2Y69

Bovine heart cytochrome c oxidase re-refined with molecular oxygen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:3ABM


Literature

A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase.

Kaila, V.R.I.Oksanen, E.Goldman, A.Bloch, D.A.Verkhovsky, M.I.Sundholm, D.Wikstrom, M.

(2011) Biochim Biophys Acta 1807: 769

  • DOI: 10.1016/j.bbabio.2010.12.016
  • Primary Citation of Related Structures:  
    2Y69

  • PubMed Abstract: 
  • Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. By reducing oxygen to water, it generates a proton gradient across the mitochondrial or bacterial membrane. Recently, two independent X-ray crystallographic studies ((Aoyama et al ...

    Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. By reducing oxygen to water, it generates a proton gradient across the mitochondrial or bacterial membrane. Recently, two independent X-ray crystallographic studies ((Aoyama et al. Proc. Natl. Acad. Sci. USA 106 (2009) 2165-2169) and (Koepke et al. Biochim. Biophys. Acta 1787 (2009) 635-645)), suggested that a peroxide dianion might be bound to the active site of oxidized CcO. We have investigated this hypothesis by combining quantum chemical calculations with a re-refinement of the X-ray crystallographic data and optical spectroscopic measurements. Our data suggest that dianionic peroxide, superoxide, and dioxygen all form a similar superoxide species when inserted into a fully oxidized ferric/cupric binuclear site (BNC). We argue that stable peroxides are unlikely to be confined within the oxidized BNC since that would be expected to lead to bond splitting and formation of the catalytic P intermediate. Somewhat surprisingly, we find that binding of dioxygen to the oxidized binuclear site is weakly exergonic, and hence, the observed structure might have resulted from dioxygen itself or from superoxide generated from O(2) by the X-ray beam. We show that the presence of O(2) is consistent with the X-ray data. We also discuss how other structures, such as a mixture of the aqueous species (H(2)O+OH(-) and H(2)O) and chloride fit the experimental data.


    Related Citations: 
    • A Peroxide Bridge between Fe and Cu Ions in the O2 Reduction Site of Fully Oxidized Cytochrome C Oxidase Could Suppress the Proton Pump.
      Aoyama, H., Muramoto, K., Shinzawa-Itoh, K., Hirata, K., Yamashita, E., Tsukihara, T., Ogura, T., Yoshikawa, S.
      (2009) Proc Natl Acad Sci U S A 106: 2165

    Organizational Affiliation

    Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland. ville.kaila@nih.gov



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 1A, N514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 2B, O227Bos 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)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 3C, P261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1D, Q169Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
EC: 1.9.3.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 5AE, R152Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 5BF, S129Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE 6A2G, T97Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
EC: 1.9.3.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1H, U86Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
EC: 1.9.3.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE VICI, V74Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE 7A1J, W80Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
EC: 1.9.3.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE 7BK, X80Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 7CL, Y63Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
EC: 1.9.3.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE 8HM, Z70Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
EC: 1.9.3.1
Find proteins for P10175 (Bos taurus)
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download Ideal Coordinates CCD File 
AA [auth A], BA [auth A], OA [auth N], PA [auth N]HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEK
Query on PEK

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HA [auth C], VA [auth P](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
PGV
Query on PGV

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IA [auth C], JA [auth C], WA [auth P], XA [auth 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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BB [auth Z], NA [auth M]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CHD
Query on CHD

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AB [auth T], FA [auth A], KA [auth C], MA [auth G], TA [auth N], YA [auth P]CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
CUA
Query on CUA

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GA [auth B], UA [auth O]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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LA [auth F], ZA [auth S]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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CA [auth A], QA [auth N]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
OXY
Query on OXY

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DA [auth A], RA [auth N]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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EA [auth A], SA [auth N]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
G, TL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.697α = 90
b = 206.991β = 90
c = 178.251γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references, Other, Version format compliance
  • Version 1.2: 2015-02-04
    Changes: Atomic model, Derived calculations, Other
  • Version 1.3: 2018-06-20
    Changes: Advisory, Data collection
  • Version 1.4: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-11-06
    Changes: Data collection, Database references, Other