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Frame — 1OCC, bovine cytochrome c oxidase
Respiratory Complex IV from bovine heart — PDB 1OCC. The 3D backbone, CuA pair, heme a, heme a₃ and CuB are deposited coordinates. PDB residue names in this file do not match textbook metal names (CU_B_* = CuA pair; CU_A_517 = CuB); the screen uses CuA / heme a / a₃–CuB. Residue numbers follow this data slice (1OCC author numbering with a 20000 offset). Bovine, not bacterial or human CIV — disclosed under organism mixing.Source: PDB 1OCC (Tsukihara et al. 1996, Science · DOI:10.1126/science.272.5265.1136)
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Overall reaction (physiological O₂)
4 cyt c(reduced) + O₂ + 8 H⁺(N) → 4 cyt c(oxidized) + 2 H₂O + 4 H⁺(P). EC 7.1.1.9. This page loads one electron, then shows O–O cleavage as a teaching beat. Do not read ⑦ as “one cyt c plus one O₂ makes two waters.” Physiology is 4 e⁻ + 4 chemical H⁺ per O₂. The other three cyt c inputs are named here, not animated. “(reduced)” = Fe²⁺ electron donor, not a red color.Source: BRENDA EC 7.1.1.9 · physiology: Yoshikawa & Shimada 2015
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Setup — CuA, heme a, a₃–CuB empty (real 1OCC)
Setup shows the real CuA pair, heme a, heme a₃ and CuB with pockets empty. No cyt c at CuA, no O₂ at the binuclear center. Static mesh — no substrates until the next steps.Source: PDB 1OCC — metals + hemes deposited; cyt c / O₂ absent in this slice
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① — cyt c (reduced) arrives at CuA
[schematic] Reduced cytochrome c (Fe²⁺, not a red color) docks beside the real CuA pair. Arrival only — the electron transfer is ②. 1OCC is COX, not a cyt c co-crystal. The schematic mesh is tinted blue; oxidized cyt c is tinted duller.Source: registered schematic — no cyt c in this 1OCC slice; entry at CuA per Tsukihara et al. 1996
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② — cyt c reduces CuA
[schematic] One electron, one arrow, in-place red→ox cross-fade. A different event from CuA → heme a.Source: registered schematic — cyt c → CuA per Tsukihara et al. 1996
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③ — CuA → heme a
Entry relay. One arrow from the CuA pair midpoint to heme a FE. Deposited CuA Cu⋯Cu 2.38 Å; heme a FE⋯heme a₃ FE 13.38 Å.Source: metal–metal re-measured from PDB 1OCC
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④ — heme a → a₃–CuB
The electron hops into the binuclear center. One arrow. heme a₃ FE⋯CuB 4.70 Å (deposited). O₂ has not bound yet.Source: a₃ FE⋯CuB re-measured from PDB 1OCC
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⑤ — O₂ binds the reduced binuclear center
[schematic] O₂ docks at reduced a₃–CuB. Arrival only — cleavage is ⑥. Literature: O₂ binds the reduced center. No O₂ ligand is in this 1OCC slice.Source: registered schematic — O₂ at reduced a₃–CuB per Yoshikawa & Shimada 2015; no O₂ in this slice
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⑥ — O–O cleavage → ferryl P
PROPOSAL [schematic] (hypothetical, lit.-based). The P-state on this page is labeled ferryl Fe(IV)=O, not a peroxide P (Yoshikawa / Rich, post-2020 consensus). His–Tyr radical chemistry is named, not drawn. Water has not formed yet.Source: proposal — ferryl P, not peroxide: Yoshikawa & Shimada 2015; radical identity not drawn
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⑦ — two H₂O form at a₃–CuB
[schematic] Cleaved O₂ cross-fades in place to two waters as a teaching product pose. Stop here: O₂ → 2 H₂O needs four electrons and four chemical protons. This page loaded one electron. The fade is not “one cyt c plus one O₂ makes two waters.” Remaining electrons and protons are named, not drawn as extra particles. O–O cleavage in the enzyme usually follows a more reduced binuclear center (2–4 e⁻ loaded), not this single-electron snapshot.Source: registered schematic — 2 H₂O product of O₂ chemistry; 4 e⁻ cycle named, not packed · Yoshikawa & Shimada 2015
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⑧ — 4 H⁺ to the P-side
PROPOSAL [schematic] (hypothetical, lit.-based). Four H⁺ marked toward the P-side. Separate from O–O cleavage and from water formation. The pump trajectory is not a measured path.Source: proposal — no deposited H/K-channel trajectory · pumping named in Yoshikawa & Shimada 2015
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⑨ — H₂O and cyt c (oxidized) leave (two directions)
[schematic] Two waters leave toward the P-side. Oxidized cyt c (Fe³⁺) leaves to pick up another electron from Complex III. A full O₂ turnover still needs three more cyt c inputs (named, not drawn). Complex V chemistry lives on the CV page.Source: display convention — separate exits; no external geometry claimed · CV etcc5.html
Legend & Fidelity
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Mechanism fidelity — measured vs. inferred
Measured layer: protein Cα, CuA pair, heme a, heme a₃, CuB (1OCC). Inferred layer: cyt c / O₂ / H₂O / H⁺ poses, hop arrows as educational path markers, ferryl P assignment, pump overlay. Å numbers on this page are deposited metal–metal distances (CuA 2.38 Å, heme a FE⋯a₃ FE 13.38 Å, a₃ FE⋯CuB 4.70 Å), not schematic seats. cyt c is a heme cartoon, not the folded protein that docks COX. The ⑦ water fade is compressed 4 e⁻ bookkeeping after a 1 e⁻ load.
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Why are cyt c, O₂, H₂O and H⁺ “[schematic]”?
This 1OCC data slice contains metals and hemes, not cytochrome c or O₂. Substrate poses are literature-based reconstructions at CuA and the binuclear center, and are labeled [schematic]. No Å is claimed for those seats.Source: PDB 1OCC ligands = metals + hemes only
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The protein mesh is static
No helix / H-channel / K-channel motion. Pumping is an overlay, not a deposited trajectory.
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Controversy — P-state is ferryl, not peroxide
Older cartoons called the first O–O product “peroxide P”. Yoshikawa and Rich (and later time-resolved work) assign P as ferryl Fe(IV)=O plus a radical. This page never labels the species “peroxide”. The cleavage step is still PROPOSAL because the radical identity (His–Tyr vs others) is not drawn.
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Physiological regulation
Complex IV is inhibited by cyanide, carbon monoxide and azide at heme a₃–CuB. This page does not animate inhibitors. See Yoshikawa & Shimada, Chem Rev 2015 (PMID:25806599).
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Kinetics scope
This tool animates one electron load plus one O₂ cleavage; it does not model timecourses, steady-state kinetics, or Km / kcat / Vmax. Compiled bovine/human CIV turnover is order-10² s⁻¹ in the literature and is not re-measured here — see BRENDA EC 7.1.1.9. Pair with a kinetics chapter. Binding order on screen is educational staging.
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Sequence
Bovine COX1 (heme a / a₃–CuB, 1OCC entity 1, 514 aa) UniProt P00396 (SIFTS) · NCBI taxonomy 9913 (Bos taurus). Residue numbers = this data slice (1OCC author + 20000 offset).
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Sources — bibliography of this page
S1 — PDB 1OCC: bovine cytochrome c oxidase; Tsukihara et al. 1996, Science 272:1136–1144, PMID:8638158, DOI 10.1126/science.272.5265.1136 (RCSB primary citation)
S2 — Yoshikawa & Shimada 2015, Chem Rev, PMID:25806599 (ferryl P, not peroxide; pump named)
S3 — BRENDA EC 7.1.1.9 (compiled turnover order-10² s⁻¹; not re-measured here)
S4 — UniProt P00396 (COX1, SIFTS on 1OCC entity 1) · NCBI taxonomy 9913
S5 — How this page is drawn: cyt c/O₂/H₂O/H⁺ = [schematic]; screen = one electron then a teaching O–O beat, not 4 cyt c; ⑦ water fade is not 1 e⁻ stoichiometry; ⑥ ferryl P = PROPOSAL; metal–metal Å from deposited 1OCC only
› The 3D protein is real 1OCC Complex IV with genuine CuA, heme a, heme a₃ and CuB. cyt c, O₂, H₂O and H⁺ are compact schematic molecules posed at the sites and labeled [schematic]. Screen = one electron + one O₂, not 4 cyt c.