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Cited by 34 publications
(21 citation statements)
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“…This probably is as nonheme iron dioxygenases often have very rigid structures where the substrate is tightly bound (Aluri and de Visser, 2007 ; Kumar et al, 2011 ; Tchesnokov et al, 2016 ; Faponle et al, 2017 ). Previous QM/MM studies on analogous nonheme iron dioxygenases indeed reproduced experimental chemoselectivities excellently using the same methods and procedures described here (Aluri and de Visser, 2007 ; Karamzadeh et al, 2010 ; Kumar et al, 2011 ; Pratter et al, 2013 ; Quesne et al, 2014 , 2016a ; Hernández-Ortega et al, 2015 ; Tchesnokov et al, 2016 ; Faponle et al, 2017 ; Timmins and de Visser, 2017 ; Timmins et al, 2017 ; Hofer and de Visser, 2018 ). Moreover, changing the QM region, basis set or density functional method did not change the ordering of the transition states.…”
Section: Resultssupporting
confidence: 65%
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“…This probably is as nonheme iron dioxygenases often have very rigid structures where the substrate is tightly bound (Aluri and de Visser, 2007 ; Kumar et al, 2011 ; Tchesnokov et al, 2016 ; Faponle et al, 2017 ). Previous QM/MM studies on analogous nonheme iron dioxygenases indeed reproduced experimental chemoselectivities excellently using the same methods and procedures described here (Aluri and de Visser, 2007 ; Karamzadeh et al, 2010 ; Kumar et al, 2011 ; Pratter et al, 2013 ; Quesne et al, 2014 , 2016a ; Hernández-Ortega et al, 2015 ; Tchesnokov et al, 2016 ; Faponle et al, 2017 ; Timmins and de Visser, 2017 ; Timmins et al, 2017 ; Hofer and de Visser, 2018 ). Moreover, changing the QM region, basis set or density functional method did not change the ordering of the transition states.…”
Section: Resultssupporting
confidence: 65%
“…In particular, we focused our computational study on the first halogenation step of the fatty acyl tethered substrate of a HctB model and took the structure reported by Pratter et al ( 2014a ). Our set-up of QM/MM models was reviewed thoroughly recently; therefore, we will summarize the main issues only briefly (Hernández-Ortega et al, 2015 ; Quesne et al, 2016a ; Hofer and de Visser, 2018 ). The model was altered from an iron(II)-water α-ketoglutarate bound structure into an iron(IV)-oxo with ligated succinate.…”
Section: Resultsmentioning
confidence: 99%
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“…46,47 Thereafter, dioxygen was placed in a position near the active site Asn residues. A standard procedure was followed for the subsequent set-up of the system, as described in more detail elsewhere, [38][39][40][48][49][50][51] and briefly summarized here. The enzyme model was set up using procedures proposed by Thiel et al 52,53 The substrate bound enzyme structure with dioxygen bound was protonated to pH 7 with the PROPKA method using the PDB2PQR web service, 54 whereby all Glu and Asp side chains were deprotonated and all Arg and Lys side chains protonated.…”
Section: Methodsmentioning
confidence: 99%