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Both His118 and His241 are monodentate on all structures described and remain so for the rest of this paper.
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2) indicates that both irons are bridged by the same oxygen on the carboxylate which binds in a bidentate fashion to one Fe.
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BP86 was selected as the functional in this investigation as there is a good correlation between the electronic structure of biferric peroxo complexes and that predicted by BP86 calcuations (Brunold, T. C.; et al. J. Am. Chem. Soc. 1998, 120, 5674-5690).
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1642296981
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note
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Geometry convergence criteria were as follows: change in total energy, ΔE < 5e-5 hartrees, maximum local energy gradient, δE/δS < 4.5e-4 hartrees/Å, δE/δS(RMS) < 3e-4 hartrees/Å, ΔS < 1.8e-3 Å, ΔS(RMS) < 1.2e-5 Å. Frequency calculations to verify that true minima had been attained were not possible as Jaguar 4.1 and subsequent Jaguar 5.0 have not implemented parallelized analytical frequency determination, Such calculations will be performed once this functionality has been added.
-
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45
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1642405781
-
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note
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The residue truncation was performed as follows: the α-carbon was replaced by a hydrogen atom with concomitant shortening of the α-C-β-C bond to 1.08 Å, with the β-C retaining its original position. This hydrogen was then frozen in all geometry optimizations.
-
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46
-
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1642417133
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note
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-. The positions of the heavy atoms (C, N, O) were frozen along with the positions of hydrogens replacing carbon atoms. Q43 and Q87 were modeled differently (as formamide and ammonia, respectively) as the R-group nitrogen of Q43 was located 2.8 Å from a carboxylate oxygen on D237 suggesting hydrogen bonding between these two residues which may have been of importance to the geometry of the active site. W/F48 residue, the second substitution from wt, was not included in the model as it does not coordinate to either iron or iron-coordinated residues.
-
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47
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1642355559
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note
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2-) by the D84E substitution and the introduction of a water molecule which is hydrogen-bonded to E84 in the variant.
-
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49
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1642290495
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note
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CD was taken on a solution at 5 °C while MCD data were taken on a glass at 1.6 K.
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1642329539
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note
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Because the CD/MCD of the R2-W48F/D84E are almost the same as the single variant, they are not included for clarity.
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-1 for the single variant and are included in Supporting Information S2.
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1642347416
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1642323193
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note
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These starting geometries included (4C, 4C), (4C, 5C), and (5C, 5C) with E84 and E204 mono- or bidentate and E115 and E238 in μ-1,3 or μ-1,1 bridging geometries.
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1642326364
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The interaction is complicated by the nonzero torsion angle between the two iron atoms and the carboxylate (ψ = 32°), which leads to mixing of the carboxylate in-plane and out-of-plane O(2p) and causes the relationship between the carboxylate orbitals to be less clear in figures 12c and 12d (in contrast with figures 12a and 12b in which the perpendicular orientation of the bridging E238 O(2p) orbitals is well illustrated).
-
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77
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0032507013
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Bollinger, J. M., Jr.; Krebs, C.; Vicol, A.; Chen, S.; Ley, B. A.; Edmondson, D. E.; Huynh, B. H. J. Am. Chem. Soc. 1998, 120, 1094-1095.
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Bollinger Jr., J.M.1
Krebs, C.2
Vicol, A.3
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Ley, B.A.5
Edmondson, D.E.6
Huynh, B.H.7
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78
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1642407428
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note
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It should be noted that the steric interaction between Y122 and E84 is not required in the geometry optimizations to reproduce the bidentate coordination of E84 to Fe1 (Figure 10). The model used for the R2-W48F/D84E active site replaces the Y122 residue with a water molecule where C is modeled by a hydrogen (with its coordinates frozen during the optimizations) and O as the water oxygen (also frozen during optimization). Thus, there is no phenyl ring present to interact with the aliphatic chain of E84, although the effects of this interaction, the addition of TIP93 and the displacement of Y122 relative to wt, are included.
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79
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0028882691
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Liu, K. E.; Nesheim, J. C.; Lee, S.-K.; Lipscomb, J. D. J. Biol. Chem. 1995, 270, 24662-24665.
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Liu, K.E.1
Nesheim, J.C.2
Lee, S.-K.3
Lipscomb, J.D.4
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80
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1642400942
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Ormo, M.; deMare, F.; Regnstrom, K.; Aberg, A.; Sahlin, M.; Ling, J.; Loehr, T. M.; Sanders-Loehr, J.; Sjoberg, B. M. J. Biol. Chem. 1992, 267.
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J. Biol. Chem.
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Ormo, M.1
DeMare, F.2
Regnstrom, K.3
Aberg, A.4
Sahlin, M.5
Ling, J.6
Loehr, T.M.7
Sanders-Loehr, J.8
Sjoberg, B.M.9
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