Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature
Abstract
1. Introduction
2. Results and Discussion
2.1. Crystals of the Rh/HEWL Adduct at 310 K
2.2. Structure of the Rh/HEWL Adduct at 310 K
2.3. Structural Comparison with Data from Literature
3. Materials and Methods
3.1. Crystallization of HEWL and Formation of Rh/HEWL Adduct at 37 °C
3.2. Data Collection at 37 °C, Structure Solution and Refinement
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
CD | Circular dichroism |
HEWL | Hen egg white lysozyme |
PDB | Protein Data Bank |
R.m.s.d. | Root mean square deviation |
RNase A | Bovine pancreatic ribonuclease |
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Crystal | |
---|---|
Temperature | 37 °C |
Crystallization condition | 0.01 M HEPES pH 7.5 and 2.00 M sodium formate |
Data collection | |
Space group | P43212 |
a = b (Å) | 80.43 |
c (Å) | 36.14 |
Resolution range (Å) | 56.87–2.12 (2.15–2.12) |
Unique reflections | 6717 (342) |
Completeness (%) | 94.0 (100.0) |
Redundancy | 11.4 (11.8) |
Rmerge (%) | 0.092 (2.788) |
Average I/σ (I) | 13.2 (0.9) |
CC1/2 | 0.998 (0.405) |
Anom. completeness (%) | 93.7 (100.0) |
Anom. redundancy | 6.4 (6.3) |
Refinement | |
Resolution range (Å) | 56.87–2.12 |
N. of reflections | 6183 |
N. of reflections (working set) | 382 |
R-factor/R-free (%) | 19.8/26.1 |
N. of atoms | 1043 |
Average B-factors (Å2) | |
All atoms | 61.2 |
Rh occupancy | 0.50/1.00/1.00/0.60/0.50 |
Rh atoms | 100.5/125.1/159.9/103.2/115.7/134.7/139.1 |
R.m.s.d. from ideality | |
Bond lengths (Å) | 0.007 |
Bond angles (°) | 1.57 |
Ramachandran values (%) | |
Most favored/Additionally allowed | 91.9/7.3 |
Outliers | 0.8 |
Rh/HEWL Adduct | Crystal at 310 K | Data from Literature | Data from Literature | Data from Literature | Data from Literature | Data from Literature | Data from Literature |
---|---|---|---|---|---|---|---|
Crystallization condition | 0.01 M HEPES pH 7.5 and 2.0 M sodium formate | 0.1 M sodium acetate, 20% ethylene glicol, 0.1 M sodium nitrate | |||||
PDB code | 9RUV | 7BE2 | 7BDZ | 7BE0 | 7BE1 | 7BEB | 7BEC |
Binding sites | Metal fragments at binding sites | ||||||
C-ter site | Rh (0.50) Rh * (0.50) Leu129 (1) Leu129 * (1) Lys13 (1) Lys13 * (1) | Rh (0.45) Rh * (0.45) Leu129 (1) Leu129 * (1) Lys13 (1) Lys13 * (1) H2O (0.5) H2O * (0.5) | Rh (0.65) Rh * (0.65) Leu129 (1) Leu129 * (1) Lys13 (1) Lys13 * (1) Act (0.60) Act (0.60) H2O (0.65) H2O * (0.65) | Rh (0.65) Rh * (0.65) Leu129 (1) Leu129 * (1) Lys13 (1) Lys13 * (1) Act (0.65) Act (0.65) H2O (0.65) H2O* (0.65) | Rh (0.65) Rh* (0.65) Leu129 (1) Leu129* (1) Lys13 (1) Lys13* (1) Act (0.65) Act (0.65) H2O (0.65) H2O * (0.65) | Rh (0.7) Rh * (0.7) Leu129 (1) Leu129 * (1) Lys13 (1) Lys13 * (1) Act (0.7) Act (0.7) H2O (0.7) H2O * (0.7) | Rh (0.4) Rh * (0.4) Leu129 (1) Leu129 * (1) Lys13 (1) Lys13 * (1) |
Lys33 site | Rh (1) Lys33 (1) H2O (1) H2O (1) H2O (1) H2O (1) | Rh (0.20) Lys33 (1) Act (0.33) | - | - | - | - | - |
His15 site | Rh (1) His15 (1) Arg14 (1) H2O (1) H2O (1) | Rh (0.35) His15 (1) Arg14 (1) H2O (0.35) H2O (0.35) | Rh (0.35) His15 (1) Arg14 (1) Act (1) H2O (0.35) H2O (0.65) | Rh (0.5) His15 (1) Arg14 (1) Act (1) H2O (0.5) | Rh (0.3) His15 (1) Arg14 (0.5) Act (1) | Rh (0.3) His15 (1) Arg14 (0.5) Act (1) H2O (0.3) H2O (0.3) | Rh (0.25) His15 (1) Arg14 (0.5) Act (1) H2O (1) |
Asp101 site | Rh (0.60) Rh (0.60) Asp101 (1) | Rh (0.40) Rh (0.40) Asp101 (1) H2O (0.40) | - | - | - | - | - |
Asn93 site | Rh (0.50) Rh (0.50) Asn93 (1) Lys96 (1) | Rh (0.30) Rh (0.30) Asn93 (1) Lys96 (1) H2O (1) | - | - | - | - | - |
Asp18 site | - | - | Rh (0.40) Rh (0.40) Asp18 (1) | Rh (0.20) Rh (0.20) Asp18 (1) H2O (0.20) | - | - | - |
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Tito, G.; Ferraro, G.; Merlino, A. Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature. Int. J. Mol. Sci. 2025, 26, 6582. https://doi.org/10.3390/ijms26146582
Tito G, Ferraro G, Merlino A. Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature. International Journal of Molecular Sciences. 2025; 26(14):6582. https://doi.org/10.3390/ijms26146582
Chicago/Turabian StyleTito, Gabriella, Giarita Ferraro, and Antonello Merlino. 2025. "Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature" International Journal of Molecular Sciences 26, no. 14: 6582. https://doi.org/10.3390/ijms26146582
APA StyleTito, G., Ferraro, G., & Merlino, A. (2025). Dirhodium Tetraacetate Binding to Lysozyme at Body Temperature. International Journal of Molecular Sciences, 26(14), 6582. https://doi.org/10.3390/ijms26146582