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References listed in PDB file
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Key reference
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Title
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Binding of n-Carboxymethyl dipeptide inhibitors to thermolysin determined by x-Ray crystallography: a novel class of transition-State analogues for zinc peptidases.
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Authors
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A.F.Monzingo,
B.W.Matthews.
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Ref.
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Biochemistry, 1984,
23,
5724-5729.
[DOI no: ]
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PubMed id
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Abstract
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The mode of binding of the specific thermolysin inhibitor
N-(1-carboxy-3-phenylpropyl)-L-leucyl-L-tryptophan (KI approximately 5 X 10(-8)
M) [Maycock, A. L., DeSousa, D. M., Payne, L. G., ten Broeke, J., Wu, M. T.,
& Patchett, A. A. (1981) Biochem. Biophys. Res. Commun. 102, 963-969] has
been determined by X-ray crystallography and refined to an R value of 17.1% at
1.9-A resolution. The inhibitor binds to thermolysin with both oxygens of the
N-carboxymethyl group liganded to the zinc to give overall pentacoordination of
the metal. The bidentate ligation of the inhibitor differs from the monodentate
binding seen previously for carboxylate-zinc interactions in thermolysin and is
closer to the bidentate geometry observed for the binding of hydroxamates
[Holmes, M. A., & Matthews, B. W. (1981) Biochemistry 20, 6912-6920]. The
geometry of the inhibitor and its interactions with the protein have a number of
elements in common with the presumed transition state formed during peptide
hydrolysis. The observed zinc ligation supports the previous suggestion that a
pentacoordinate intermediate participates in the mechanism of catalysis.
However, the alpha-amino nitrogen of the inhibitor is close to Glu-143,
suggesting that this residue might accept a proton from an attacking water
molecule (as proposed before) and subsequently donate this proton to the leaving
nitrogen. By analogy with thermolysin, it is proposed that a related mechanism
should be considered for peptide cleavage by carboxypeptidase A.(ABSTRACT
TRUNCATED AT 250 WORDS)
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Secondary reference #1
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Title
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Structures of two thermolysin-Inhibitor complexes that differ by a single hydrogen bond.
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Authors
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D.E.Tronrud,
H.M.Holden,
B.W.Matthews.
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Ref.
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Science, 1987,
235,
571-574.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Crystallographic structural analysis of phosphoramidates as inhibitors and transition-State analogs of thermolysin.
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Authors
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D.E.Tronrud,
A.F.Monzingo,
B.W.Matthews.
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Ref.
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Eur J Biochem, 1986,
157,
261-268.
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PubMed id
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Secondary reference #3
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Title
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An interactive computer graphics study of thermolysin-Catalyzed peptide cleavage and inhibition by n-Carboxymethyl dipeptides.
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Authors
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D.G.Hangauer,
A.F.Monzingo,
B.W.Matthews.
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Ref.
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Biochemistry, 1984,
23,
5730-5741.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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Structural analysis of the inhibition of thermolysin by an active-Site-Directed irreversible inhibitor.
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Authors
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M.A.Holmes,
D.E.Tronrud,
B.W.Matthews.
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Ref.
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Biochemistry, 1983,
22,
236-240.
[DOI no: ]
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PubMed id
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Secondary reference #5
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Title
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Structure of a mercaptan-Thermolysin complex illustrates mode of inhibition of zinc proteases by substrate-Analogue mercaptans.
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Authors
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A.F.Monzingo,
B.W.Matthews.
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Ref.
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Biochemistry, 1982,
21,
3390-3394.
[DOI no: ]
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PubMed id
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Secondary reference #6
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Title
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Structure of thermolysin refined at 1.6 a resolution.
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Authors
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M.A.Holmes,
B.W.Matthews.
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Ref.
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J Mol Biol, 1982,
160,
623-639.
[DOI no: ]
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PubMed id
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Figure 3.
FIG. 3. Conformational diagram for the backbone of thermolysin. Residues that are outside the
``allowed'' regions for a hard-sphere model are numbered.
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Figure 4.
FIG. 4. Stereo diagram illustrating the apparent thermal motion of t,he thermolysin molecule. Larger
circles correspond to residues with greater apparen motion. The radius of each c~wlr l\as obtained 1)~
taking the verage R value for all atoms in that residue, subtracting a constant value of 4.0 AZ (in order
to make differences in apparent motion more obvious) and drawing the circle at t,hr SO'?; probabilit?
level (Johson, 196.5).
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #7
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Title
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Binding of hydroxamic acid inhibitors to crystalline thermolysin suggests a pentacoordinate zinc intermediate in catalysis.
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Authors
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M.A.Holmes,
B.W.Matthews.
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Ref.
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Biochemistry, 1981,
20,
6912-6920.
[DOI no: ]
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PubMed id
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Secondary reference #8
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Title
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Binding of the biproduct analog l-Benzylsuccinic acid to thermolysin determined by X-Ray crystallography.
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Authors
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M.C.Bolognesi,
B.W.Matthews.
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Ref.
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J Biol Chem, 1979,
254,
634-639.
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PubMed id
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Secondary reference #9
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Title
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Comparison of the structures of carboxypeptidase a and thermolysin.
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Authors
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W.R.Kester,
B.W.Matthews.
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Ref.
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J Biol Chem, 1977,
252,
7704-7710.
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PubMed id
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Secondary reference #10
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Title
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A crystallographic study of the complex of phosphoramidon with thermolysin. A model for the presumed catalytic transition state and for the binding of extended substances.
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Authors
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L.H.Weaver,
W.R.Kester,
B.W.Matthews.
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Ref.
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J Mol Biol, 1977,
114,
119-132.
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PubMed id
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Secondary reference #11
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Title
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Crystallographic study of the binding of dipeptide inhibitors to thermolysin: implications for the mechanism of catalysis.
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Authors
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W.R.Kester,
B.W.Matthews.
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Ref.
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Biochemistry, 1977,
16,
2506-2516.
[DOI no: ]
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PubMed id
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Secondary reference #12
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Title
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Role of calcium in the thermal stability of thermolysin.
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Authors
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F.W.Dahlquist,
J.W.Long,
W.L.Bigbee.
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Ref.
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Biochemistry, 1976,
15,
1103-1111.
[DOI no: ]
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PubMed id
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Secondary reference #13
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Title
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Evidence of homologous relationship between thermolysin and neutral protease a of bacillus subtilis.
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Authors
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P.L.Levy,
M.K.Pangburn,
Y.Burstein,
L.H.Ericsson,
H.Neurath,
K.A.Walsh.
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Ref.
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Proc Natl Acad Sci U S A, 1975,
72,
4341-4345.
[DOI no: ]
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PubMed id
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Secondary reference #14
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Title
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The structure and stability of thermolysin.
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Authors
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L.H.Weaver,
W.R.Kester,
L.F.Ten eyck,
B.W.Matthews.
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Ref.
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Experientia Suppl, 1976,
26,
31-39.
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PubMed id
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Secondary reference #15
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Title
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The conformation of thermolysin.
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Authors
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B.W.Matthews,
L.H.Weaver,
W.R.Kester.
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Ref.
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J Biol Chem, 1974,
249,
8030-8044.
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PubMed id
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Secondary reference #16
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Title
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Binding of lanthanide ions to thermolysin.
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Authors
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B.W.Matthews,
L.H.Weaver.
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Ref.
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Biochemistry, 1974,
13,
1719-1725.
[DOI no: ]
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PubMed id
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Secondary reference #17
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Title
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The structure of thermolysin: an electron density map at 2-3 a resolution.
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Authors
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P.M.Colman,
J.N.Jansonius,
B.W.Matthews.
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Ref.
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J Mol Biol, 1972,
70,
701-724.
[DOI no: ]
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PubMed id
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Figure 5.
Fra. 5. Schematic diagram, seen from above, of the optical comparator used to build to
thermolyein model after Richards, 1968).
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Figure 9.
FIG. 9. (a) Key showing tho position of the major binding sites of Llra heavy BWIUS used to
determirw thn phase trnglaa fur L~IC therrnolysin elootron density map. and for the folluwing
diEcmnoe maps. The calcum positions LIY dotcnninod from tho throo -dinmtional map BK+
indicated in this Figure by crosses. DA&IA, imnrcury acetic acd.
(b) DifYeronce electron density bdween atrontillm-thnrmolynin and native themolysin. Tho
mnoutmn of this and the following maps are 2-4 L%
(c) DifGrence electron den&y betweau barium-lborxnolyuin au3 uetivo thermolyti.
(d) Diffeence obctro density between dysprosium-thermolyain and native thomolysin.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #18
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Title
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Amino-Acid sequence of thermolysin
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Authors
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K.Titani,
M.A.Hermodson,
L.H.Ericsson,
K.A.Walsh,
H.Neurath.
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Ref.
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nature new biol, 1972,
238,
35.
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Secondary reference #19
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Title
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Three dimensional structure of thermolysin
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Authors
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B.W.Matthews,
J.N.Jansonius,
P.M.Colman,
B.P.Schoenborn,
D.Duporque.
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Ref.
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nature new biol, 1972,
238,
37.
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Secondary reference #20
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Title
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Structure of thermolysin
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Authors
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B.W.Matthews,
P.M.Colman,
J.N.Jansonius,
K.Titani,
K.A.Walsh,
H.Neurath.
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Ref.
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nature new biol, 1972,
238,
41.
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Secondary reference #21
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Title
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The gamma turn. Evidence for a new folded conformation in proteins
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Author
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B.W.Matthews.
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Ref.
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macromolecules, 1972,
5,
818.
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Secondary reference #22
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Title
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Rare earths as isomorphous calcium replacements for protein crystallography.
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Authors
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P.M.Colman,
L.H.Weaver,
B.W.Matthews.
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Ref.
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Biochem Biophys Res Commun, 1972,
46,
1999-2005.
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PubMed id
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