Coordination of a Dirhodium(II) Center to Methionine and Cysteine Side Chains: Evidence from X-Ray Structure of the Adduct Formed by Dirhodium Tetraacetate with a C-Phycocyanin
Abstract
1. Introduction

2. Results and Discussion
2.1. Structure of the diRh/GpPC Adduct
2.2. Comparison with Literature Data
2.3. In Solution Secondary Structure and Thermal Stability Analysis of diRh/GpPC Adduct
3. Materials and Methods
3.1. Crystallization of GpPC and Formation of the diRh/GpPC Adduct
3.2. Data Collection, Structure Solution, and Refinement
3.3. Circular Dichroism
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
| bpy | Bipyridine |
| diRh | dirhodium |
| ESI-MS | Electrospray ionization mass spectrometry |
| EXAFS | extended X-ray absorption fine structure |
| GpPC | C-phycocyanin from Galdiera phlegrea |
| HEWL | Hen Egg White Lysozyme |
| HSA | Human serum albumin |
| MS | Mass spectrometry |
| PCB | phycocyanobilin |
| PDB | Protein Data Bank |
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| PDB Deposition Code | 9T05 |
|---|---|
| Crystallization conditions | 0.10–0.20 M magnesium chloride, 0.10 M Hepes, pH 6.5, and 9.0–10.0% (w/v) PEG 4000 |
| Crystallization temperature (K) | 293 |
| Soaking temperature (K) | 293 |
| Data collection | |
| Data collection temperature (K) | 100 |
| Wavelength (Å) | 0.9537 |
| a (Å)/b (Å)/c (Å) | 60.586/188.500/207.212 |
| (αβ) per asymmetric unit | 6 (12 chains: A, C, E, G, I, K for the α-chains and B, D, F, H, J, L for the β-chains) |
| Resolution range (Å) | 188.5–2.17 (2.31–2.17) |
| Unique reflections | 102,746 (5138) |
| Completeness (%) | 94.2 (63.6) |
| Redundancy | 12.9 (11.6) |
| † Rmerge (%) | 0.340 (2.13) |
| Rpim | 0.100 (0.656) |
| Average I/σ(I) | 6.6 (1.4) |
| CC1/2 | 0.996 (0.564) |
| Anomalous completeness (%) | 94.2 (65.5) |
| Anomalous redundancy | 6.7 (6.0) |
| Refinement | |
| Resolution range (Å) | 139.83–2.17 |
| N. of reflections (working set) | 97,759 |
| N. of reflections (test set) | 5000 |
| R-factor/R-free (%) | 22.7/26.3 |
| N. of non-H atoms | 16,492 |
| Rh occupancy at Met30β binding site | 0.50/0.50–B/0.50/0.50–D/0.50/0.50–F/0.50/0.50–H/0.50/0.50–J/0.60/0.60–L |
| Rh occupancy at Cys73α binding site | 0.40/0.40–A/0.25/0.25–C/0.30/0.30–E/0.35/0.35–G/0.20/0.20–I/0.25/0.25–K |
| Average B-factors (Å2) All atoms | 35.7 |
| B-factors (Å2) of Rh atoms at Met30β binding site | 44.0/48.8–B/47.7/49.1–D/58.6/59.7–F/43.5/49.6–H/33.8/34.1–J/24.0/26.7–L |
| B-factors (Å2) of Rh atoms at Cys73α binding site | 37.2/62.5–A/47.8/52.8–C/48.4/61.8–E/40.7/65.7–G/30.9/57.0–I/54.0/58.5–K |
| R.m.s. deviations | |
| Bond lengths (Å) | 0.008 |
| Bond angles (°) | 1.73 |
| Ramachandran statistics (Coot analysis) | |
| Favored regions (%)/Outliers(%) | 96.9/0.63 |
| Dirhodium/GpPC Adduct | |||||||
|---|---|---|---|---|---|---|---|
| Chain B | Chain D | Chain F | Chain H | Chain J | Chain L | ||
| Met30β | Rh—Rh (Å) | 2.38 | 2.38 | 2.39 | 2.38 | 2.41 | 2.36 |
| Rh—SD (Å) | 2.47 | 2.39 | 2.51 | 2.51 | 2.44 | 2.44 | |
| Rh—Oeq (Å) | 2.04 ± 0.01 | 2.04 ± 0.01 | 2.05 ± 0.01 | 2.05 ± 0.01 | 2.05 ± 0.01 | 2.04 ± 0.01 | |
| Rh—Oax a (Å) | 2.33 | 2.33 | 2.33 | 2.33 | 2.34 | 2.34 | |
| SD—Rh—Rh (°) | 170.5 | 172.8 | 177.1 | 172.1 | 173.3 | 176.6 | |
| Oeq—Rh—Rh b (°) | 87.4 ± 4.8 | 87.1 ± 6.0 | 88.2 ± 0.7 | 87.8 ± 3.2 | 87.6 ± 2.4 | 86.5 ± 2.8 | |
| Oeq—Rh—SD (°) | 92.2 ± 10.3 | 92.5 ± 7.0 | 91.6 ± 2.5 | 92.0 ± 9.6 | 92.2 ± 7.6 | 93.6 ± 2.3 | |
| Oax a—Rh—Rh (°) | 175.3 | 161.5 | 169.4 | 173.5 | 177.1 | 168.8 | |
| Chain A | Chain C | Chain E | Chain G | Chain I | Chain K | ||
| Cys73α | Rh—Rh (Å) | 2.41 | 2.40 | 2.40 | 2.40 | 2.38 | 2.39 |
| Rh—SG (Å) | 2.13 | 2.47 | 2.26 | 2.14 | 2.08 | 2.47 | |
| SG—Rh—Rh (°) | 179.3 | 179.8 | 177.8 | 178.1 | 90.0 | 178.8 | |
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Ferraro, G.; Imbimbo, P.; Troisi, R.; Monti, D.M.; Merlino, A. Coordination of a Dirhodium(II) Center to Methionine and Cysteine Side Chains: Evidence from X-Ray Structure of the Adduct Formed by Dirhodium Tetraacetate with a C-Phycocyanin. Int. J. Mol. Sci. 2025, 26, 11492. https://doi.org/10.3390/ijms262311492
Ferraro G, Imbimbo P, Troisi R, Monti DM, Merlino A. Coordination of a Dirhodium(II) Center to Methionine and Cysteine Side Chains: Evidence from X-Ray Structure of the Adduct Formed by Dirhodium Tetraacetate with a C-Phycocyanin. International Journal of Molecular Sciences. 2025; 26(23):11492. https://doi.org/10.3390/ijms262311492
Chicago/Turabian StyleFerraro, Giarita, Paola Imbimbo, Romualdo Troisi, Daria Maria Monti, and Antonello Merlino. 2025. "Coordination of a Dirhodium(II) Center to Methionine and Cysteine Side Chains: Evidence from X-Ray Structure of the Adduct Formed by Dirhodium Tetraacetate with a C-Phycocyanin" International Journal of Molecular Sciences 26, no. 23: 11492. https://doi.org/10.3390/ijms262311492
APA StyleFerraro, G., Imbimbo, P., Troisi, R., Monti, D. M., & Merlino, A. (2025). Coordination of a Dirhodium(II) Center to Methionine and Cysteine Side Chains: Evidence from X-Ray Structure of the Adduct Formed by Dirhodium Tetraacetate with a C-Phycocyanin. International Journal of Molecular Sciences, 26(23), 11492. https://doi.org/10.3390/ijms262311492

