Table I Protein-DNA complexes studied by NMR site patlern Panern/protein sequet DNA fragment NMR Summary of direct protein-DNA interactions side-chains tp(C39S GAAAGCCATTAGAG Ile47 Thy 8. Ade 9 and Ade 10 strand B AssI "LASLIRLTPTQVKIWFQNHRYKTK TGIGTCAAGIGGCTT le]. Ades and Guag strand a GUnS de10 and Cyull strand B: Gua9 and Assi Lae repressor HPS6 HTH LACI FAMILY "LYDVAEYAGVSYQTVSRVV AATTGTGAGCGS Thy6 strand a: Cyty and Thy& strand B [ 2] Cyn and Thys strand B CRYSTALLIN BE "VTLYDVAEYAGVSYQT Thy strand GAATTGTGAGCGCT CyclO and Thy strand B CACAATIC ly7, Guas and Thy strand a Ade7 and Cys strand B CGTACTAGTTAACTA ua2 and Thy3 strand a VDLLKNAYQNDLHLPLLNLM GTACG LTPDEREALGTRVRIVEELL I5 strand a VLLKSD ETs_domain_2 7 KPKMNYEKLSRGLR TCGAGCCGGAAGTICGA Args Guas, Gua9 strand a: Cyu. Cy19 and Thy 10 strand B kell and Gual2 strand a: Thy ll and Cyul2 strand B Myb_I CCTAACTGACA HWTEEEDRII wSVIAKHLKGRIGKQCRE Adel strand a IWAEIAKLLPGRTDNAIKNHWNSTM Asg ly4 strand bN. Jamin, F. Toma / Progress in Nuclear Magnetic Resonance Spectroscopy 38 (2001) 83±114 94Table 1 Protein±DNA complexes studied by NMR Protein name Prosite pattern Pattern/protein sequencea DNAb fragment used in NMR study Summary of direct protein±DNA interactions Ref. Amino acid side-chains Nucleic acid side-chains Antp(C39S) Homeobox_1 34IAHALSLTERQIKIWFQNR GAAAGCCATTAGAG Ile47 Thy 8, Ade 9 and Ade 10 strand b [1] RMKWK Gln50 Cyt 6, Cyt 7 and Ade8 strand a; Thy8 strand b Asn51 Ade10 strand b Met54 Thy9 strand a Vnd/NK-2 Homeobox_1 34LASLIRLTPTQVKIWFQNHRYKTK TGTGTCAAGTGGCTT Lys3 Ade7, Ade8 and Gua9 strand a [48] Arg5 Cyt6 and Ade7 strand a; Ade 5 strand b Ile47 Ade8 and Ade7 strand a Gln50 Ade10 and Cyt11 strand b; Gua9 and Thy10 strand a Asn51 Ade7 and Ade8 strand a Tyr54 Thy8, Cyt9 and Ade10 strand b Lae repressor HP56 HTH_LACI_FAMILY 6LYDVAEYAGVSYQTVSRVV AATTGTGAGCGc Tyr17 Thy6 strand a; Cyt9 and Thy8 strand b [2] Gln18 Cyt7 and Thy8 strand b CRYSTALLIN_BETA 4VTLYDVAEYAGVSYQT Ser21 Thy8 strand b GAMMA Arg22 Gua5 strand a Asn25 Thy8 strand b Gln26 Cyt7 strand b His29 Thy3 strand a HP62 GAATTGTGAGCGCT Leu6 Cyt10 and Thy9 strand b [55] CACAATTC Tyr7 Cyt10 strand b Tyr17 Thy7, Gua8 and Thy9 strand a Gln18 Ade7 and Cyt8 strand b His29 Thy4 strand a Leu56 Gua13 strand b Trp repressor ± 1QSPYSAAMAEQRHQEWLRF CGTACTAGTTAACTA Arg69 Gua2 and Thy3 strand a [29] VDLLKNAYQNDLHLPLLNLM GTACG Lys72 Gua16 strand a LTPDEREALGTRVRIVEELL Ile79 Gua16 or Ade15 strand a RGEMSQRELKNELGAGIATI Ala80 Ade15 strand a TRGSNSLKAAPVELRQWLEE Thr83 Ade4 strand a VLLKSD Arg84 Cyt13 strand a hETS1 ETS_domain_2 71KPKMNYEKLSRGLRYY TCGAGCCGGAAGTTCGA Arg81 Gua8, Gua9 strand a; Cyt8, Cyt9 and Thy10 strand b [58] ETS_domain_1 27LWQFLLELL Gly82 Thy10 and Thy11 strand b Arg84 Gua8 and Gua9 strand a Tyr85 Ade11 and Gua12 strand a; Thy11 and Cyt12 strand b Mouse c-Myb Myb_1 95WTKEEDQRV CCTAACTGACA Lys41 Gua7 strand a [61] 147WTEEEDRII Glu45 Cyt6 strand a; Cyt8 strand b Myb_2 115WSVIAKHLKGRIGKQCRE Lys95 Gua6 strand b RWHNHL Asn96 Ade4 strand a 166WAEIAKLLPGRTDNAIKNHWNSTM Asn99 Thy4 strand b