PMID- 32525689
OWN - NLM
STAT- MEDLINE
DCOM- 20201204
LR  - 20240402
IS  - 1520-510X (Electronic)
IS  - 0020-1669 (Print)
IS  - 0020-1669 (Linking)
VI  - 59
IP  - 13
DP  - 2020 Jul 6
TI  - A Water Molecule Residing in the Fe(a3)(3+)...Cu(B)(2+) Dinuclear Center of the 
      Resting Oxidized as-Isolated Cytochrome c Oxidase: A Density Functional Study.
PG  - 8906-8915
LID - 10.1021/acs.inorgchem.0c00724 [doi]
AB  - Although the dinuclear center (DNC) of the resting oxidized "as-isolated" 
      cytochrome c oxidase (CcO) is not a catalytically active state, its detailed 
      structure, especially the nature of the bridging species between the Fe(a3)(3+) 
      and Cu(B)(2+) metal sites, is still both relevant and unsolved. Recent 
      crystallographic work has shown an extended electron density for a peroxide type 
      dioxygen species (O1-O2) bridging the Fe(a3) and Cu(B) centers. In this paper, 
      our density functional theory (DFT) calculations show that the observed peroxide 
      type electron density between the two metal centers is most likely a mistaken 
      analysis due to overlap of the electron density of a water molecule located at 
      different positions between apparent O1 and O2 sites in DNCs of different CcO 
      molecules with almost the same energy. Because the diffraction pattern and the 
      resulting electron density map represent the effective long-range order averaged 
      over many molecules and unit cells in the X-ray structure, this averaging can 
      lead to an apparent observed superposition of different water positions between 
      the Fe(a3)(3+) and Cu(B)(2+) metal sites.
FAU - Han Du, Wen-Ge
AU  - Han Du WG
AUID- ORCID: 0000-0001-5876-1943
AD  - Department of Integrative Structural and Computational Biology, The Scripps 
      Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, 
      United States.
FAU - McRee, Duncan
AU  - McRee D
AD  - Department of Integrative Structural and Computational Biology, The Scripps 
      Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, 
      United States.
FAU - Gotz, Andreas W
AU  - Gotz AW
AUID- ORCID: 0000-0002-8048-6906
AD  - San Diego Supercomputer Center, University of California San Diego, 9500 Gilman 
      Drive MC0505, La Jolla, California 92093, United States.
FAU - Noodleman, Louis
AU  - Noodleman L
AUID- ORCID: 0000-0001-8176-4448
AD  - Department of Integrative Structural and Computational Biology, The Scripps 
      Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, 
      United States.
LA  - eng
GR  - R01 GM100934/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20200611
PL  - United States
TA  - Inorg Chem
JT  - Inorganic chemistry
JID - 0366543
RN  - 059QF0KO0R (Water)
RN  - 789U1901C5 (Copper)
RN  - E1UOL152H7 (Iron)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
SB  - IM
MH  - Copper/*chemistry
MH  - Density Functional Theory
MH  - Electron Transport Complex IV/*chemistry
MH  - Iron/*chemistry
MH  - Models, Chemical
MH  - Water/*chemistry
PMC - PMC8114904
COIS- The authors declare no competing financial interest.
EDAT- 2020/06/12 06:00
MHDA- 2020/12/15 06:00
PMCR- 2021/05/12
CRDT- 2020/06/12 06:00
PHST- 2020/06/12 06:00 [pubmed]
PHST- 2020/12/15 06:00 [medline]
PHST- 2020/06/12 06:00 [entrez]
PHST- 2021/05/12 00:00 [pmc-release]
AID - 10.1021/acs.inorgchem.0c00724 [doi]
PST - ppublish
SO  - Inorg Chem. 2020 Jul 6;59(13):8906-8915. doi: 10.1021/acs.inorgchem.0c00724. Epub 
      2020 Jun 11.