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 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    3ABK

  • 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-reduction site, which consists of haem and a Cu atom (the haem a(3)-Cu(B) site) ...

    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 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)
Membrane Entity: Yes 
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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)
Membrane Entity: Yes 
UniProt
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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)
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1D, Q147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5AE, R109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5BF, S98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2G, T85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1H, U85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CI, V73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 7A1J, W59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7BK, X56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7CL, Y47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8BM, Z46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
EC: 1.9.3.1
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
SA [auth C], TB [auth P], XA [auth G], ZB [auth T]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
TGL (Subject of Investigation/LOI)
Query on TGL

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AB [auth L], CC [auth Y], IB [auth N], JA [auth B], NB [auth O], VA [auth D]TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
 Ligand Interaction
HEA (Subject of Investigation/LOI)
Query on HEA

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AA [auth A], BA [auth A], CB [auth N], DB [auth N]HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEK (Subject of Investigation/LOI)
Query on PEK

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OA [auth C], PA [auth C], RB [auth P], XB [auth T], YA [auth G], YB [auth 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 (Subject of Investigation/LOI)
Query on PSC

Download Ideal Coordinates CCD File 
KA [auth B], VB [auth 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 (Subject of Investigation/LOI)
Query on PGV

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AC [auth U], GA [auth A], HA [auth A], JB [auth N], KB [auth N], QA [auth C], RA [auth C], SB [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 (Subject of Investigation/LOI)
Query on DMU

Download Ideal Coordinates CCD File 
BB [auth M], DC [auth Z], PB [auth P], UA [auth C]DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CHD (Subject of Investigation/LOI)
Query on CHD

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BC [auth W], LA [auth B], MB [auth O], NA [auth C], QB [auth P], TA [auth C], UB [auth P], ZA [auth J]CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
 Ligand Interaction
CUA
Query on CUA

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

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

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DA [auth A], FB [auth N]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NO
Query on NO

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CA [auth A], EB [auth N]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
MG
Query on MG

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EA [auth A], GB [auth N]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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FA [auth A], HB [auth N]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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MA [auth C], OB [auth P]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, NL-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO
G, TL-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC
I, VL-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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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