Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis

MD data of bd-II from M. smegmatis Table S5. List of molecular dynamics (MD) simulations. The MD system with around 280,000 atoms (see Methods). Heme b558, heme b595 and heme d (FeIII-E113C) were modelled in their oxidized state while heme-d (FeII-O2), was modelled in their reduced state, whereas the MQ was modelled as menaquinol in MQN and MQC, and as menaquinone in MQ1, MQ2, and MQ3. a,b Resides modeled in their neutral/anionic states, respecitvely. Simulation MQN MQC heme d ligand F117 Length (ns) Protonationa,b Number of O2 molecules in the simulation box ============================================================================= S1 QH2 QH2 E113 inward 2 x 600 E120a, E57b 7 S2 QH2 QH2 E113 outward 2 x 600 E120a, E57b 7 S3 QH2 QH2 E113 inward 2 x 600 E57b 7 S4 QH2 QH2 E113 outward 2 x 600 E57b 7 S5 - - E113 inward 2 x 600 E120a, E57b 55 S6 - - E113 outward 2 x 600 E120a, E57b 55 S7 QH2 QH2 O2 inward 2 x 600 E120a, E57b 7 S8 QH2 QH2 O2 outward 2 x 600 E120a, E57b 7 S9 QH2 QH2 O2 inward 2 x 600 E113a, E120a, E57b 55 S10 QH2 QH2 O2 outward 2 x 600 E113a, E120a, E57b 55 =============================================================================QM/MM dataQM/MM optimized models from Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis using B3LYP-D3/def2-TZVP(Fe)/def2-SVP(C,N,O,H) Heme-d model and surrounding residues at different oxidation states (Fe3+/Fe2+) and protonation states of Glutamate E113. Includes also the O2 bound model. QM-optimized models DFT optimized cluster models from Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis using B3LYP-D3/def2-TZVP(Fe)/def2-SVP(C,N,O,H) Heme-d model and surrounding residues at different oxidation states (Fe3+/Fe2+) and protonation states of Glutamate E113 and Glutamate E57. Includes also the O2 bound models.