› 2eim

X-ray diffraction
2.6Å resolution

Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state

Released:
DOI: 10.2210/pdb2eim/pdb
PDB 2eim coloured by chain and viewed from the front.
PDB 2eim coloured by chain and viewed from the side.
PDB 2eim coloured by chain and viewed from the top.
Source organism: Bos taurus
Primary publication:
A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase.
Muramoto K, Hirata K, Shinzawa-Itoh K, Yoko-o S, Yamashita E, Aoyama H, Tsukihara T, Yoshikawa S
Proc Natl Acad Sci U S A 104 7881-6 (2007)
PMID: 17470809

Function and Biology Details

Reaction catalysed: 
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero 26-mer (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
Cytochrome c oxidase subunit 1 Chains: A, N
Molecule details ›
Chains: A, N
Length: 514 amino acids
Theoretical weight: 57.09 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00396 (Residues: 1-514; Coverage: 100%)
Gene names: COI, COXI, MT-CO1, MTCO1
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Structure domains: Cytochrome c oxidase-like, subunit I domain
Cytochrome c oxidase subunit 2 Chains: B, O
Molecule details ›
Chains: B, O
Length: 227 amino acids
Theoretical weight: 26.07 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P68530 (Residues: 1-227; Coverage: 100%)
Gene names: COII, COX2, COXII, MT-CO2, MTCO2
Sequence domains:
Structure domains:
Cytochrome c oxidase subunit 3 Chains: C, P
Molecule details ›
Chains: C, P
Length: 261 amino acids
Theoretical weight: 29.96 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00415 (Residues: 1-261; Coverage: 100%)
Gene names: COIII, COXIII, MT-CO3, MTCO3
Sequence domains: Cytochrome c oxidase subunit III
Structure domains:
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial Chains: D, Q
Molecule details ›
Chains: D, Q
Length: 147 amino acids
Theoretical weight: 17.18 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00423 (Residues: 23-169; Coverage: 87%)
Gene names: COX4, COX4I1
Sequence domains: Cytochrome c oxidase subunit IV
Structure domains: Cytochrome c oxidase subunit IV
Cytochrome c oxidase subunit 5A, mitochondrial Chains: E, R
Molecule details ›
Chains: E, R
Length: 109 amino acids
Theoretical weight: 12.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00426 (Residues: 44-152; Coverage: 72%)
Gene name: COX5A
Sequence domains: Cytochrome c oxidase subunit Va
Structure domains: Cytochrome c oxidase, subunit Va/VI
Cytochrome c oxidase subunit 5B, mitochondrial Chains: F, S
Molecule details ›
Chains: F, S
Length: 98 amino acids
Theoretical weight: 10.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00428 (Residues: 32-129; Coverage: 76%)
Gene name: COX5B
Structure domains: Cytochrome c oxidase, subunit Vb
Cytochrome c oxidase subunit 6A2, mitochondrial Chains: G, T
Molecule details ›
Chains: G, T
Length: 85 amino acids
Theoretical weight: 9.63 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07471 (Residues: 13-97; Coverage: 88%)
Gene names: COX6A, COX6A2
Structure domains: Cytochrome c oxidase, subunit VIa
Cytochrome c oxidase subunit 6B1 Chains: H, U
Molecule details ›
Chains: H, U
Length: 85 amino acids
Theoretical weight: 10.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00429 (Residues: 2-86; Coverage: 99%)
Gene names: COX6B, COX6B1
Sequence domains: Cytochrome oxidase c subunit VIb
Structure domains: Cytochrome c oxidase, subunit VIb
Cytochrome c oxidase subunit 6C Chains: I, V
Molecule details ›
Chains: I, V
Length: 73 amino acids
Theoretical weight: 8.54 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P04038 (Residues: 2-74; Coverage: 99%)
Gene name: COX6C
Sequence domains: Cytochrome c oxidase subunit VIc
Structure domains: Mitochondrial cytochrome c oxidase subunit VIc/VIIs
Cytochrome c oxidase subunit 7A1, mitochondrial Chains: J, W
Molecule details ›
Chains: J, W
Length: 59 amino acids
Theoretical weight: 6.68 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P07470 (Residues: 22-80; Coverage: 74%)
Gene names: COX7A, COX7A1, COX7AH
Sequence domains: Cytochrome c oxidase subunit VII
Structure domains: Cytochrome c oxidase, subunit VIIa
Cytochrome c oxidase subunit 7B, mitochondrial Chains: K, X
Molecule details ›
Chains: K, X
Length: 56 amino acids
Theoretical weight: 6.37 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P13183 (Residues: 25-80; Coverage: 70%)
Gene name: COX7B
Structure domains: Cytochrome C Oxidase, chain K
Cytochrome c oxidase subunit 7C, mitochondrial Chains: L, Y
Molecule details ›
Chains: L, Y
Length: 47 amino acids
Theoretical weight: 5.45 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00430 (Residues: 17-63; Coverage: 75%)
Gene names: COX7C, COX7CP1
Structure domains: Cytochrome c oxidase subunit VIIc
Cytochrome c oxidase subunit 8B, mitochondrial Chains: M, Z
Molecule details ›
Chains: M, Z
Length: 46 amino acids
Theoretical weight: 4.97 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P10175 (Residues: 25-70; Coverage: 66%)
Gene names: COX8B, COX8H
Sequence domains: Cytochrome oxidase c subunit VIII
Structure domains: Cytochrome c oxidase, subunit 8

Ligands and Environments

13 bound ligands:
Ligand CU 2 x CU
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand ZN 6 x ZN
Ligand HEA 4 x HEA
Ligand PGV 8 x PGV
Ligand CHD 8 x CHD
Ligand CUA 2 x CUA
Ligand TGL 6 x TGL
Ligand PSC 2 x PSC
Ligand DMU 4 x DMU
Ligand PEK 6 x PEK
Ligand CDL 4 x CDL
3 modified residues:
Ligand FME 4 x FME
Ligand TPO 2 x TPO
Ligand SAC 2 x SAC

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 183.909Å b: 206.721Å c: 178.337Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.256

Quick links

Citations

14 review citations

Non-redox cycling mechanisms of oxidative stress induced by PM metals.
Samet et al. (2020)
13 more

1 mention without citation

A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase.
Muramoto et al. (2007)