3ABK

Bovine heart cytochrome c oxidase at the NO-bound fully reduced state (50K)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray structure of the NO-bound Cu(B) in bovine cytochrome c oxidase

Ohta, K.Muramoto, K.Shinzawa-Itoh, K.Yamashita, E.Yoshikawa, S.Tsukihara, T.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 251-253

  • DOI: 10.1107/S1744309109055109
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The X-ray crystallographic structure of nitric oxide-treated bovine heart cytochrome c oxidase (CcO) in the fully reduced state has been determined at 50 K under light illumination. In this structure, nitric oxide (NO) is bound to the CcO oxygen-redu ...

    The X-ray crystallographic structure of nitric oxide-treated bovine heart cytochrome c oxidase (CcO) in the fully reduced state has been determined at 50 K under light illumination. In this structure, nitric oxide (NO) is bound to the CcO oxygen-reduction site, which consists of haem and a Cu atom (the haem a(3)-Cu(B) site). Electron density for the NO molecule was observed close to Cu(B). The refined structure indicates that NO is bound to Cu(B) in a side-on manner.


    Organizational Affiliation

    Institute for Protein Research, Osaka University, OLABB, 6-2-6 Furuedai, Suita, Osaka 565-0874, Japan.



Macromolecules

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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: 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

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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)
Go to UniProtKB:  P07471

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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)
Go to UniProtKB:  P04038

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c oxidase polypeptide 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: 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)
Go to UniProtKB:  P13183

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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)
Go to UniProtKB:  P00430

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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
Small Molecules
Ligands 15 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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B, D, L, N, O, Y
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

Download CCD File 
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

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B, R
(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, U
(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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C, M, P, Z
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CHD
Query on CHD

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B, C, J, O, 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
NO
Query on NO

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A, N
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 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
FME
Query on FME
A,N, B,O
L-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO
A,N, B,O, G,T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC
A,N, B,O, G,T, I,V
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.247α = 90
b = 207.944β = 90
c = 177.997γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Database references