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References listed in PDB file
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Key reference
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Title
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Restrained least squares refinement of native (calcium) and cadmium-Substituted carp parvalbumin using X-Ray crystallographic data at 1.6-A resolution.
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Authors
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A.L.Swain,
R.H.Kretsinger,
E.L.Amma.
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Ref.
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J Biol Chem, 1989,
264,
16620-16628.
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PubMed id
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Abstract
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Carp parvalbumin coordinates calcium through one carbonyl oxygen atom and the
oxygen-containing side chains of 5 amino acid residues, or 4 residues and a
water molecule, in a helix-loop-helix structural motif. Other calcium-binding
proteins, including calmodulin and troponin C, also possess this unique
calcium-binding design, which is designated EF-hand or calmodulin fold.
Parvalbumin has two such sites, labeled CD and EF. Each of the calcium-binding
sites of refined structures of proteins belonging to this group has a 7-oxygen
coordination sphere except those of the structure of parvalbumin as it was
reported in 1975. This structure had been refined at 1.9 A using difference
Fourier techniques on film data. The CD site appeared to be 6-coordinate and the
EF site 8-coordinate. Results of NMR experiments using 113Cd-substituted
parvalbumin, however, indicate that the sites are similar to one another with
coordination number greater than 6. To resolve the inconsistency between
crystallographic and NMR results, 1.6 A area detector data was collected for
native and cadmium-substituted parvalbumin; the structures have been refined to
R factors of 18.7% and 16.4%, respectively, with acceptable geometry and low
errors in atomic coordinates. Differences between the parvalbumin structure
described in 1975 and the present structure are addressed, including the
discovery of 7-coordination for both the CD and EF sites.
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Secondary reference #1
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Title
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The coordination polyhedron of ca==2+==,Cd==2+== in parvalbumin
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Authors
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A.L.Swain,
E.L.Amma.
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Ref.
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inorg chim acta, 1989,
163,
5.
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Secondary reference #2
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Title
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Refinement of the structure of carp muscle calcium-Binding parvalbumin by model building and difference fourier analysis.
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Authors
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P.C.Moews,
R.H.Kretsinger.
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Ref.
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J Mol Biol, 1975,
91,
201-225.
[DOI no: ]
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PubMed id
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Figure 1.
FIQ. 1. In the F-6i difference Fourier map positive regions are indicated by stippling and negative
regions by horizontal hatching. The conour level is O-2 electron/A3. We observed that a methyl
group or xygen atom omitted in the structure factor calculstion will appear in the dp map four
contour levels high. Neighboring molecules (2, 8, 6, 4, 5 and 7) are indicated by large numerals;
refer to the packing diagram, Fig. 2. Van der W&s' areas are drawn about each atom at a radius
appropriate to level s = 26/80. This section passes near the EF calcium in at z = 23*7/40
y = l&8/80, I = 26-l/80. The diagonally hatched areas represent regions of the solvent accessible
to solvent molecues considered to be spheres of 1.5 A van der W&s radius. The numbered
circles refer o the solvent molecules included in the structure factor calculation (Table 7).
Since we frequently labeled the atomic sites on our Fourier maps as well as generating many
lists of co-ordinates, etc., we adopted the one letter code for amino acids and used the following
code for labeling atoms :
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Figure 2.
Fro. 2. The 8 neighboring moleaules whose contacts are listed in Table 7 are shown. Portiom
of moleoules 2, 8, 6, 4, 6 and 7 me shown in Fig. 1. The CD and EF calcium biing loops as well
as N and C-termial and a-carbon 81 me indicated in the central molecule.
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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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Terbium replacement of calcium in carp muscle calcium-Binding parvalbumin: an X-Ray crystallographic study.
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Authors
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P.C.Moews,
R.H.Kretsinger.
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Ref.
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J Mol Biol, 1975,
91,
229-232.
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PubMed id
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Secondary reference #4
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Title
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Troponin and parvalbumin calcium binding regions predicted in myosin light chain and t4 lysozyme.
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Authors
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R.M.Tufty,
R.H.Kretsinger.
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Ref.
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Science, 1975,
187,
167-169.
[DOI no: ]
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PubMed id
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Secondary reference #5
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Title
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Calcium binding proteins and natural membranes
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Author
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R.H.Kretsinger.
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Ref.
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perspectives in membrane ...
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Secondary reference #6
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Title
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The coordination of calcium ions by carp muscle calcium binding proteins a, B and c.
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Authors
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C.J.Coffee,
R.A.Bradshaw,
R.H.Kretsinger.
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Ref.
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Adv Exp Med Biol, 1974,
48,
211-233.
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PubMed id
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Secondary reference #7
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Title
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Carp muscle calcium-Binding protein. I. Characterization of the tryptic peptides and the complete amino acid sequence of component b.
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Authors
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C.J.Coffee,
R.A.Bradshaw.
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Ref.
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J Biol Chem, 1973,
248,
3305-3312.
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PubMed id
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Secondary reference #8
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Title
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Carp muscle calcium-Binding protein. Ii. Structure determination and general description.
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Authors
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R.H.Kretsinger,
C.E.Nockolds.
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Ref.
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J Biol Chem, 1973,
248,
3313-3326.
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PubMed id
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Secondary reference #9
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Title
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Carp muscle calcium-Binding protein. 3. Phase refinement using the tangent formula.
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Authors
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W.A.Hendrickson,
J.Karle.
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Ref.
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J Biol Chem, 1973,
248,
3327-3334.
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PubMed id
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Secondary reference #10
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Title
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Gene duplication in carp muscle calcium binding protein.
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Author
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A.D.Mclachlan.
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Ref.
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Nat New Biol, 1972,
240,
83-85.
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PubMed id
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Secondary reference #11
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Title
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Gene triplication deduced from the tertiary structure of a muscle calcium binding protein.
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Author
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R.H.Kretsinger.
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Ref.
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Nat New Biol, 1972,
240,
85-88.
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PubMed id
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Secondary reference #12
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Title
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Structure of a calcium-Binding carp myogen.
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Authors
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C.E.Nockolds,
R.H.Kretsinger,
C.J.Coffee,
R.A.Bradshaw.
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Ref.
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Proc Natl Acad Sci U S A, 1972,
69,
581-584.
[DOI no: ]
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PubMed id
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Secondary reference #13
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Title
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The structure of a calcium-Binding protein from carp muscle.
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Authors
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R.H.Kretsinger,
C.E.Nockolds,
C.J.Coffee,
R.A.Bradshaw.
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Ref.
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Cold Spring Harb Symp Quant Biol, 1972,
36,
217-220.
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PubMed id
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