1OCO

BOVINE HEART CYTOCHROME C OXIDASE IN CARBON MONOXIDE-BOUND STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.

Yoshikawa, S.Shinzawa-Itoh, K.Nakashima, R.Yaono, R.Yamashita, E.Inoue, N.Yao, M.Fei, M.J.Libeu, C.P.Mizushima, T.Yamaguchi, H.Tomizaki, T.Tsukihara, T.

(1998) Science 280: 1723-1729

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from ...

    Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from the O2 reduction site exchanges its effective accessibility to the matrix aqueous phase for one to the cytosolic phase concomitantly with a significant decrease in the pK of its carboxyl group, on reduction of the metal sites. The movement indicates the aspartate as the proton pumping site. A tyrosine acidified by a covalently linked imidazole nitrogen is a possible proton donor for the O2 reduction by the enzyme.


    Related Citations: 
    • Structures of Metal Sites of Oxidized Bovine Heart Cytochrome C Oxidase at 2.8 A
      Tsukihara, T.,Aoyama, H.,Yamashita, E.,Tomizaki, T.,Yamaguchi, H.,Shinzawa-Itoh, K.,Nakashima, R.,Yaono, R.,Yoshikawa, S.
      (1995) Science 269: 1069
    • The Whole Structure of the 13-Subunit Oxidized Cytochrome C Oxidase at 2.8 A
      Tsukihara, T.,Aoyama, H.,Yamashita, E.,Tomizaki, T.,Yamaguchi, H.,Shinzawa-Itoh, K.,Nakashima, R.,Yaono, R.,Yoshikawa, S.
      (1996) Science 272: 1136


    Organizational Affiliation

    Department of Life Science, Himeji Institute of Technology and CREST, Japan Science and Technology Corporation (JST), Kamigohri Akoh, Hyogo 678-1297, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
A, N
514Bos taurusMutation(s): 0 
Gene Names: MT-CO1 (COI, COXI, MTCO1)
EC: 1.9.3.1
Find proteins for P00396 (Bos taurus)
Go to Gene View: MT-CO1
Go to UniProtKB:  P00396
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
B, O
227Bos taurusMutation(s): 0 
Gene Names: MT-CO2 (COII, COX2, COXII, MTCO2)
Find proteins for P68530 (Bos taurus)
Go to Gene View: MT-CO2
Go to UniProtKB:  P68530
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
C, P
261Bos taurusMutation(s): 0 
Gene Names: MT-CO3 (COIII, COXIII, MTCO3)
Find proteins for P00415 (Bos taurus)
Go to Gene View: MT-CO3
Go to UniProtKB:  P00415
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
D, Q
147Bos taurusMutation(s): 0 
Gene Names: COX4I1 (COX4)
Find proteins for P00423 (Bos taurus)
Go to Gene View: COX4I1
Go to UniProtKB:  P00423
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
E, R
109Bos taurusMutation(s): 0 
Gene Names: COX5A
Find proteins for P00426 (Bos taurus)
Go to Gene View: COX5A
Go to UniProtKB:  P00426
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
F, S
98Bos taurusMutation(s): 0 
Gene Names: COX5B
Find proteins for P00428 (Bos taurus)
Go to Gene View: COX5B
Go to UniProtKB:  P00428
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
G, T
84Bos taurusMutation(s): 0 
Gene Names: COX6A2 (COX6A)
Find proteins for P07471 (Bos taurus)
Go to Gene View: COX6A2
Go to UniProtKB:  P07471
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
H, U
85Bos taurusMutation(s): 0 
Gene Names: COX6B1 (COX6B)
Find proteins for P00429 (Bos taurus)
Go to Gene View: COX6B1
Go to UniProtKB:  P00429
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
I, V
73Bos taurusMutation(s): 0 
Gene Names: COX6C
Find proteins for P04038 (Bos taurus)
Go to Gene View: COX6C
Go to UniProtKB:  P04038
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
J, W
59Bos taurusMutation(s): 0 
Gene Names: COX7A1 (COX7A, COX7AH)
Find proteins for P07470 (Bos taurus)
Go to Gene View: COX7A1
Go to UniProtKB:  P07470
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
K, X
56Bos taurusMutation(s): 0 
Gene Names: COX7B
Find proteins for P13183 (Bos taurus)
Go to Gene View: COX7B
Go to UniProtKB:  P13183
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
L, Y
47Bos taurusMutation(s): 0 
Gene Names: COX7C (COX7CP1)
Find proteins for P00430 (Bos taurus)
Go to Gene View: COX7C
Go to UniProtKB:  P00430
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
M, Z
46Bos taurusMutation(s): 0 
Gene Names: COX8B (COX8H)
Find proteins for P10175 (Bos taurus)
Go to UniProtKB:  P10175
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download SDF File 
Download CCD File 
A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
F, S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A, B, N, O
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, N
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 189.100α = 90.00
b = 210.500β = 90.00
c = 178.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
TSUKIdata scaling
X-PLORphasing
TSUKIdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-07-09 
  • Released Date: 1999-07-22 
  • Deposition Author(s): Tsukihara, T., Yao, M.

Revision History 

  • Version 1.0: 1999-07-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance