370
• Primary Citation Related Structures: 
  7QHR


• PubMed Abstract: 
  

  X-ray diffraction data demonstrate that the adduct formed upon the reaction of dirhodium(II,II) tetraacetate with RNase A reacts with imidazole, leading to the formation of an unexpected product with the imidazole that binds the dirhodium center at an equatorial site rather than an axial site. The origin of this result has been dissected using quantum-chemical calculations.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Via Cintia, Napoli I-80126, Italy.
Department of Physics "Ettore Pancini", University of Naples Federico II, Via Cintia, Napoli I-80126, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.31 kDa 
• Atom Count: 2,324 
• 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, B	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
D1O (Subject of Investigation/LOI)	C [auth A], F [auth B]	tri-(mi2-acetato-(O, O')-diaqua-dirhodium(II, II) C6 H14 O8 Rh2 WOIABTFBXKXYRQ-UHFFFAOYSA-L
D5A (Subject of Investigation/LOI)	G [auth B]	trans-mi2-acetato-(O, O')-N-imidazyl-pentaaqua-dirhodium(II, II) C5 H11 N2 O7 Rh2 BYUCGAKRVFARFM-UHFFFAOYSA-H
CJI (Subject of Investigation/LOI)	E [auth A]	cis-mi2-acetato-(O, O')-N-imidazyl-pentaaqua-dirhodium(II, II) C5 H10 N2 O6 Rh2 BEADRPPWUGELIN-UHFFFAOYSA-I
D3I (Subject of Investigation/LOI)	D [auth A]	octaaqua-dirhodium (II, II) fragment H2 O2 Rh2 PVWOYIBLLHKGIL-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.5	α = 90
b = 32.53	β = 90.295
c = 72.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Loreto, D., Merlino, A.

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Funding Organization	Location	Grant Number
Not funded	Italy	--

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 2.0: 2022-06-15
  Changes: Database references, Non-polymer description
• Version 3.0: 2024-01-31
  Changes: Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
• Version 3.1: 2024-11-13
  Changes: Structure summary