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If we compare the calculated and experimental STD values of individual protons, the calculated values are signiﬁcantly smaller than the experimental values for the N-acetyl methyl group of N-acetyl neuraminic acid and for H6 of glucose. This is not surprising since in the crystal structure the N-acetyl methyl group is too far from the protein methyl groups to experience a “direct” saturation transfer. 67) calculated at different protein/ligand ratios are in general indicative of a moderate overall ﬁt between experimental and calculated values.
Jayalakshmi Fig. 8 Structure of UDP-Gal with labeling of the residues (G galactose, R ribose, U uracil) and torsion angles. 5 × 10–6 M a H5U has a systematic error due to resonance overlap Quantitative Analysis of STD-NMR Spectra 41 Figure 9 shows a comparison of the energy-minimized structure and the CORCEMSA-ST structure for the ligand, along with the protein residues in the binding pocket. The discrepancy between experimental and SICOpredicted STDs for the H5U may be the result of systematic error from the overlap of H5U and H1R resonances .
Thus, in our model, the saturation originates from P2 and P2 and spreads to all other protons (ligand and protein) according to Scheme 2 (DD stands for exchange through dipole–dipole relaxation). Scheme 2 Under these conditions, the expression for the observable magnetization in an intermolecular NOE (INOE) experiment in which the P2 and P2 protons are instantaneously saturated by rf irradiation is given by : I(t) = I0 + 1 – exp – R + K t (R + K)–1 Q , (1) where t is the time period for which the protons remain saturated.
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