Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 14.72 kDa 
• Atom Count: 1125 
• Residue Count: 129 
• Unique protein chains: 1

4UWV

Lysozyme soaked with a ruthenium based CORM with a pyridine ligand (complex 8)

• DOI: 10.2210/pdb4UWV/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2014-08-14 Released: 2014-12-10 
• Deposition Author(s): Santos, M.F.A., Mukhopadhyay, A., Romao, M.J., Romao, C.C., Santos-Silva, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

A Contribution to the Rational Design of Ru(Co)3Cl2L Complexes for in Vivo Delivery of Co.

Seixas, J.D., Santos, M.F.A., Mukhopadhyay, A., Coelho, A.C., Reis, P.M., Veiros, L.F., Marques, A.R., Penacho, N., Goncalves, A.M.L., Romao, M.J., Bernardes, G.J.L., Santos-Silva, T., Romao, C.C.

(2015) Dalton Trans 44: 5058

• PubMed: 25427784 
• DOI: 10.1039/c4dt02966f
• Primary Citation of Related Structures:  
  4UWN, 4UWU, 4UWV


• PubMed Abstract: 
  

A few ruthenium based metal carbonyl complexes, e.g. CORM-2 and CORM-3, have therapeutic activity attributed to their ability to deliver CO to biological targets. In this work, a series of related complexes with the formula [Ru(CO)3Cl2L] (L = DMSO (3), L-H3CSO(CH2)2CH(NH2)CO2H) (6a); D,L-H3CSO(CH2)2CH(NH2)CO2H (6b); 3-NC5H4(CH2)2SO3Na (7); 4-NC5H4(CH2)2SO3Na (8); PTA (9); DAPTA (10); H3CS(CH2)2CH(OH)CO2H (11); CNCMe2CO2Me (12); CNCMeEtCO2Me (13); CN(c-C3H4)CO2Et) (14)) were designed, synthesized and studied. The effects of L on their stability, CO release profile, cytotoxicity and anti-inflammatory properties are described. The stability in aqueous solution depends on the nature of L as shown using HPLC and LC-MS studies. The isocyanide derivatives are the least stable complexes, and the S-bound methionine oxide derivative is the more stable one. The complexes do not release CO gas to the headspace, but release CO2 instead. X-ray diffraction of crystals of the model protein Hen Egg White Lysozyme soaked with 6b (4UWN) and 8 (4UWN) shows the addition of Ru(II)(CO)(H2O)4 at the His15 binding site. Soakings with 7(4UWN) produced the metallacarboxylate [Ru(COOH)(CO)(H2O)3](+) bound to the His15 site. The aqueous chemistry of these complexes is governed by the water-gas shift reaction initiated with the nucleophilic attack of HO(-) on coordinated CO. DFT calculations show this addition to be essentially barrierless. The complexes have low cytotoxicity and low hemolytic indices. Following i.v. administration of CORM-3, the in vivo bio-distribution of CO differs from that obtained with CO inhalation or with heme oxygenase stimulation. A mechanism for CO transport and delivery from these complexes is proposed.

---

Organizational Affiliation: 

Instituto de Tecnologia Química e Biológica-António Xavier da Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RU	A	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO	A	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.22	α = 90
b = 80.22	β = 90
c = 37.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-14 
• Released Date: 2014-12-10 
Deposition Author(s): Santos, M.F.A., Mukhopadhyay, A., Romao, M.J., Romao, C.C., Santos-Silva, T.

Revision History 

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation