| _version_ | 1866901287054868480 |
|---|---|
| author | Gamiz-Hernandez, Ana Kaila, Ville R. I. |
| author_facet | Gamiz-Hernandez, Ana Kaila, Ville R. I. |
| contents | <p>MD data of bd-II from M. smegmatis</p> <p>Table S5. List of molecular dynamics (MD) simulations. The MD system with around 280,000 atoms (see Methods). <br>Heme b558, heme b595 and heme d (FeIII-E113C) were modelled in their oxidized state while heme-d (FeII-O2), was <br>modelled in their reduced state, whereas the MQ was modelled as menaquinol in MQN and MQC, and as menaquinone <br>in MQ1, MQ2, and MQ3. a,b Resides modeled in their neutral/anionic states, respecitvely. <br><br>Simulation MQN MQC heme d ligand F117 Length (ns) Protonationa,b Number of O2 molecules in the simulation box <br>============================================================================= <br> S1 QH2 QH2 E113 inward 2 x 600 E120a, E57b 7 <br> S2 QH2 QH2 E113 outward 2 x 600 E120a, E57b 7 <br> S3 QH2 QH2 E113 inward 2 x 600 E57b 7 <br> S4 QH2 QH2 E113 outward 2 x 600 E57b 7 <br> S5 - - E113 inward 2 x 600 E120a, E57b 55 <br> S6 - - E113 outward 2 x 600 E120a, E57b 55 <br> S7 QH2 QH2 O2 inward 2 x 600 E120a, E57b 7 <br> S8 QH2 QH2 O2 outward 2 x 600 E120a, E57b 7 <br> S9 QH2 QH2 O2 inward 2 x 600 E113a, E120a, E57b 55 <br>S10 QH2 QH2 O2 outward 2 x 600 E113a, E120a, E57b 55 <br>=============================================================================<br><br>QM/MM data<br>QM/MM optimized models from <br>Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis <br>using B3LYP-D3/def2-TZVP(Fe)/def2-SVP(C,N,O,H) <br>Heme-d model and surrounding residues at different oxidation states (Fe3+/Fe2+) and <br>protonation states of Glutamate E113. <br>Includes also the O2 bound model.<br><br><br></p> <p>QM-optimized models</p> <p>DFT optimized cluster models from <br>Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis <br>using B3LYP-D3/def2-TZVP(Fe)/def2-SVP(C,N,O,H) <br>Heme-d model and surrounding residues at different oxidation states (Fe3+/Fe2+) and <br>protonation states of Glutamate E113 and Glutamate E57. <br>Includes also the O2 bound models.<br><br></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15385662 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis Gamiz-Hernandez, Ana Kaila, Ville R. I. <p>MD data of bd-II from M. smegmatis</p> <p>Table S5. List of molecular dynamics (MD) simulations. The MD system with around 280,000 atoms (see Methods). <br>Heme b558, heme b595 and heme d (FeIII-E113C) were modelled in their oxidized state while heme-d (FeII-O2), was <br>modelled in their reduced state, whereas the MQ was modelled as menaquinol in MQN and MQC, and as menaquinone <br>in MQ1, MQ2, and MQ3. a,b Resides modeled in their neutral/anionic states, respecitvely. <br><br>Simulation MQN MQC heme d ligand F117 Length (ns) Protonationa,b Number of O2 molecules in the simulation box <br>============================================================================= <br> S1 QH2 QH2 E113 inward 2 x 600 E120a, E57b 7 <br> S2 QH2 QH2 E113 outward 2 x 600 E120a, E57b 7 <br> S3 QH2 QH2 E113 inward 2 x 600 E57b 7 <br> S4 QH2 QH2 E113 outward 2 x 600 E57b 7 <br> S5 - - E113 inward 2 x 600 E120a, E57b 55 <br> S6 - - E113 outward 2 x 600 E120a, E57b 55 <br> S7 QH2 QH2 O2 inward 2 x 600 E120a, E57b 7 <br> S8 QH2 QH2 O2 outward 2 x 600 E120a, E57b 7 <br> S9 QH2 QH2 O2 inward 2 x 600 E113a, E120a, E57b 55 <br>S10 QH2 QH2 O2 outward 2 x 600 E113a, E120a, E57b 55 <br>=============================================================================<br><br>QM/MM data<br>QM/MM optimized models from <br>Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis <br>using B3LYP-D3/def2-TZVP(Fe)/def2-SVP(C,N,O,H) <br>Heme-d model and surrounding residues at different oxidation states (Fe3+/Fe2+) and <br>protonation states of Glutamate E113. <br>Includes also the O2 bound model.<br><br><br></p> <p>QM-optimized models</p> <p>DFT optimized cluster models from <br>Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis <br>using B3LYP-D3/def2-TZVP(Fe)/def2-SVP(C,N,O,H) <br>Heme-d model and surrounding residues at different oxidation states (Fe3+/Fe2+) and <br>protonation states of Glutamate E113 and Glutamate E57. <br>Includes also the O2 bound models.<br><br></p> |
| title | Structure and functional dynamics of the qOR-2 type bd oxidase from Mycobacterium smegmatis |
| url | https://doi.org/10.5281/zenodo.15385662 |