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3s39, resolution 4.80Å ()
Ligands: , , , ,
Gene: cbaa (Thermus thermophilus), cbab, cbac (Thermus thermophilus), cbad (Thermus thermophilus)
Activity: Cytochrome-c oxidase, with EC number
Related: 3s33, 3s38, 3s3a, 3s3b, 3s3c, 3s3d

Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml

Structure of Thermus thermophilus cytochrome ba3 oxidase 60s after Xe depressurization

Publication Abstract from PubMed

We use a form of "freeze-trap, kinetic-crystallography" to explore the migration of Xe atoms away from the dinuclear heme-a3/CuB center in Thermus thermophilus cytochrome ba3 oxidase. This enzyme is a member of the heme-copper oxidase super-family, and is thus crucial for dioxygen dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O2 diffusion channel in cytochrome ba3 oxidase that is continuous, Y-shaped, 18-20 A in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a3-CuB center in the active site. To understand movement of gas molecules within the O2 channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 seconds while undergoing out-gassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 --> Xe5 --> Xe3 --> Xe4 sites, suggesting that ingress of O2 is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.

Mobility of Xe atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase., Luna VM, Fee JA, Deniz AA, Stout CD, Biochemistry. 2012 May 19. PMID:22607023

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3s39 is a 3 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA.


  • Luna VM, Fee JA, Deniz AA, Stout CD. Mobility of Xe atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase. Biochemistry. 2012 May 19. PMID:22607023 doi:10.1021/bi3003988

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