EzCatDB: M00062

DB codeM00062
RLCP classification10.100012.100.10200
10.12100.110.10080
10.100110.100.10300
CATH domainDomain 11.20.210.10Catalytic domain
Domain 22.60.40.420Catalytic domain
Domain 31.10.287.90
Domain 41.10.287.70
Domain 51.20.120.80
Domain 61.20.5.160
E.C.1.9.3.1
CSA1ar1

CATH domainRelated DB codes (homologues)
1.20.210.10M00194
2.60.40.420T00215,T00216,M00115,M00194

Enzyme Name
Swiss-protKEGG

P98002P08306P06030P77921
Protein nameCytochrome c oxidase subunit 1-betaCytochrome c oxidase subunit 2Cytochrome c oxidase subunit 3Cytochrome c oxidase subunit 4cytochrome-c oxidase
cytochrome oxidase
cytochrome a3
cytochrome aa3
Warburg's respiratory enzyme
indophenol oxidase
indophenolase
complex IV (mitochondrial electron transport)
ferrocytochrome c oxidase
NADH cytochrome c oxidase
SynonymsEC 1.9.3.1
Cytochrome c oxidase polypeptide I-beta
Cytochrome aa3 subunit 1-beta
EC 1.9.3.1
Cytochrome c oxidase polypeptide II
Cytochrome aa3 subunit 2
Oxidase aa(3) subunit 2
EC 1.9.3.1
Cytochrome c oxidase polypeptide III
Cytochrome aa3 subunit 3
Oxidase aa(3) subunit 3
EC 1.9.3.1
Cytochrome c oxidase polypeptide IV
Cytochrome aa3 subunit 4

KEGG pathways
MAP codePathways
MAP00190Oxidative phosphorylation

Swiss-prot:Accession NumberP98002P08306P06030P77921
Entry nameCOX1B_PARDECOX2_PARDECOX3_PARDECOX4_PARDE
Activity4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.
Subunit



Subcellular locationCell inner membrane, Multi-pass membrane protein.Cell inner membrane, Multi-pass membrane protein.Cell inner membrane, Multi-pass membrane protein.Cell inner membrane, Single-pass membrane protein.
CofactorBinds 1 copper B ion per subunit.,Binds 2 heme groups per subunit.Binds 2 copper A ions per subunit.



CofactorsSubstratesProducts
KEGG-idC00070C00032C00032C00034C00126C00007C00080C00125C00001
CompoundCopperHeme AHeme A3ManganeseFerrocytochrome cO2H+Ferricytochrome cH2O
Typeheavy metalaromatic ring (with nitrogen atoms),carboxyl group,heavy metalaromatic ring (with nitrogen atoms),carboxyl group,heavy metalheavy metalamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide groupothersothersamide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide groupH2O
1ar1ABound:_CUBound:HEA 1Bound:HEA 2Analogue:_MGUnboundUnbound
Unbound
1qleABound:_CUBound:HEA 1Bound:HEA 2Bound:_MNUnboundUnbound
Unbound
1ar1B01Bound:2x_CUUnboundUnboundUnboundUnboundUnbound
Unbound
1qleB01Bound:CUAUnboundUnboundUnboundUnboundUnbound
Unbound
1ar1B02UnboundUnboundUnboundUnboundUnboundUnbound
Unbound
1qleB02UnboundUnboundUnboundUnboundUnboundUnbound
Unbound
1qleC01UnboundUnboundUnboundUnboundUnboundUnbound
Unbound
1qleC02UnboundUnboundUnboundUnboundUnboundUnbound
Unbound
1qleDUnboundUnboundUnboundUnboundUnboundUnbound
Unbound

Active-site residues
resource
literature [10], [26]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
1ar1AASP 124;GLU 278;TYR 280;HIS 325;LYS 354
HIS 94;HIS 413(Heme A);HIS 411(Heme A3);HIS 276;TYR 280;HIS 325;HIS 326(Copper B);HIS 403;ASP 404(Manganese);GLU 56;HIS 59;GLY 61;GLN 63(Calcium)
PHE 412;ARG 473;ARG 474
1qleAASP 124;GLU 278;TYR 280;HIS 325;LYS 354
HIS 94;HIS 413(Heme A);HIS 411(Heme A3);HIS 276;TYR 280;HIS 325;HIS 326(Copper B);HIS 403;ASP 404(Manganese);GLU 56;HIS 59;GLY 61;GLN 63(Calcium)
PHE 412;ARG 473;ARG 474
1ar1B01TRP 121
HIS 181;CYS 216;CYS 220;MET 227(Copper A1);CYS 216;GLU 218;CYS 220;HIS 224(Copper A2);GLU 218;SER 217(Manganese)

1qleB01TRP 121
HIS 181;CYS 216;CYS 220;MET 227(Copper A1);CYS 216;GLU 218;CYS 220;HIS 224(Copper A2);GLU 218;SER 217(Manganese)

1ar1B02


1qleB02


1qleC01


1qleC02


1qleD



References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]Fig.5
[10]Fig.5, p.666-668
[11]Fig.1
[14]p.463-464
[16]Fig.5, p.13827-13828
[17]p.10550-10552
[18]Fig.4, p.2473-2475
[21]p.828-832, Fig.13
[22]Fig.1, p.719-720
[23]Fig.1
[24]Fig.1, Fig.6, p.371-373
[25]

[26]Fig.6, p.102-106
[27]

[32]Fig.6, p.987-988
[34]Fig.1
[37]p.6-7
[43]Fig.1
[45]p.51-59

references
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PubMed ID6307293
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Year1983
Volume113
Pages575-80
AuthorsYanagita Y, Sone N, Kagawa Y
TitleProton pumping and oxidase activity of thermophilic cytochrome oxidase remain after its extensive proteolysis.
[2]
PubMed ID2883179
JournalJ Biochem (Tokyo)
Year1986
Volume100
Pages1465-70
AuthorsSone N
TitleMeasurement of proton pump activity of the thermophilic bacterium PS3 and Nitrobacter agilis at the cytochrome oxidase level using total membrane and heptyl thioglucoside.
[3]
PubMed ID8407882
JournalJ Biochem (Tokyo)
Year1993
Volume114
Pages88-95
AuthorsYumoto I, Takahashi S, Kitagawa T, Fukumori Y, Yamanaka T
TitleThe molecular features and catalytic activity of CuA-containing aco3-type cytochrome c oxidase from a facultative alkalophilic Bacillus.
[4]
PubMed ID8068652
JournalBiochemistry
Year1994
Volume33
Pages9731-40
AuthorsHaltia T, Semo N, Arrondo JL, Goni FM, Freire E
TitleThermodynamic and structural stability of cytochrome c oxidase from Paracoccus denitrificans.
[5]
PubMed ID7577945
JournalBiochemistry
Year1995
Volume34
Pages13565-9
AuthorsEchabe I, Haltia T, Freire E, Goni FM, Arrondo JL
TitleSubunit III of cytochrome c oxidase influences the conformation of subunits I and II: an infrared study.
[6]
PubMed ID7779804
JournalBiochemistry
Year1995
Volume34
Pages7586-92
AuthorsHosler JP, Espe MP, Zhen Y, Babcock GT, Ferguson-Miller S
TitleAnalysis of site-directed mutants locates a non-redox-active metal near the active site of cytochrome c oxidase of Rhodobacter sphaeroides.
[7]
PubMed ID7727443
JournalBiochemistry
Year1995
Volume34
Pages5824-30
AuthorsLappalainen P, Watmough NJ, Greenwood C, Saraste M
TitleElectron transfer between cytochrome c and the isolated CuA domain: identification of substrate-binding residues in cytochrome c oxidase.
[8]
PubMed ID7632682
JournalBiochemistry
Year1995
Volume34
Pages9819-25
AuthorsWang J, Takahashi S, Hosler JP, Mitchell DM, Ferguson-Miller S, Gennis RB, Rousseau DL
TitleTwo conformations of the catalytic site in the aa3-type cytochrome c oxidase from Rhodobacter sphaeroides.
[9]
PubMed ID7552705
JournalNat Struct Biol
Year1995
Volume2
Pages842-6
AuthorsOstermeier C, Iwata S, Ludwig B, Michel H
TitleFv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID95379947
PubMed ID7651515
JournalNature
Year1995
Volume376
Pages660-9
AuthorsIwata S, Ostermeier C, Ludwig B, Michel H
TitleStructure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans.
Related Swiss-protP98002,P08306,P06030,P77921
[11]
PubMed ID8718868
JournalBiochemistry
Year1996
Volume35
Pages10776-83
AuthorsHosler JP, Shapleigh JP, Mitchell DM, Kim Y, Pressler MA, Georgiou C, Babcock GT, Alben JO, Ferguson-Miller S, Gennis RB
TitlePolar residues in helix VIII of subunit I of cytochrome c oxidase influence the activity and the structure of the active site.
[12]
PubMed ID8547262
JournalBiochemistry
Year1996
Volume35
Pages824-8
AuthorsMitchell DM, Adelroth P, Hosler JP, Fetter JR, Brzezinski P, Pressler MA, Aasa R, Malmstrom BG, Alben JO, Babcock GT, Gennis RB, Ferguson-Miller S
TitleA ligand-exchange mechanism of proton pumping involving tyrosine-422 of subunit I of cytochrome oxidase is ruled out.
[13]
PubMed ID8825522
JournalCurr Biol
Year1996
Volume6
Pages36-8
AuthorsGennis RB, Ferguson-Miller S
TitleProtein structure: proton-pumping oxidases.
[14]
CommentsREVIEW
Medline ID96391941
PubMed ID8794157
JournalCurr Opin Struct Biol
Year1996
Volume6
Pages460-6
AuthorsOstermeier C, Iwata S, Michel H
TitleCytochrome c oxidase.
Related Swiss-protP98002
[15]
PubMed ID8955368
JournalFEBS Lett
Year1996
Volume397
Pages303-7
AuthorsLubben M, Gerwert K
TitleRedox FTIR difference spectroscopy using caged electrons reveals contributions of carboxyl groups to the catalytic mechanism of haem-copper oxidases.
[16]
PubMed ID9374859
JournalBiochemistry
Year1997
Volume36
Pages13824-9
AuthorsAdelroth P, Ek MS, Mitchell DM, Gennis RB, Brzezinski P
TitleGlutamate 286 in cytochrome aa3 from Rhodobacter sphaeroides is involved in proton uptake during the reaction of the fully-reduced enzyme with dioxygen.
[17]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS)
Medline ID98021406
PubMed ID9380672
JournalProc Natl Acad Sci U S A
Year1997
Volume94
Pages10547-53
AuthorsOstermeier C, Harrenga A, Ermler U, Michel H
TitleStructure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment.
Related PDB1ar1
Related Swiss-protP98002,P08306
[18]
PubMed ID9485395
JournalBiochemistry
Year1998
Volume37
Pages2470-6
AuthorsAdelroth P, Gennis RB, Brzezinski P
TitleRole of the pathway through K(I-362) in proton transfer in cytochrome c oxidase from R. sphaeroides.
[19]
PubMed ID9922138
JournalBiochemistry
Year1998
Volume37
Pages17726-34
AuthorsKarlin S, Zhu ZY, Karlin KD
TitleExtended metal environments of cytochrome c oxidase structures.
[20]
PubMed ID9585552
JournalBiochemistry
Year1998
Volume37
Pages7378-89
AuthorsSalgado J, Warmerdam G, Bubacco L, Canters GW
TitleUnderstanding the electronic properties of the CuA site from the soluble domain of cytochrome c oxidase through paramagnetic 1H NMR.
[21]
PubMed ID9893941
JournalBiochimie
Year1998
Volume80
Pages821-36
AuthorsPapa S, Capitanio N, Villani G, Capitanio G, Bizzoca A, Palese LL, Carlino V, De Nitto E
TitleCooperative coupling and role of heme a in the proton pump of heme-copper oxidases.
[22]
PubMed ID9533684
JournalBiophys J
Year1998
Volume74
Pages708-21
AuthorsKannt A, Lancaster CR, Michel H
TitleThe coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase.
[23]
PubMed ID9492306
JournalEur J Biochem
Year1998
Volume251
Pages367-73
AuthorsWitt H, Malatesta F, Nicoletti F, Brunori M, Ludwig B
TitleCytochrome-c-binding site on cytochrome oxidase in Paracoccus denitrificans.
[24]
PubMed ID9538216
JournalJ Biochem (Tokyo)
Year1998
Volume123
Pages369-75
AuthorsIwata S
TitleStructure and function of bacterial cytochrome c oxidase.
[25]
PubMed ID9478966
JournalJ Biol Chem
Year1998
Volume273
Pages5132-6
AuthorsWitt H, Malatesta F, Nicoletti F, Brunori M, Ludwig B
TitleTryptophan 121 of subunit II is the electron entry site to cytochrome-c oxidase in Paracoccus denitrificans. Involvement of a hydrophobic patch in the docking reaction.
[26]
PubMed ID9443344
JournalProteins
Year1998
Volume30
Pages100-7
AuthorsHofacker I, Schulten K
TitleOxygen and proton pathways in cytochrome c oxidase.
[27]
PubMed ID9660711
JournalScience
Year1998
Volume280
Pages1712-3
AuthorsGennis RB
TitleCytochrome c oxidase: one enzyme, two mechanisms?
[28]
PubMed ID10029521
JournalBiochemistry
Year1999
Volume38
Pages2287-94
AuthorsVillani G, Capitanio N, Bizzoca A, Palese LL, Carlino V, Tattoli M, Glaser P, Danchin A, Papa S
TitleEffects of site-directed mutagenesis of protolytic residues in subunit I of Bacillus subtilis aa3-600 quinol oxidase. Role of lysine 304 in proton translocation.
[29]
PubMed ID10481041
JournalFEBS Lett
Year1999
Volume458
Pages83-6
AuthorsHellwig P, Soulimane T, Buse G, Mantele W
TitleSimilarities and dissimilarities in the structure-function relation between the cytochrome c oxidase from bovine heart and from Paracoccus denitrificans as revealed by FT-IR difference spectroscopy.
[30]
PubMed ID10462045
JournalFEBS Lett
Year1999
Volume456
Pages365-9
AuthorsPfitzner U, Kirichenko A, Konstantinov AA, Mertens M, Wittershagen A, Kolbesen BO, Steffens GC, Harrenga A, Michel H, Ludwig B
TitleMutations in the Ca2+ binding site of the Paracoccus denitrificans cytochrome c oxidase.
[31]
CommentsX-ray crystallography
PubMed ID10559205
JournalJ Biol Chem
Year1999
Volume274
Pages33296-9
AuthorsHarrenga A, Michel H
TitleThe cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction.
Related PDB1qle
[32]
CommentsCOVALENT BOND
Medline ID99268331
PubMed ID10338009
JournalProtein Sci
Year1999
Volume8
Pages985-90
AuthorsBuse G, Soulimane T, Dewor M, Meyer HE, Bluggel M
TitleEvidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase.
Related Swiss-protP98002
[33]
PubMed ID10891065
JournalBiochemistry
Year2000
Volume39
Pages7863-7
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TitleProton translocation by cytochrome c oxidase can take place without the conserved glutamic acid in subunit I.
[34]
PubMed ID10828950
JournalBiochemistry
Year2000
Volume39
Pages6365-72
AuthorsRiistama S, Puustinen A, Verkhovsky MI, Morgan JE, Wikstrom M
TitleBinding of O(2) and its reduction are both retarded by replacement of valine 279 by isoleucine in cytochrome c oxidase from Paracoccus denitrificans.
[35]
PubMed ID11352755
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Year2001
Volume40
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[36]
PubMed ID11425307
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Year2001
Volume40
Pages7806-11
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TitleDynamics of nitric oxide in the active site of reduced cytochrome c oxidase aa3.
[37]
PubMed ID11341911
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Year2001
Volume1544
Pages1-9
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PubMed ID11513871
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Year2001
Volume503
Pages142-6
AuthorsKannt A, Ostermann T, Muller H, Ruitenberg M
TitleZn(2+) binding to the cytoplasmic side of Paracoccus denitrificans cytochrome c oxidase selectively uncouples electron transfer and proton translocation.
[39]
PubMed ID11374571
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Year2001
Volume57A
Pages1123-31
AuthorsHellwig P, Rost B, Mantele W
TitleRedox dependent conformational changes in the mixed valence form of the cytochrome c oxidase from p. The reorganization of glutamic acid 278 is coupled to the electron transfer from/to heme a and the binuclear center. denitrificans.
[40]
PubMed ID12071962
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Year2002
Volume269
Pages2980-8
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[41]
PubMed ID11950842
JournalJ Biol Chem
Year2002
Volume277
Pages22402-6
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[42]
PubMed ID11825904
JournalJ Biol Chem
Year2002
Volume277
Pages13563-8
AuthorsPinakoulaki E, Pfitzner U, Ludwig B, Varotsis C
TitleThe role of the cross-link His-Tyr in the functional properties of the binuclear center in cytochrome c oxidase.
[43]
PubMed ID11986672
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Year2002
Volume417
Pages99-102
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[44]
PubMed ID11870867
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Year2002
Volume47
Pages75-85
AuthorsFlock D, Helms V
TitleProtein--protein docking of electron transfer complexes: cytochrome c oxidase and cytochrome c.
[45]
PubMed ID12783267
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Year2003
Volume147
Pages47-74
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TitleCytochrome c oxidase--structure, function, and physiology of a redox-driven molecular machine.
[46]
PubMed ID15518562
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Year2004
Volume43
Pages14118-27
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TitleNO binding and dynamics in reduced heme-copper oxidases aa3 from Paracoccus denitrificans and ba3 from Thermus thermophilus.
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PubMed ID15041635
JournalBiophys J
Year2004
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Pages1873-89
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TitleDynamic water networks in cytochrome C oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations.
[48]
PubMed ID14672950
JournalJ Biol Chem
Year2004
Volume279
Pages10293-303
AuthorsPaumann M, Lubura B, Regelsberger G, Feichtinger M, Kollensberger G, Jakopitsch C, Furtmuller PG, Peschek GA, Obinger C
TitleSoluble CuA domain of cyanobacterial cytochrome c oxidase.

comments
This enzyme, cytochrome c oxidase, is so-called "Complex IV (mitochondrial electron transport).
Although this enzyme is partially homologous to that from T. thermophilus (Bacteria) (M00194 in EzCatDB), the subunit/domain compositions seem to be slightly different from the counterpart enzyme.
Bacterial enzymes are composed of 3 or 4 subunits. Of the three or four subunits, subunits I and II form the functional core of the enzyme complex. The subunit I binds a copper ion (CuB), two heme groups (heme A and heme A3), along with manganese ion bound at the interface with the subunit II. The subunit II binds a binuclear copper ion pair, CuA. Heme A3 and CuB form a binuclear centre for O2 reduction.
Taken together, this enzyme catalyzes the following reactions, electron transfers and dioxygen reduction, coupling with proton pumping.
4 cyt c(red) + 8 H+(in) + O2 = 4 cyt c(ox) + 2 H2O + 4 H+(out)
According to the literature [7], [10], [45], this enzyme catalyzes the following reactions:
(A) Electron transfer from cytochrome c (substrate;ferrocytochrome c) to CuA (subunit II):
(B) Electron transfer from CuA (subunit II) to heme A (subunit I):
(C) Electron transfer from heme A (subunit I) to binculear center (heme A3 & CuB) (subunit I):
(D) Reduction of dioxygen (O2) to H2O (at the binuclear center):
(E) Proton pump
According to the literature [10], the following reaction proceeds as follows:
(A) Electron transfer from cytochrome c (substrate;ferrocytochrome c) to CuA (subunit II):
(A1) Indirect transfer through Trp121 (subunit II) to Met227 bound to CuA-1 (see [10], [25]).
(B) Electron transfer from CuA (subunit II) to heme A (subunit I):
(B1) Indirect transfer through His224 (subunit II), mainchain carbonyl oxygen of Arg473 and mainchain amide of Arg474 (subunit I), and propionate (carboxylate) group of heme A.
(C) Electron transfer from heme A (subunit I) to binculear center (heme A3 & CuB) (subunit I):
(C1) Indirect transfer through His413 bound to heme A iron, mainchain of Phe412, and His411 bound to heme A3 iron (see [10]).

createdupdated
2004-04-192009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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