-
2
-
-
0025303335
-
Zinc coordination, function, and structure of zinc enzymes and other proteins
-
Vallee BL, Auld DS. Zinc coordination, function, and structure of zinc enzymes and other proteins. Biochemistry 1990;29:5647-5659.
-
(1990)
Biochemistry
, vol.29
, pp. 5647-5659
-
-
Vallee, B.L.1
Auld, D.S.2
-
3
-
-
7744244599
-
Recent advances in zinc enzymology
-
Lipscomb WN, Strater N. Recent advances in zinc enzymology. Chem Rev 1996;96:2375-2434.
-
(1996)
Chem Rev
, vol.96
, pp. 2375-2434
-
-
Lipscomb, W.N.1
Strater, N.2
-
6
-
-
2542428546
-
Structure and mechanism of the RNA polymerase II transcription machinery
-
Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol 2004;11:394-403.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 394-403
-
-
Hahn, S.1
-
7
-
-
1142274214
-
Structural basis of transcription: An RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms
-
Bushneil DA, Westover KD, Davis R, Kornberg RD. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science 2004;303:983-988.
-
(2004)
Science
, vol.303
, pp. 983-988
-
-
Bushneil, D.A.1
Westover, K.D.2
Davis, R.3
Kornberg, R.D.4
-
8
-
-
0034607658
-
Zinc Stoichiometry of yeast RNA polymerase II and characterization of mutations in the zinc-binding domain of the largest subunit
-
Donaldson IM, Friesen JD. Zinc Stoichiometry of yeast RNA polymerase II and characterization of mutations in the zinc-binding domain of the largest subunit. J Biol Chem 2000;275:13780-13788.
-
(2000)
J Biol Chem
, vol.275
, pp. 13780-13788
-
-
Donaldson, I.M.1
Friesen, J.D.2
-
9
-
-
0035827332
-
Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 A resolution
-
Gnatt AL, Fu J, Bushneil DA, Kornberg RD. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 2001;292:1876-1882.
-
(2001)
Science
, vol.292
, pp. 1876-1882
-
-
Gnatt, A.L.1
Fu, J.2
Bushneil, D.A.3
Kornberg, R.D.4
-
10
-
-
0035827346
-
Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution
-
Cramer P, Bushneil DA, Kornberg RD, Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution. Science 2001; 292:1863-1876.
-
(2001)
Science
, vol.292
, pp. 1863-1876
-
-
Cramer, P.1
Bushneil, D.A.2
Kornberg, R.D.3
-
11
-
-
0036516460
-
Matrix metalloproteinases: A tail of a frog that became a prince
-
Brinckerhoff CE, Matrisian LM. Matrix metalloproteinases: a tail of a frog that became a prince. Nat Rev Mol Cell Biol 2002;3:207-214.
-
(2002)
Nat Rev Mol Cell Biol
, vol.3
, pp. 207-214
-
-
Brinckerhoff, C.E.1
Matrisian, L.M.2
-
12
-
-
0036512208
-
New functions for the matrix metalloproteinases in cancer progression
-
Egeblad M, Werb Z. New functions for the matrix metalloproteinases in cancer progression. Nat Rev Cancer 2002;2:161-174.
-
(2002)
Nat Rev Cancer
, vol.2
, pp. 161-174
-
-
Egeblad, M.1
Werb, Z.2
-
13
-
-
0037192458
-
Matrix metalloproteinase inhibitors and cancer: Trials and tribulations
-
Coussens LM, Fingleton B, Matrisian LM. Matrix metalloproteinase inhibitors and cancer: trials and tribulations. Science 2002;295: 2387-2392.
-
(2002)
Science
, vol.295
, pp. 2387-2392
-
-
Coussens, L.M.1
Fingleton, B.2
Matrisian, L.M.3
-
14
-
-
0037057707
-
Reaction path of protein farnesyltransferase at atomic resolution
-
Long SB, Casey PJ, Beese LS. Reaction path of protein farnesyltransferase at atomic resolution. Nature 2002;419:645-650.
-
(2002)
Nature
, vol.419
, pp. 645-650
-
-
Long, S.B.1
Casey, P.J.2
Beese, L.S.3
-
15
-
-
0030909826
-
Crystal structure of protein farnesyltransferase at 2.25 Angstrom resolution
-
Park HW, Boduluri SR, Moomaw JF, Casey PJ, Beese LS. Crystal structure of protein farnesyltransferase at 2.25 Angstrom resolution. Science 1997;275:1800-1804.
-
(1997)
Science
, vol.275
, pp. 1800-1804
-
-
Park, H.W.1
Boduluri, S.R.2
Moomaw, J.F.3
Casey, P.J.4
Beese, L.S.5
-
16
-
-
24344434552
-
Farnesyltransferase: Theoretical studies on peptide substrate entrance - thiol or thiolate coordination?
-
Sousa SF, Fernandes PA, Ramos MJ. Farnesyltransferase: theoretical studies on peptide substrate entrance - thiol or thiolate coordination? J Mol Struct (THEOCHEM) 2005;729:125-129.
-
(2005)
J Mol Struct (THEOCHEM)
, vol.729
, pp. 125-129
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
18
-
-
11244321501
-
Farnesyltransferase - new insights into the zinc-coordination sphere paradigm: Evidence for a carboxylate-shift mechanism
-
Sousa SF, Fernandes PA, Ramos MJ. Farnesyltransferase - new insights into the zinc-coordination sphere paradigm: evidence for a carboxylate-shift mechanism. Biophys J 2005;88:483-494.
-
(2005)
Biophys J
, vol.88
, pp. 483-494
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
19
-
-
0043022293
-
Structural characterization of the zinc site in protein farnesyltransferase
-
Tobin DA, Pickett JS, Hartman HL, Fierke CA, Penner-Hahn JE. Structural characterization of the zinc site in protein farnesyltransferase. J Am Chem Soc 2003;125:9962-9969.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 9962-9969
-
-
Tobin, D.A.1
Pickett, J.S.2
Hartman, H.L.3
Fierke, C.A.4
Penner-Hahn, J.E.5
-
20
-
-
0032726199
-
Class B β-lactamases: The importance of being metallic
-
Cricco JA, Vila AJ. Class B β-lactamases: the importance of being metallic. Curr Pharm Des 1999;5:915-927.
-
(1999)
Curr Pharm Des
, vol.5
, pp. 915-927
-
-
Cricco, J.A.1
Vila, A.J.2
-
21
-
-
11244317355
-
Metallo-β-lactamases: Two binding sites for one catalytic metal ion?
-
Heinz U, Adolph HW. Metallo-β-lactamases: two binding sites for one catalytic metal ion? Cell Mol Life Sci 2004;61:2827-2839.
-
(2004)
Cell Mol Life Sci
, vol.61
, pp. 2827-2839
-
-
Heinz, U.1
Adolph, H.W.2
-
22
-
-
0034055985
-
Function and mechanism of zinc metalloenzymes
-
McCall KA, Huang CC, Fierke CA. Function and mechanism of zinc metalloenzymes. J Nutr 2000;130:1437-1446.
-
(2000)
J Nutr
, vol.130
, pp. 1437-1446
-
-
McCall, K.A.1
Huang, C.C.2
Fierke, C.A.3
-
23
-
-
0032464349
-
Analysis of zinc binding sites in protein crystal structures
-
Alberts IL, Nadassy K, Wodak SJ. Analysis of zinc binding sites in protein crystal structures. Protein Sci 1998;7:1700-1716.
-
(1998)
Protein Sci
, vol.7
, pp. 1700-1716
-
-
Alberts, I.L.1
Nadassy, K.2
Wodak, S.J.3
-
24
-
-
0017411710
-
Protein data bank - computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. Protein data bank - computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
25
-
-
33846840870
-
The carboxylate-shift in zinc enzymes: A computational study
-
Sousa SF, Fernandes PA, Ramos MJ. The carboxylate-shift in zinc enzymes: a computational study. J Am Chem Soc 2007;129:1378-1385.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 1378-1385
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
26
-
-
0033532088
-
The crystal structure of the monomeric human SOD mutant F50E/G51E/E133Q at atomic resolution. The enzyme mechanism revisited
-
Ferraroni M, Rypniewski W, Wilson KS, Viezzoli MS, Banci L, Bertini I, Mangani S. The crystal structure of the monomeric human SOD mutant F50E/G51E/E133Q at atomic resolution. The enzyme mechanism revisited. J Mol Biol 1999;288:413-426.
-
(1999)
J Mol Biol
, vol.288
, pp. 413-426
-
-
Ferraroni, M.1
Rypniewski, W.2
Wilson, K.S.3
Viezzoli, M.S.4
Banci, L.5
Bertini, I.6
Mangani, S.7
-
27
-
-
2342475729
-
Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans
-
Zhou Z, Song X, Li Y, Gong W. Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans. J Mol Biol 2004;339:207-215.
-
(2004)
J Mol Biol
, vol.339
, pp. 207-215
-
-
Zhou, Z.1
Song, X.2
Li, Y.3
Gong, W.4
-
28
-
-
0034050126
-
X-ray structure of β-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration
-
Mitsuhashi S, Mizushima T, Yamashita E, Yamamoto M, Kumasaka T, Moriyama H, Ueki T, Miyachi S, Tsukihara T. X-ray structure of β-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration. J Biol Chem 2000;275:5521-5526.
-
(2000)
J Biol Chem
, vol.275
, pp. 5521-5526
-
-
Mitsuhashi, S.1
Mizushima, T.2
Yamashita, E.3
Yamamoto, M.4
Kumasaka, T.5
Moriyama, H.6
Ueki, T.7
Miyachi, S.8
Tsukihara, T.9
-
29
-
-
3142653228
-
Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases
-
Bae E, Phillips GN, Jr. Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases. J Biol Chem 2004;279:28202-28208.
-
(2004)
J Biol Chem
, vol.279
, pp. 28202-28208
-
-
Bae, E.1
Phillips Jr., G.N.2
-
30
-
-
34247548408
-
Theoretical Studies on farnesyltransferase: Evidence for thioether product coordination to the active-site zinc sphere
-
Sousa SF, Fernandes PA, Ramos MJ. Theoretical Studies on farnesyltransferase: evidence for thioether product coordination to the active-site zinc sphere. J Comput Chem 2007;28:1160-1168.
-
(2007)
J Comput Chem
, vol.28
, pp. 1160-1168
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
31
-
-
33845671721
-
Theoretical studies on farnesyltransferase: The distances paradox explained
-
Sousa SF, Fernandes PA, Ramos MJ. Theoretical studies on farnesyltransferase: the distances paradox explained. Proteins 2007;66:205-218.
-
(2007)
Proteins
, vol.66
, pp. 205-218
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
32
-
-
0032569201
-
Theoretical study of the substrate mechanism of ribonucleotide reductase
-
Siegbahn PEM. Theoretical study of the substrate mechanism of ribonucleotide reductase. J Am Chem Soc 1998;120:8417-8429.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 8417-8429
-
-
Siegbahn, P.E.M.1
-
33
-
-
0033597076
-
Theoretical study of arginine - carboxylate interactions
-
Melo A, Ramos MJ, Floriano WB, Gomes JANF, Leão JFR, Magalhães AL, Maigret B, Nascimento MC, Reuter N. Theoretical study of arginine - carboxylate interactions. J Mol Struct (THEOCHEM) 1999;463:81-90.
-
(1999)
J Mol Struct (THEOCHEM)
, vol.463
, pp. 81-90
-
-
Melo, A.1
Ramos, M.J.2
Floriano, W.B.3
Gomes, J.A.N.F.4
Leão, J.F.R.5
Magalhães, A.L.6
Maigret, B.7
Nascimento, M.C.8
Reuter, N.9
-
34
-
-
0032708644
-
Carboxylate binding modes in zinc proteins: A theoretical study
-
Ryde U. Carboxylate binding modes in zinc proteins: a theoretical study. Biophys J 1999;77:2777-2787.
-
(1999)
Biophys J
, vol.77
, pp. 2777-2787
-
-
Ryde, U.1
-
35
-
-
0037950581
-
Theoretical studies on the mechanism of inhibition of ribonucleotide reductase by (E)-2′-fluoromethylene-2′- deoxycitidine-5′-diphosphate
-
Fernandes PA, Ramos MJ. Theoretical studies on the mechanism of inhibition of ribonucleotide reductase by (E)-2′-fluoromethylene-2′- deoxycitidine-5′-diphosphate. J Am Chem Soc 2003;125:6311-6322.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 6311-6322
-
-
Fernandes, P.A.1
Ramos, M.J.2
-
36
-
-
0347228946
-
Theoretical studies on the mode of inhibition of ribonucleotide reductase by 2′-substituted substrate analogues
-
Fernandes PA, Ramos MJ. Theoretical studies on the mode of inhibition of ribonucleotide reductase by 2′-substituted substrate analogues. Chem Eur J 2003;9:5916-5925.
-
(2003)
Chem Eur J
, vol.9
, pp. 5916-5925
-
-
Fernandes, P.A.1
Ramos, M.J.2
-
37
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 1988;37:785-789.
-
(1988)
Phys Rev B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
38
-
-
0000189651
-
Density-functional thermochemistry. III. The role of exact exchange
-
Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 1993;98:5648-5652.
-
(1993)
J Chem Phys
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
39
-
-
0344791553
-
Approximate density functional theory as a practical tool in molecular energetics and dynamics
-
Ziegler T. Approximate density functional theory as a practical tool in molecular energetics and dynamics. Chem Rev 1991;91:651-667.
-
(1991)
Chem Rev
, vol.91
, pp. 651-667
-
-
Ziegler, T.1
-
40
-
-
58149324166
-
A comparison of the accuracy of different functionals
-
Bauschlicher CW. A comparison of the accuracy of different functionals. Chem Phys Lett 1995;246:40-44.
-
(1995)
Chem Phys Lett
, vol.246
, pp. 40-44
-
-
Bauschlicher, C.W.1
-
41
-
-
0000840558
-
The performance of density functional/Hartree-Fock hybrid methods: The bonding in cationic first-row transition metal methylene complexes
-
Holthausen MC, Mohr M, Koch W. The performance of density functional/Hartree-Fock hybrid methods: the bonding in cationic first-row transition metal methylene complexes. Chem Phys Lett 1995;240:245-252.
-
(1995)
Chem Phys Lett
, vol.240
, pp. 245-252
-
-
Holthausen, M.C.1
Mohr, M.2
Koch, W.3
-
42
-
-
21944454332
-
A comparison of density functional theory with ab initio approaches for systems involving first transition row metals
-
Ricca A, Bauschlicher CW. A comparison of density functional theory with ab initio approaches for systems involving first transition row metals. Theor Chim Acta 1995;92:123-131.
-
(1995)
Theor Chim Acta
, vol.92
, pp. 123-131
-
-
Ricca, A.1
Bauschlicher, C.W.2
-
43
-
-
35448991944
-
-
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchin HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malik DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Lahan A, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian03 2004, Revision C. 02. Wallingford, CT: Gaussian; 2004
-
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchin HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malik DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Lahan A, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian03 2004, Revision C. 02. Wallingford, CT: Gaussian; 2004.
-
-
-
-
44
-
-
36549092018
-
Energy-adjusted ab initio pseudopotentials for the first row transition elements
-
Dolg M, Wedig U, Stoll H, Preuss H. Energy-adjusted ab initio pseudopotentials for the first row transition elements. J Chem Phys 1987;86:866-872.
-
(1987)
J Chem Phys
, vol.86
, pp. 866-872
-
-
Dolg, M.1
Wedig, U.2
Stoll, H.3
Preuss, H.4
-
45
-
-
11744322674
-
Energy-adjusted ab initio pseudopotentials for the second and third row transition elements
-
Andrae D, Haussermann U, Dolg M, Stoll H, Preuss H. Energy-adjusted ab initio pseudopotentials for the second and third row transition elements. Theor Chim Acta 1990;77:123-141.
-
(1990)
Theor Chim Acta
, vol.77
, pp. 123-141
-
-
Andrae, D.1
Haussermann, U.2
Dolg, M.3
Stoll, H.4
Preuss, H.5
-
46
-
-
18744407471
-
Pseudopotential calculations of transition metal compounds: Scope and limitations
-
Frenking G, Antes I, Bohme M, Dapprich S, Ehlers AW, Jonas V, Neubaus A, Otto M, Stegmann R, Veldkamp A, Vyboishchikov SF. Pseudopotential calculations of transition metal compounds: scope and limitations. Rev Comput Chem 1996;8:63-144.
-
(1996)
Rev Comput Chem
, vol.8
, pp. 63-144
-
-
Frenking, G.1
Antes, I.2
Bohme, M.3
Dapprich, S.4
Ehlers, A.W.5
Jonas, V.6
Neubaus, A.7
Otto, M.8
Stegmann, R.9
Veldkamp, A.10
Vyboishchikov, S.F.11
-
47
-
-
0000609585
-
Hydration of zinc ions: A comparison with magnesium and beryllium ions
-
Bock CW, Katz AK, Glusker JP. Hydration of zinc ions: a comparison with magnesium and beryllium ions. J Am Chem Soc 1995;117: 3754-3765.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 3754-3765
-
-
Bock, C.W.1
Katz, A.K.2
Glusker, J.P.3
|