ROS production, scavenging and redox buffering. A weak-field effect on an electron-transfer branching ratio may be far too small to measure as a rate change, but ROS signalling is threshold-like, so the same small change can register as a transcriptional response. That is why the ROS-responsive programme is the best-evidenced node in the whole atlas, and equally why it cannot identify a mechanism: an amplifier reports that something moved upstream, never what. The map deliberately includes enzymes with no spin route at all — the peroxiredoxin/thioredoxin system is pure two-electron thiol chemistry with no radical intermediate and no metal — so that "redox" is not read as a synonym for "magnetically addressable". The heme peroxidases do cycle through a genuine porphyrin radical, but it is exchange-coupled to the ferryl iron and extremely short-lived, and that caveat travels with the annotation. Derived from: Figure 3 panel C and Figure 5 of Porterfield & Barker, "Plant Responses to Near-Null Magnetic Fields" — expanded to the scavenging network and bound to Arabidopsis loci flavin_semiquinone iron_sulfur_4Fe4S iron_sulfur_2Fe2S ros_leak_site 1H 14N 57Fe 33S CHEBI:58210 AT5G37510 AT5G08530 AT4G02580 AT5G11770 GO:0005747 7.1.1.2 The FMN site forms a flavin semiquinone during turnover and is a known superoxide-producing leak site, and the Fe/S chain performs sequential one-electron transfers — both of the physical routes the radical-pair and hyperfine arguments require. No published experiment has applied a near-null field and measured plant complex I activity, so this is a hypothesis with a mechanism, not a result. Electron transfer along the Fe/S chain is fast relative to plausible singlet-triplet mixing times, so a coherent radical-pair effect here is harder to argue than at the flavin. Treat the flavin and the cluster chain as separate hypotheses rather than one. ros_leak_site CHEBI:18421 CHEBI:16240 AT4G25100 AT2G28190 Reactive oxygen species production differed between geomagnetic and near-null field conditions in lima bean. Near-null magnetic field alters ROS-associated transcriptomic and metabolomic programmes in Arabidopsis. As in the mitochondrion, the amplifier rather than the mechanism: threshold behaviour converts a small change in electron branching into a signal. ros_leak_site 1.3.3.6 Acyl-CoA oxidase is a flavoprotein that reduces O2 directly to H2O2 as part of its normal catalytic cycle — one of the few places in the cell where peroxide production is the intended chemistry rather than a leak. During germination that makes the peroxisome a major ROS source at exactly the stage the review argues matters most. A flavin semiquinone is not well established in the acyl-CoA oxidase mechanism, and the enzyme's own catalase-rich compartment quenches the product quickly. Classed only as a ROS source, not as a radical-pair site. ros_leak_site CHEBI:18421 CHEBI:16240 AT3G10920 Near-null magnetic field exposure alters ROS-associated transcriptomic and metabolomic programmes in Arabidopsis. Reactive oxygen species and mitochondria jointly regulate seed germination, establishing the route from mitochondrial ROS to a developmental outcome. Not a magnetosensitive mechanism itself — it is the amplifier. A field effect too small to measure as a rate change can still register here, because ROS signalling is threshold-like. structural_context AT1G08830 AT2G28190 AT3G10920 AT4G25100 1.15.1.1 heme_electron_carrier 57Fe 1H AT1G07890 AT3G09640 1.11.1.11 Catalysis proceeds through Compound I, an oxoferryl porphyrin pi-cation radical — a genuine protein-based radical intermediate, and one of the few in the redox network rather than the electron transport chains. The porphyrin radical is strongly exchange-coupled to the ferryl iron and extremely short-lived. Structurally it is a radical; whether it could ever be a spin-correlated pair with a geomagnetically relevant lifetime is untested and doubtful. heme_electron_carrier 57Fe 1H AT1G20630 AT4G35090 AT1G20620 1.11.1.6 Like ascorbate peroxidase, catalase cycles through a Compound I porphyrin radical. Its relevance here is positional: it is the enzyme standing between germination beta-oxidation and oxidative damage. structural_context AT3G06050 1.11.1.24 flavin_semiquinone 1H 14N CHEBI:57692 AT3G24170 AT1G19570 AT3G52880 1.8.1.7 1.8.5.1 1.6.5.4 Glutathione reductase and monodehydroascorbate reductase are FAD enzymes, so the same flavin semiquinone chemistry applies here as at complex I and FNR. MDAR is notable for acting on a stable organic radical — monodehydroascorbate — as its actual substrate. The monodehydroascorbate radical is free in solution rather than held in a protein pocket, so it has no correlated partner and tumbles freely. It is a radical, not a radical pair. structural_context CHEBI:29073 CHEBI:57925 CHEBI:57783 C00072 C00051 C00005 structural_context CHEBI:57783 CHEBI:58349 C00005 C00006 structural_context Transcriptomics and metabolomics of ROS modulation in near-null magnetic field-induced Arabidopsis: field reduction alters ROS-associated transcriptional and metabolic programmes. Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport, establishing a route from respiratory state to stress signalling. This entity carries demonstrated near-null-field evidence but NO proposed quantum route, and is classed structural_context to say so explicitly. It is the amplifier's output: threshold-like signalling turns an upstream change too small to measure directly into a transcriptional response. That sensitivity is what makes it the best-evidenced node in the atlas and simultaneously a poor discriminator — it reports that something moved upstream, never what. direct_influence direct_influence direct_influence catalysis electron_transfer electron_transfer electron_transfer redox_feedback redox_feedback energy_feedback redox_feedback direct_influence redox_feedback redox_feedback