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PDBsum entry 3cyt
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Electron transport (heme protein)
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PDB id
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3cyt
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Redox conformation changes in refined tuna cytochrome c.
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Authors
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T.Takano,
R.E.Dickerson.
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Ref.
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Proc Natl Acad Sci U S A, 1980,
77,
6371-6375.
[DOI no: ]
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PubMed id
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Abstract
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Tuna ferrocytochrome c and ferricytochrome c have been refined independently at
high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3%
and 20.8%, respectively. Small but significant conformational differences are
seen surrounding a buried water molecule that is hydrogen bonded to Asn-52,
Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer
to the heme and the heme has moved 0.15 A out of its heme crevice; both changes
lead to a more polar microenvironment for the heme. Chemical modification
studies, patterns of evolutionary conservatism, structural differences in
bacterial cytochromes, and x-ray studies all agree that the "active
site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87
(thus containing the evolutionary conservative 72-87 loop) and has the buried
water molecule just below its surface and the opening of the heme crevice
slightly to one side.
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Secondary reference #1
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Title
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Conformation change of cytochrome c. I. Ferrocytochrome c structure refined at 1.5 a resolution.
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Authors
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T.Takano,
R.E.Dickerson.
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Ref.
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J Mol Biol, 1981,
153,
79-94.
[DOI no: ]
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PubMed id
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Figure 3.
FIG. 3. Full ide-chains on m m-carbon skeleton. (a) Front view, and (b) view from Met80 side
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Figure 6.
FIG. 6. Electron density map of the haem region viewed along the haem plane normal, with the final
atomic model superimposed. The maps consist of 7 sections of spacing 0.5 a. Cntours start from O&/A3
i increments of 1.2e/A3.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Conformation change of cytochrome c. Ii. Ferricytochrome c refinement at 1.8 a and comparison with the ferrocytochrome structure.
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Authors
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T.Takano,
R.E.Dickerson.
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Ref.
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J Mol Biol, 1981,
153,
95.
[DOI no: ]
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PubMed id
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Figure 4.
Fro. 4. ain-chain tereo diagrams showing the 12 water-molecules, W, that are common to both
ferri- and ferrocgtochrome c. Three are inside the protein molecule : the first between the 2 propionic acid
groups. the second in he 20's loop near His18 and the third just below the bured propionate.
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Figure 6.
FI. 6. Superposition of the 2 oxidized molecules: outer (olid lines) and inner molecule (open lines).
They are essentially identical except for both amin and carboxyl termini, which have large
temper&we factrs and are themselves less well defined. (a) Front \-iew : (b) side I-irw.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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Cytochrome c and the evolution of energy metabolism.
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Author
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R.E.Dickerson.
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Ref.
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Sci Am, 1980,
242,
137-153.
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PubMed id
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Secondary reference #4
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Title
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Internal mobility of ferrocytochrome c.
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Authors
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S.H.Northrup,
M.R.Pear,
J.A.Mccammon,
M.Karplus,
T.Takano.
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Ref.
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Nature, 1980,
287,
659-660.
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PubMed id
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Secondary reference #5
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Title
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Tuna cytochrome c at 2.0 a resolution. Ii. Ferrocytochrome structure analysis.
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Authors
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T.Takano,
B.L.Trus,
N.Mandel,
G.Mandel,
O.B.Kallai,
R.Swanson,
R.E.Dickerson.
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Ref.
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J Biol Chem, 1977,
252,
776-785.
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PubMed id
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Secondary reference #6
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Title
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Tuna cytochrome c at 2.0 a resolution. I. Ferricytochrome structure analysis.
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Authors
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R.Swanson,
B.L.Trus,
N.Mandel,
G.Mandel,
O.B.Kallai,
R.E.Dickerson.
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Ref.
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J Biol Chem, 1977,
252,
759-775.
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PubMed id
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Secondary reference #7
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Title
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The structure of ferrocytochrome c at 2.45 a resolution.
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Authors
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T.Takano,
O.B.Kallai,
R.Swanson,
R.E.Dickerson.
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Ref.
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J Biol Chem, 1973,
248,
5234-5255.
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PubMed id
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Secondary reference #8
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Title
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The structure and history of an ancient protein.
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Author
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R.E.Dickerson.
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Ref.
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Sci Am, 1972,
226,
58.
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PubMed id
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