3ASN

Bovine heart cytochrome C oxidase in the fully oxidized state measured at 1.7470 angstrom wavelength


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase

Suga, M.Yano, N.Muramoto, K.Shinzawa-Itoh, K.Maeda, T.Yamashita, E.Tsukihara, T.Yoshikawa, S.

(2011) Acta Crystallogr D Biol Crystallogr 67: 742-744

  • DOI: 10.1107/S0907444911022803
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Fully oxidized cytochrome c oxidase (CcO) under enzymatic turnover is capable of pumping protons, while fully oxidized CcO as isolated is not able to do so upon one-electron reduction. The functional difference is expected to be a consequence of stru ...

    Fully oxidized cytochrome c oxidase (CcO) under enzymatic turnover is capable of pumping protons, while fully oxidized CcO as isolated is not able to do so upon one-electron reduction. The functional difference is expected to be a consequence of structural differences: [Fe(3+)-OH(-)] under enzymatic turnover versus [Fe(3+)-O(2)(2-)-Cu(2+)] for the as-isolated CcO. However, the electron density for O(2)(2-) is equally assignable to Cl(-). An anomalous dispersion analysis was performed in order to conclusively demonstrate the absence of Cl(-) between the Fe(3+) and Cu(2+). Thus, the peroxide moiety receives electron equivalents from cytochrome c without affecting the oxidation states of the metal sites. The metal-site reduction is coupled to the proton pump.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P00415 (Bos taurus)
Go to UniProtKB:  P00415

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 4 isoform 1
D, Q
147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
EC: 1.9.3.1
Find proteins for P00423 (Bos taurus)
Go to UniProtKB:  P00423

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 5A
E, R
109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
Find proteins for P00426 (Bos taurus)
Go to UniProtKB:  P00426

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 5B
F, S
98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
Find proteins for P00428 (Bos taurus)
Go to UniProtKB:  P00428

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6A2
G, T
85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
EC: 1.9.3.1
Find proteins for P07471 (Bos taurus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
EC: 1.9.3.1
Find proteins for P00429 (Bos taurus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
Find proteins for P04038 (Bos taurus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7B
K, X
56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
Find proteins for P13183 (Bos taurus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7C
L, Y
47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
EC: 1.9.3.1
Find proteins for P00430 (Bos taurus)
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P00396 (Bos taurus)
Go to UniProtKB:  P00396

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 7A1
J, W
59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
EC: 1.9.3.1
Find proteins for P07470 (Bos taurus)
Go to UniProtKB:  P07470

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 8B
M, Z
46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
EC: 1.9.3.1
Find proteins for P10175 (Bos taurus)
Go to UniProtKB:  P10175

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Find proteins for P68530 (Bos taurus)
Go to UniProtKB:  P68530
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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C, G, P, T
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
TGL
Query on TGL

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A, D, L, N
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
 Ligand Interaction
HEA
Query on HEA

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A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEK
Query on PEK

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C, G, P, T
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
 Ligand Interaction
PSC
Query on PSC

Download CCD File 
B, O
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
 Ligand Interaction
PGV
Query on PGV

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A, C, N, P
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
 Ligand Interaction
DMU
Query on DMU

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M, Z
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CHD
Query on CHD

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B, C, G, J, P, W
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
CUA
Query on CUA

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B, O
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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F, S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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A, N
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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C, P
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
G,T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC
G,T, I,V
L-PEPTIDE LINKINGC5 H9 N O4SER
FME
Query on FME
A,N, G,T, I,V
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.826α = 90
b = 204.098β = 90
c = 177.829γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references