-
1
-
-
0036940303
-
Metal ions in the structure and function of RNA
-
Pyle A.M. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7 (2002) 679-690
-
(2002)
J. Biol. Inorg. Chem.
, vol.7
, pp. 679-690
-
-
Pyle, A.M.1
-
2
-
-
16244363320
-
Metal ions and RNA folding: a highly charged topic with a dynamic future
-
Woodson S.A. Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr. Opin. Chem. Biol. 9 (2005) 104-109
-
(2005)
Curr. Opin. Chem. Biol.
, vol.9
, pp. 104-109
-
-
Woodson, S.A.1
-
4
-
-
0027247579
-
Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena
-
Christian E.L., and Yarus M. Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena. Biochemistry 32 (1993) 4475-4480
-
(1993)
Biochemistry
, vol.32
, pp. 4475-4480
-
-
Christian, E.L.1
Yarus, M.2
-
5
-
-
0031790171
-
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor
-
Basu S., Rambo R.P., Strauss-Soukup J., Cate J.H., Ferre-D'Amare A.R., Strobel S.A., and Doudna J.A. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nature Struct. Biol. 5 (1998) 986-992
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 986-992
-
-
Basu, S.1
Rambo, R.P.2
Strauss-Soukup, J.3
Cate, J.H.4
Ferre-D'Amare, A.R.5
Strobel, S.A.6
Doudna, J.A.7
-
6
-
-
0017361887
-
A crystallographic study of metal-binding to yeast phenylalanine transfer RNA
-
Jack A., Ladner J.E., Rhodes D., Brown R.S., and Klug A. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J. Mol. Biol. 111 (1977) 315-328
-
(1977)
J. Mol. Biol.
, vol.111
, pp. 315-328
-
-
Jack, A.1
Ladner, J.E.2
Rhodes, D.3
Brown, R.S.4
Klug, A.5
-
7
-
-
0033862354
-
The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited
-
Shi H., and Moore P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited. Rna 6 (2000) 1091-1105
-
(2000)
Rna
, vol.6
, pp. 1091-1105
-
-
Shi, H.1
Moore, P.B.2
-
8
-
-
0029820625
-
Crystal structure of a group I ribozyme domain: principles of RNA packing
-
Cate J.H., Gooding A.R., Podell E., Zhou K., Golden B.L., Kundrot C.E., et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273 (1996) 1678-1685
-
(1996)
Science
, vol.273
, pp. 1678-1685
-
-
Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Zhou, K.4
Golden, B.L.5
Kundrot, C.E.6
-
9
-
-
0030929889
-
A magnesium ion core at the heart of a ribozyme domain
-
Cate J.H., Hanna R.L., and Doudna J.A. A magnesium ion core at the heart of a ribozyme domain. Nature Struct. Biol. 4 (1997) 553-558
-
(1997)
Nature Struct. Biol.
, vol.4
, pp. 553-558
-
-
Cate, J.H.1
Hanna, R.L.2
Doudna, J.A.3
-
10
-
-
0035085466
-
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions
-
Juneau K., Podell E., Harrington D.J., and Cech T.R. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure (Camb.) 9 (2001) 221-231
-
(2001)
Structure (Camb.)
, vol.9
, pp. 221-231
-
-
Juneau, K.1
Podell, E.2
Harrington, D.J.3
Cech, T.R.4
-
11
-
-
0036786231
-
Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly
-
Batey R.T., and Doudna J.A. Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly. Biochemistry 41 (2002) 11703-11710
-
(2002)
Biochemistry
, vol.41
, pp. 11703-11710
-
-
Batey, R.T.1
Doudna, J.A.2
-
12
-
-
0030856333
-
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
-
Correll C.C., Freeborn B., Moore P.B., and Steitz T.A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91 (1997) 705-712
-
(1997)
Cell
, vol.91
, pp. 705-712
-
-
Correll, C.C.1
Freeborn, B.2
Moore, P.B.3
Steitz, T.A.4
-
13
-
-
4344569647
-
The contribution of metal ions to the structural stability of the large ribosomal subunit
-
Klein D.J., Moore P.B., and Steitz T.A. The contribution of metal ions to the structural stability of the large ribosomal subunit. Rna 10 (2004) 1366-1379
-
(2004)
Rna
, vol.10
, pp. 1366-1379
-
-
Klein, D.J.1
Moore, P.B.2
Steitz, T.A.3
-
14
-
-
0038737980
-
2+ binding in the group I intron core
-
2+ binding in the group I intron core. J. Mol. Biol. 329 (2003) 229-238
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 229-238
-
-
Rangan, P.1
Woodson, S.A.2
-
15
-
-
0034625314
-
2+ binding to tRNA revisited: the non-linear Poisson-Boltzmann model
-
2+ binding to tRNA revisited: the non-linear Poisson-Boltzmann model. J. Mol. Biol. 299 (2000) 813-825
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 813-825
-
-
Misra, V.K.1
Draper, D.E.2
-
17
-
-
0032707136
-
Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain
-
Basu S., and Strobel S.A. Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain. Rna 5 (1999) 1399-1407
-
(1999)
Rna
, vol.5
, pp. 1399-1407
-
-
Basu, S.1
Strobel, S.A.2
-
18
-
-
0020417286
-
Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena
-
Kruger K., Grabowski P.J., Zaug A.J., Sands J., Gottschling D.E., and Cech T.R. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31 (1982) 147-157
-
(1982)
Cell
, vol.31
, pp. 147-157
-
-
Kruger, K.1
Grabowski, P.J.2
Zaug, A.J.3
Sands, J.4
Gottschling, D.E.5
Cech, T.R.6
-
22
-
-
0032893740
-
A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution
-
Yoshida A., Sun S., and Piccirilli J.A. A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution. Nature Struct. Biol. 6 (1999) 318-321
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 318-321
-
-
Yoshida, A.1
Sun, S.2
Piccirilli, J.A.3
-
23
-
-
0033600571
-
Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme
-
Shan S.O., and Herschlag D. Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme. Biochemistry 38 (1999) 10958-10975
-
(1999)
Biochemistry
, vol.38
, pp. 10958-10975
-
-
Shan, S.O.1
Herschlag, D.2
-
24
-
-
0037176844
-
Identification of an active site ligand for a group I ribozyme catalytic metal ion
-
Szewczak A.A., Kosek A.B., Piccirilli J.A., and Strobel S.A. Identification of an active site ligand for a group I ribozyme catalytic metal ion. Biochemistry 41 (2002) 2516-2525
-
(2002)
Biochemistry
, vol.41
, pp. 2516-2525
-
-
Szewczak, A.A.1
Kosek, A.B.2
Piccirilli, J.A.3
Strobel, S.A.4
-
26
-
-
0031967099
-
The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme
-
Ortoleva-Donnelly L., Szewczak A.A., Gutell R.R., and Strobel S.A. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. Rna 4 (1998) 498-519
-
(1998)
Rna
, vol.4
, pp. 498-519
-
-
Ortoleva-Donnelly, L.1
Szewczak, A.A.2
Gutell, R.R.3
Strobel, S.A.4
-
27
-
-
0034665747
-
A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme
-
Strauss-Soukup J.K., and Strobel S.A. A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme. J. Mol. Biol. 302 (2000) 339-358
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 339-358
-
-
Strauss-Soukup, J.K.1
Strobel, S.A.2
-
28
-
-
30944458838
-
Atomic level architecture of group I introns revealed
-
Vicens Q., and Cech T.R. Atomic level architecture of group I introns revealed. Trends Biochem. Sci. 31 (2006) 41-51
-
(2006)
Trends Biochem. Sci.
, vol.31
, pp. 41-51
-
-
Vicens, Q.1
Cech, T.R.2
-
29
-
-
2342522611
-
Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron
-
Luptak A., and Doudna J.A. Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron. Nucl. Acids Res. 32 (2004) 2272-2280
-
(2004)
Nucl. Acids Res.
, vol.32
, pp. 2272-2280
-
-
Luptak, A.1
Doudna, J.A.2
-
30
-
-
3042848954
-
Crystal structure of a self-splicing group I intron with both exons
-
Adams P.L., Stahley M.R., Kosek A.B., Wang J., and Strobel S.A. Crystal structure of a self-splicing group I intron with both exons. Nature 430 (2004) 45-50
-
(2004)
Nature
, vol.430
, pp. 45-50
-
-
Adams, P.L.1
Stahley, M.R.2
Kosek, A.B.3
Wang, J.4
Strobel, S.A.5
-
31
-
-
8644229237
-
Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site
-
Guo F., Gooding A.R., and Cech T.R. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol. Cell 16 (2004) 351-362
-
(2004)
Mol. Cell
, vol.16
, pp. 351-362
-
-
Guo, F.1
Gooding, A.R.2
Cech, T.R.3
-
32
-
-
11444263264
-
Crystal structure of a phage Twort group I ribozyme-product complex
-
Golden B.L., Kim H., and Chase E. Crystal structure of a phage Twort group I ribozyme-product complex. Nature Struct. Mol. Biol. 12 (2005) 82-89
-
(2005)
Nature Struct. Mol. Biol.
, vol.12
, pp. 82-89
-
-
Golden, B.L.1
Kim, H.2
Chase, E.3
-
33
-
-
24644492337
-
Structural evidence for a two-metal-ion mechanism of group I intron splicing
-
Stahley M.R., and Strobel S.A. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 309 (2005) 1587-1590
-
(2005)
Science
, vol.309
, pp. 1587-1590
-
-
Stahley, M.R.1
Strobel, S.A.2
-
34
-
-
0023047647
-
Ribozyme inhibitors: deoxyguanosine and dideoxyguanosine are competitive inhibitors of self-splicing of the Tetrahymena ribosomal ribonucleic acid precursor
-
Bass B.L., and Cech T.R. Ribozyme inhibitors: deoxyguanosine and dideoxyguanosine are competitive inhibitors of self-splicing of the Tetrahymena ribosomal ribonucleic acid precursor. Biochemistry 25 (1986) 4473-4477
-
(1986)
Biochemistry
, vol.25
, pp. 4473-4477
-
-
Bass, B.L.1
Cech, T.R.2
-
35
-
-
9344232753
-
Crystal structure of a group I intron splicing intermediate
-
Adams P.L., Stahley M.R., Gill M.L., Kosek A.B., Wang J., and Strobel S.A. Crystal structure of a group I intron splicing intermediate. Rna 10 (2004) 1867-1887
-
(2004)
Rna
, vol.10
, pp. 1867-1887
-
-
Adams, P.L.1
Stahley, M.R.2
Gill, M.L.3
Kosek, A.B.4
Wang, J.5
Strobel, S.A.6
-
36
-
-
9344236009
-
RNA kink turns to the left and to the right
-
Strobel S.A., Adams P.L., Stahley M.R., and Wang J. RNA kink turns to the left and to the right. Rna 10 (2004) 1852-1854
-
(2004)
Rna
, vol.10
, pp. 1852-1854
-
-
Strobel, S.A.1
Adams, P.L.2
Stahley, M.R.3
Wang, J.4
-
37
-
-
0035094475
-
Geometry of metal-ligand interactions in proteins
-
Harding M.M. Geometry of metal-ligand interactions in proteins. Acta Crystallog. sect. D 57 (2001) 401-411
-
(2001)
Acta Crystallog. sect. D
, vol.57
, pp. 401-411
-
-
Harding, M.M.1
-
38
-
-
0036014793
-
Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium
-
Harding M.M. Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallog. sect. D 58 (2002) 872-874
-
(2002)
Acta Crystallog. sect. D
, vol.58
, pp. 872-874
-
-
Harding, M.M.1
-
39
-
-
33744797086
-
RNA splicing: group I intron crystal structures reveal the basis of splice site selection and metal ion catalysis
-
Stahley M.R., and Strobel S.A. RNA splicing: group I intron crystal structures reveal the basis of splice site selection and metal ion catalysis. Curr. Opin. Struct. Biol. 16 (2006) 319-326
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 319-326
-
-
Stahley, M.R.1
Strobel, S.A.2
-
40
-
-
0035340961
-
Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction
-
Shan S., Kravchuk A.V., Piccirilli J.A., and Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry 40 (2001) 5161-5171
-
(2001)
Biochemistry
, vol.40
, pp. 5161-5171
-
-
Shan, S.1
Kravchuk, A.V.2
Piccirilli, J.A.3
Herschlag, D.4
-
41
-
-
0024427177
-
The guanosine binding site of the Tetrahymena ribozyme
-
Michel F., Hanna M., Green R., Bartel D.P., and Szostak J.W. The guanosine binding site of the Tetrahymena ribozyme. Nature 342 (1989) 391-395
-
(1989)
Nature
, vol.342
, pp. 391-395
-
-
Michel, F.1
Hanna, M.2
Green, R.3
Bartel, D.P.4
Szostak, J.W.5
-
42
-
-
0031984645
-
Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site
-
Strobel S.A., Ortoleva-Donnelly L., Ryder S.P., Cate J.H., and Moncoeur E. Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nature Struct. Biol. 5 (1998) 60-66
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 60-66
-
-
Strobel, S.A.1
Ortoleva-Donnelly, L.2
Ryder, S.P.3
Cate, J.H.4
Moncoeur, E.5
-
43
-
-
0028951325
-
Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns
-
Allain F.H., and Varani G. Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns. Nucl. Acids Res. 23 (1995) 341-350
-
(1995)
Nucl. Acids Res.
, vol.23
, pp. 341-350
-
-
Allain, F.H.1
Varani, G.2
-
44
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
45
-
-
3543012707
-
Crystallography and NMR system: a new software suite for macromolecular structure determination
-
Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
-
(1998)
Acta Crystallog. sect. D
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
-
46
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
-
(1997)
Acta Crystallog. sect. D
, vol.53
, pp. 240-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
49
-
-
0035964342
-
Electrostatics of nanosystems: application to microtubules and the ribosome
-
Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98 (2001) 10037-10041
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
50
-
-
3242886771
-
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky T.J., Nielsen J.E., McCammon J.A., and Baker N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucl. Acids Res. 32 (2004) W665-W667
-
(2004)
Nucl. Acids Res.
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
|