From: An overview of the structures of protein-DNA complexes
PDB code | DNA-binding subunits | Protein name | Species | Resolution /Ã… | DNA sequence |
---|---|---|---|---|---|
I. Helix-turn-helix group | Â | Â | Â | Â | Â |
1. Cro and Repressor family | Â | Â | Â | Â | Â |
1lmb* | 3,4 | Repressor | Phage ? | 1.8 | -AATACCACTGGCGGTGATATTATAT-CACCGCCAGTGGTAT- |
1lli | A,B | Repressor mutant | Phage ? | 2.1 | -AATACCACTGGCGGTGATATTATAT-CACCGCCAGTGGTAT- |
1per | L,R | Repressor | Phage 434 | 2.5 | AAGTACAGTTTTTCTTG-TATTATA--CAAGAAAAACTGTACT |
1rpe | L,R | Repressor | Phage 434 | 2.5 | -TATACAATGTATCTTG-TTTGACAAACAAGATACATTGTAT- |
2or1 | L,R | Repressor | Phage 434 | 2.5 | AAGTACAAACTTTCTTG-TATTATA--CAAGAAAGTTTGTACT |
3cro | L,R | Cro | Phage 434 | 2.5 | AAGTACAAACTTTCTTG-TATTATA--CAAGAAAGTTTGTACT |
6cro | A | Cro | Phage ? | 3.0 | AAGTACAAACTTTCTTG-TATTATA-CAAGAAAGTTTGTACT |
3orc | A | Cro | Phage ? | 3.0 | AAGTACAAACTTTCTTG-TATTATA--CAAGAAAGTTTGTACT |
2. Homeodomain family | Â | Â | Â | Â | Â |
1fjl*†| A,B,C,G | Paired protein | D. melanogaster | 2.0 | AATAATCTGATTACTGTAATCAGATTAT |
1hdd | C,D | Engrailed homeodomain | D. melanogaster | 2.8 | --TTTTGCCATGTAATTACCTAAATTAGGTAATTACATGGCAAA |
1apl | C,D | Mat a-2 | S. cerevisiae | 2.7 | --ACATGTAATTCATTTACACGCTGCGTGTAAATGAATTACATG |
1yrn | A,B | Mat a-1/a-2 | S. cerevisiae | 2.5 | -TACATGTAATTTATT-ACATCATATGATGTAATAAATTACATG |
1au7 | A1(5-76), | Pit-1 POU domain | R. norvegicus | 2.3 | TTGCGTAGCGTTACGTATATTCCGCTAATCGAT |
 | A2(103-160), |  |  |  |  |
 | B1(5-75), |  |  |  |  |
 | B2(102-161) |  |  |  |  |
1oct | C1(5-75) | Oct-1 POU domain | H. sapiens | 3.0 | TGTATTGCAAATAAGGACCTTATTTGCATAC |
 | C1(102-161) |  |  |  |  |
2hdd | A,B | Engrailed homeodomain | D. melanogaster | 1.9 | TGTTTTTGATAAGATCTTATCAAAAAC |
3hdd | A,B | Engrailed homeodomain | D. melanogaster | 2.2 | --TTTTGCCATGTAATTACCTAAATTAGGTAATTACATGGCAAA |
9ant | A,B | Antennapedia homeodomain | D. melanogaster | 2.4 | --TTTTGCCATGTAATTACCTAAATTAGGTAATTACATGGCAAA |
6pax | A | Paired domain | H. sapiens | 2.5 | GATGACCTAATAGGGAAAATAACACGAA |
1akh | A,B | Mat a-1/a-2 | S. cerevisiae | 2.5 | TACATGTAAAAATTACATCATATGA |
1b72 | A,B | Homeodomain | H. sapiens | 2.35 | ACTCTATGATTGATCGTAATGCGCAAACG |
1b8I | A,B | Homeodomain | D. melanogaster | 2.4 | TTTACGTTTAAAAGCTTAATAAACG |
1mnm | C,D | Mat a-2 | S. cerevisiae | 2.25 | GATTACCTAATAGGGAAATTTACACG |
 |  |  |  |  | * * * |
3. LacI repressor family | Â | Â | Â | Â | Â |
1wet*†| A,C | Purine repressor | E. coli | 2.6 | AACGAAAACGTTTTCGT |
1bdh†| A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
1bdi†| A,C | Purine repressor | E. coli | 3.0 | TACGCAAACGTTTGCGT |
1pnr†| A,C | Purine repressor | E. coli | 2.7 | AACGAAAACGTTTTCG- |
2pua†| A,C | Purine repressor | E. coli | 2.9 | TACGCAAACGTTTGCGT |
2pub†| A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
2puc†| A,C | Purine repressor | E. coli | 2.6 | TACGCAAACGTTTGCGT |
2pud†| A,C | Purine repressor | E. coli | 2.6 | TACGCAAACGTTTGCGT |
2pue†| A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
2puf†| A,C | Purine repressor | E. coli | 3.0 | TACGCAAACGTTTGCGT |
2pug†| A,C | Purine repressor | E. coli | 2.7 | AACGAAAATTTTTCGT- |
1vpw†| A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
1qpz†| A,C | Purine repressor | E. coli | 2.5 | TACGCAAATTTTTCGT- |
1zay†| A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
 |  |  |  |  | *** *** *** |
4. Endonuclease Fok I family ‡ |  |  |  |  |  |
1fok* | A | Endonuclease FokI | F. okeanokoites | 2.8 | TCGGATGATAACGCTAGTCA |
5. ?d-resolvase family ‡ |  |  |  |  |  |
1gdt* | A,B | ?d-resolvase | E. coli | 3.0 | GCAGTGTCCGATAATTTATAAA |
6. Hin recombinase family ‡ |  |  |  |  |  |
1hcr* | A | Artificial Hin recombinase | Artificial | 1.8 | TGTTTTTGATAAGA |
7. RAP1 family | Â | Â | Â | Â | Â |
1ign* | A,B | RAP1 | S. cerevisiae | 2.25 | CCGCACACCCACACACCAG |
8. Prd paired domain family | Â | Â | Â | Â | Â |
1pdn* | C | Prd paired domain | D. melanogaster | 2.5 | AACGTCACGGTTGAC |
9. Tc3 transposase family ‡ |  |  |  |  |  |
1tc3* | C | Transposase TC3 | C. elegans | 2.45 | AGGGGGGGTCCTATAGAACTT |
10. Trp repressor family | Â | Â | Â | Â | Â |
1trr* | A,B,D,E, | Trp repressor | E. coli | 2.4 | AGCGTACTAGTACGCT |
 | G,H,J,K |  |  |  |  |
11. Diptheria Tox repressor family | Â | Â | Â | Â | Â |
1ddn* | A,B,C,D | Diptheria Tox repressor | E. coli | 3.0 | ATATAATTAGGATAGCTTTACCTAATTATTTTA |
12. Transcription factor IIB | Â | Â | Â | Â | Â |
1d3u* | B | TF IIB | P. woesei | 2.4 | AGAGTAAAGTTTAAATACTTATAT |
1vol | A | TF IIB | H. sapiens | 2.7 | ------ GGCTATAAAAGGGCTG-- |
1c9b | A,E,I,M,Q | TF IIB | H. sapiens | 2.65 | --GGGCGCCTATAAAAGGGG---- |
 |  |  |  |  | * ***** |
'Winged' HTH | Â | Â | Â | Â | Â |
13. Interferon regulatory factor | Â | Â | Â | Â | Â |
2irf* | G,H,I,J, K, L | Interferon regulatory factor-2 | M. musculus | 2.2 | AAGTGAAAGCGA |
1if1 | A,B | Interferon regulatory factor | M. musculus | 3.0 | AACTGTAAGCTTT |
14. Catabolite gene activator protein family | Â | Â | Â | Â | Â |
2cgp* | C | Catabolite gene activator | E. coli | 2.2 | -------------------------GTCACATTAAT-------------------- |
1ber | A,B | Catabolite gene activator | E. coli | 2.5 | --------GCGAAAAGTGTGACATATGTCACACTTTTCGGCGAAAAGTGTGACATATGTCACACTT |
1cgp | A,B | Catabolite gene activator | E. coli | 3.0 | ACTTTTCGGCGAAAAGTGTGACATATGTCACACTTTTCGGCGAAAAGTGTGACATAT--------- |
1run | A,B | Catabolite gene activator | E. coli | 2.7 | --------GCGAAAAATGTGATCTAGATCACATTTTTCGGCGAAAAATGTGATCTAGATCACATTT |
1ruo | A,B | Catabolite gene activator | E. coli | 2.7 | --------GCGAAAAATGTGATCTAGATCACATTTTTCGGCGAAAAATGTGATCTAGATCACATTT |
 |  |  |  |  | ******* ************ *********** ****** |
15. Transcription factor family | Â | Â | Â | Â | Â |
3hts*†| B | Heat shock transcription factor | K. lactis | 1.75 | GGTTCTAGAACC---- |
1cf7 | A,B | E2F-DP | H. sapiens | 2.6 | -ATTTTCGCGCGGTTT |
 |  |  |  |  | ** * ** |
16. Ets domain family | Â | Â | Â | Â | Â |
1bc8* | C | Sap-1 | H. sapiens | 1.93 | TACCGGAAGTAACTTCCGGT |
1bc7 | C | Sap-1 | H. sapiens | 2.01 | TACCGGAAGTAACTTCCGGT |
1pue | E,F | TF PU.1 | M. musculus | 2.1 | -AAAAAGGGGAAGTGGG--- |
1awc | A,B | GABP-a | M. musculus | 2.15 | -AACGACCGGAAGTACACCGGA |
 |  |  |  |  | ** ** * |
II. Zinc-coordinating group | Â | Â | Â | Â | Â |
17. ßßa-zinc finger family |  |  |  |  |  |
1aay* | A1(103-133), A2(134-161), A3(162-187) | Zif268 zinc finger | M. musculus | 1.6 | --AGCGTGGGCGTTACGCC-CACGC |
1zaa | C1(3-33), C2(34-61), C3(62-87) | Zif268 zinc finger | M. musculus | 2.1 | --AGCGTGGGCGTTACGCC-CACGC------------- |
2drp | A1(103-135), A2(137-164), D1(102-135), D2(137-165) | Tramtrack protein | D. melanogaster | 2.8 | AATAAGGATAACGTCCGTCGGACGTTATCCTTATTA-- |
1ubd | C1(295-323), C2(324-351), C3(352-381), C4(382-408) | Zinc finger | H. sapiens | 2.5 | -AGGGTCTCCAATTTTGAAGCGCGCTTCAAAATGG--- |
1mey | C1(1-31), C2(32-59), C3(60-84), F1(1-31), F2(32-59), F3(60-84), G | Consensus zinc finger | Artificial | 2.2 | ---ATGAGGCAGAACTTAGTTCTGCCTCA-------- |
1a1g | A1(103-132), A2(133-159), A3(160186) | DSNR (Zif268 variant) | M. musculus | 1.9 | ---AGCGTGGGCGTTACGCCCACGC |
1a1h | " | QSGR (Zif268 variant) | M. musculus | 1.6 | ---AGCGTGGGCGTTACGCCCACGC |
1a1I | " | RADR (Zif268 variant) | M. musculus | 1.9 | ---AGCGTGGGCGTTACGCCCACGC |
1a1j | " | " | M. musculus | 1.6 | ---AGCGTGGGCGTTACGCCCACGC |
1a1k | " | " | M. musculus | 2.0 | ---AGCGTGGGCGTTACGCCCACGC |
1a1l | " | Zif268 zinc finger | M. musculus | 2.3 | ---AGCGTGGGCGTTACGCCCACGC |
2gli | A1(103-135) | Five-zinc finger | H. sapiens | 2.6 | ---AGCGTGGGCGTTACGCCCACGC |
 | A2(136-167) | " | " | " | ---TTTCGTCTTGGGTGGTCCACG |
 | A3(168-196) | " | " | " |  |
 | A4(197-228) | " | " | " |  |
 | A5(229-257) | " | " | " |  |
18. Hormone-nuclear receptor family | Â | Â | Â | Â | Â |
2nll* | A,B | Retinoic acid receptor | H. sapiens | 1.9 | ---CAGGTCAT-TTCAGGTCAGCTGACCTGAAATGACCTG-- |
1hcq | A,B,E,F | Estrogen receptor | H. sapiens | 2.4 | --CCAGGTCAC-AGTGACCTGCCAGGTCACTG-TGACCTG-- |
1glu | A,B | Glucococorticoid receptor | R. norvegicus | 2.9 | --CCAGAACATCGATGTTCTGCCAGAACATCGATGTTCTG-- |
1lat | A,B | Glucococorticoid receptor | R. norvegicus | 1.9 | TTCCAGAACATGTTCTGGATTCCAGAACAT----GTTCTGGA |
1by4 | A,B,C,D | Retinoic acid receptor | H. sapiens | 2.1 | ---CAGGACATCTAGTAAATTCCAGATCTTACGTTGTCTG-- |
1cit | A | Orphan nuclear receptor | H. sapiens | 2.7 | --CCAGAACATCGAGCCTCTGCCAGAACATCGTTGTTCTG-- |
1a6y | A,B | Orphan nuclear receptor | H. sapiens | 2.3 | -TCCAGGACATCGCTAAGCTTGCTGGTCATTGCGGTTCTG |
 |  |  |  |  | *** *** ***** |
19. Loop-sheet-helix family | Â | Â | Â | Â | Â |
1tsr* | A,B,C | p53 tumor suppressor | H. sapiens | 2.2 | TTTCCTAGACTTGCCCAATTAATAATTGGGCAAGTCTAGGAA |
1tup | A,B,C | p53 tumor suppressor | H. sapiens | 2.2 | TTTCCTAGACTTGCCCAATTAATAATTGGGCAAGTCTAGGAA |
20. GAL4-type family: | Â | Â | Â | Â | Â |
1zme* | C,D | Proline utilization | S. cerevisiae | 2.5 | -ACGGGAAGCCAACTCCG- |
1d66 | A,B | GAL4 | S. cerevisiae | 2.7 | CCGGAGGACAGTCCTCCGG |
 |  |  |  |  | * * * ***** |
III. Zipper-type group | Â | Â | Â | Â | Â |
21. Leucine zipper family | Â | Â | Â | Â | Â |
2dgc*†| A,C | GCN4 | S. cerevisiae | 2.2 | ---TGGAGATGACGTCATCTCC-- |
1dgc†| A,C | GCN4 | S. cerevisiae | 3.0 | ---TGGAGATGACGTCATCTCC-- |
1ysa | C,D | GCN4 | S. cerevisiae | 2.9 | ---TTCCTATGAGCTCATCCAGTT |
1a02 | F | C-Fos | H. sapiens | 2.7 | TTGGGAAATTTCTTTCATAG---- |
 | J | C-Jun |  |  |  |
 |  |  |  |  | * **** |
22. Helix-loop-helix family | Â | Â | Â | Â | Â |
1am9* | A,B,C,D | Srebp-1A | H. sapiens | 2.3 | -TTGCAAGTGGGGTGATCCATGA--------------- |
1hlo | A,B | Max | H. sapiens | 2.8 | -CACCACGTGGTGTGGTGCACCA--------------- |
1an4 | A,B | USF | H. sapiens | 2.9 | AGGCCACGTGACCGG-GGTACATCCGGTGCACT----- |
1an2 | A,C | Max | M. musculus | 2.9 | AGGTCACGTGACCTACACCACATCCAGTGCACTGGATG |
1mdy | A,B,C,D | Myod | M. musculus | 3.0 | TCAACAGCTGTTGA---TCAACAGCTGTTGAC------ |
1a0a | A,B | Pho4 | S. cerevisiae | 2.8 | Â |
 |  |  |  |  | ** ** ***** |
IV. Other a-helix group | Â | Â | Â | Â | Â |
23. Papillomavirus-1 E2 family | Â | Â | Â | Â | Â |
2bop*†| A,C | Papillomavirus-1 E2 | Bovine | 1.7 | CCGACCGACGTCGGTCG |
 |  |  | papillomavirus |  |  |
24. Histone family | Â | Â | Â | Â | Â |
1aoi* | A,B,C,D,E,F,G,H | Histone | X. laevis | 2.8 | ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTC |
 |  |  |  |  | CATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGG |
 |  |  |  |  | AGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT |
25. EBNA1 nuclear protein family | Â | Â | Â | Â | Â |
1b3t* | A,B | Ebna-1 | H. herpesvirus 4 | 2.2 | GGGAAGCATAGCTTCCC |
26. Skn-1 transcription factor | Â | Â | Â | Â | Â |
1skn* | P | Skn-1 | C. elegans | 2.5 | TGACAATGTCATCCC |
27. Cre recombinase family ‡ |  |  |  |  |  |
1crx* | A,B | Cre recombinase | Bacteriophage P1 | 2.4 | TATAACTTCGTATAG |
28. High mobility group family | Â | Â | Â | Â | Â |
1qrv* | A,B | High mobility group-1 | D. melanogaster | 2.2 | GCGATATCGC------ |
1ckt | A | High mobility group-1 | R. norvegicus | 2.5 | CCCCTCTGGACCTTCC |
 |  |  |  |  | ** |
29. MADS box family | Â | Â | Â | Â | Â |
1mnm* | A,B | Pheromone transcription | S. cerevisiae | 2.25 | GATTACCTAATAGGGAAATTTACACG |
 |  | factor MCM-1 |  |  |  |
V. ß-sheet group |  |  |  |  |  |
30. TATA box-binding family | Â | Â | Â | Â | Â |
1ytb* | B | TATA box-binding protein | S. cerevisiae | 1.8 | --GTATATAAAACGGGTGGCGTTTTATATAC----- |
1ytf | A | TATA box-binding protein | S. cerevisiae | 2.5 | ----TGTATGTATATAAAACGTTTTATATACATACA |
1ais | A | TATA box-binding protein | P. woesei | 2.1 | AACTTACTTTIIAAAGCTTGAATGAAAAATTTCA-- |
1cdw | A | TATA box-binding protein | H. sapiens | 1.9 | CTGCTATAAAAGGCTGCAGCCTTTTATAGCAG---- |
1tgh | A | TATA box-binding protein | H. sapiens | 2.0 | --------CGTATATATACGCGTATATATACG---- |
1vol | B | TATA-box-BP | H. sapiens | 2.7 | ----TGATCCCTTAAACTCGCTTGTATATGA----- |
1d3u | A | TATA-box-BP | P. woesei | 2.4 | ---CTTAATCGCTATATCCGTTTCTATAGCTTTCA- |
1c9b | B,F,J,N,R | TATA-box-BP | H. sapiens | 2.65 | --GCTATAACGGTTAACGTTATTGTATAGCCAA--- |
 |  |  |  |  | * **** |
VI. ß-hairpin/ribbon group |  |  |  |  |  |
31. MetJ repressor protein | Â | Â | Â | Â | Â |
1cma* | A,B | Met repressor | E. coli | 2.8 | TTAGACGTCTAGACGTCTA |
32. Tus replication terminator family | Â | Â | Â | Â | Â |
1ecr* | A | Tus replication terminator | E. coli | 2.7 | TTAGTTACAACATACT |
33. Integration host factor family | Â | Â | Â | Â | Â |
1ihf* | A,B | Integration host factor | E. coli | 2.5 | CGGTGCAACAAATTGATAAGCAATGCTTTTTTGGC |
34. Transcription factor T-domain | Â | Â | Â | Â | Â |
1xbr* | A,B | T-domain | X. laevis | 2.5 | AATTTCACACCTAGGTGTGAAAATT |
35. Hyperthermophile DNA-BP. | Â | Â | Â | Â | Â |
1azp* | A | Sac7D | S. acidocaldarius | 1.6 | GCGATCGC |
1azq | A | Sac7D | S. acidocaldarius | 1.94 | GCGATCGC |
1bnz | A | 7A | S. acidocaldarius | 2.0 | GTAATTAC |
1bf4 | A | Ss07D | S. acidocaldarius | 1.6 | GTAATTAC |
 |  |  |  |  | **** |
36. Arc repressor | Â | Â | Â | Â | Â |
1bdt* | A,B,C,D | Arc repressor | Bacteriophage P22 | 2.5 | TATAGTAGAGTGCTTCTATCAT |
1bdv | A,B,C,D | Arc repressor | Bacteriophage P22 | 2.8 | TATAGTAGAGTGCTTCTATCAT |
1par | A,B,C,D | Arc repressor | Bacteriophage P22 | 2.6 | TATAGTAGAGTGCTTCTATCAT |
VII. Other | Â | Â | Â | Â | Â |
37. Rel homology region family | Â | Â | Â | Â | Â |
1a3q* | A, B | NF ?B p52 | H. sapiens | 2.1 | GATTCCCCGGGGAATTCCCC------ |
1nfk | A,B | NF-?B p50 | M. musculus | 2.3 | GAATTCCCTGGGAATTCCC------- |
1svc | P,T | NF-?B p50 | H. sapiens | 2.6 | ----AGATGGGGAATCCCCTAGA--- |
1vkx | A,B | NF ?B p50/p65 | M. musculus | 2.9 | ------CTGGGGAATTTCCCAG---- |
1ram | A,B | NF ?B p65 | M. musculus | 2.7 | GGGACTTTCCGAAATTCCCC------ |
1bvo | A | Gambif1 TF | A. gambiae | 2.7 | ---CGGGCTGGAAATTTCCAGCCG-- |
1a02 | N | Nfat | H. sapiens | 2.7 | ------TTGGGAAATTTCTTTCATAG |
 |  |  |  |  | * *** * |
38. Stat protein family | Â | Â | Â | Â | Â |
1bf5* | A | Stat-1 | H. sapiens | 2.9 | ACAGTTTCCCGTAAATGC |
VIII. Enzyme group | Â | Â | Â | Â | Â |
39. Methyltransferase family | Â | Â | Â | Â | Â |
6mht* | A | Hhal methyltransferase | H. haemolyticus | 2.05 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
4mht | A | Hhal methyltransferase | H. haemolyticus | 2.7 | ---GATAG-GCTATC-GATAGCGCTATC---------- |
1mht | A | Hhal methyltransferase | H. haemolyticus | 2.8 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
3mht | A | Hhal methyltransferase | H. haemolyticus | 2.7 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
5mht | A | HhaI methyltransferase | H. haemolyticus | 2.7 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
7mht | A | HhaI methyltransferase | H. haemolyticus | 2.87 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
8mht | A | HhaI methyltransferase | H. haemolyticus | 2.76 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
9mht | A | HhaI methyltransferase | H. haemolyticus | 2.87 | ---GATAG-GCTATC-GATAGCGCTATC---------- |
10mh | A | HhaI methyltransferase | H. haemolyticus | 2.55 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
1dct | A,B | HaeIII methyltransferase | H. aegyptus | 2.8 | ---ACCAGCAG-GCCACC-AGTGTCACTGGTGGCCTGCTGG |
 |  |  |  |  | ** ** * * ** ** |
40. Endonuclease PvuII family | Â | Â | Â | Â | Â |
3pvi* | A,B | Endonuclease PvuII | P. vulgaris | 1.59 | TGACCAGCTGGTC |
2pvi | A,B | Endonuclease PvuII | P. vulgaris | 1.76 | TGACCAGCTGGTC |
1pvi | A,B | Endonuclease PvuII | P. vulgaris | 2.8 | TGACCAGCTGGTC |
41. Endonuclease EcoRV family | Â | Â | Â | Â | Â |
1rva* | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGATATCTTAAA---GATATCTT- |
1rvb | A,B | Endonuclease EcoRV | E. coli | 2.1 | ------AAAGATATCTTAAA---GATATCTT- |
1rvc | A,B | Endonuclease EcoRV | E. coli | 2.1 | ------AAAGATATCTTAAA---GATATCTT- |
2rve | A,B | Endonuclease EcoRV | E. coli | 3.0 | CGAGCTCGCGAGCTCGCGAGCTCGCGAGCTCG |
4rve†| A,B,C,G | Endonuclease EcoRV | E. coli | 3.0 | -------GGGATATCCCGG----GATATCCC- |
1rve | A,B | Endonuclease EcoRV | E. coli | 2.5 | ------AAAGATATCTTAAA----GATATCTT- |
1rv5 | A,B | Endonuclease EcoRV | E. coli | 2.1 | ------CGGGATATCCC CGG---GATATCCC- |
1bgb | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGATATCTTAAA---GATATCTT- |
1bss | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGATATCTTAAA---GATATCTT- |
1bua | A,B | Endonuclease EcoRV | E. coli | 2.15 | ------AAAGACATCTT--------------- |
1bsu | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGACATCTT--------------- |
 |  |  |  |  | ** **** * |
42. Endonuclease EcoRI family | Â | Â | Â | Â | Â |
1qps*†| A,M | Endonuclease EcoRI | E. coli | 2.5 | TCGCGAATTCGCG |
1eri†| A,C | Endonuclease EcoRI | E. coli | 2.7 | TCGCGAATTCGCG |
1qrh†| A | Endonuclease EcoRI | E. coli | 2.5 | TCGCGAATTCGCG |
1qri†| A | Endonuclease EcoRI | E. coli | 2.6 | TCGCGAATTCGCG |
43. Endonuclease BamHI family | Â | Â | Â | Â | Â |
3bam* | A,B | Endonuclease BamHI | B. amyloliquefaciens | 1.8 | TATGGATCCATATATG |
1bhm | A,B | Endonuclease BamHI | B. amyloliquefaciens | 2.2 | TATGGATCCATA---- |
 |  |  |  |  | ************ |
44. Endonuclease V family | Â | Â | Â | Â | Â |
1vas* | A | Endonuclease V | Phage T4 | 2.75 | ATCGCGTTGCGCTTAGCGCAACGCCGA |
45. Dnase I family | Â | Â | Â | Â | Â |
2dnj* | A | Deoxyribonuclease I | B. taurus | 2.0 | GCGATCGCGCGATC-- |
1dnk | A | Deoxyribonuclease I | B. taurus | 2.3 | GGTATACGGCTATACC |
 |  |  |  |  | * ** * ** |
46. DNA mismatch endonuclease | Â | Â | Â | Â | Â |
1cw0* | A | DNA mismatch endonuclease | E. coli | 2.3 | ACGTACCTGGCTAGCTAGGTACGT |
47. DNA polymerase-ß family |  |  |  |  |  |
1bpy* | A | DNA polymerase-ß | H. sapiens | 2.2 | CCGACCACGCATCAGC |
1bpx | A | " | " | 2.4 | CCGACCACGCATCAGC |
1bpz | A | " | " | 2.6 | CCGACCACGCATCAGC |
1zqa | A | " | " | 2.7 | CATTAGAATCTAATG- |
1zqf | A | " | " | 2.9 | CATTAGAATCTAATG- |
1zqi | A | " | " | 2.7 | CATTAGAATCTAATG- |
1zqn | A | " | " | 3.0 | CATTAGAATCTAATG- |
1zqp | A | " | " | 2.8 | CATCTG--TCAGATG- |
7ice | A | " | " | 2.8 | CATCTG--TCAGATG- |
7icg | A | " | " | 3.0 | CATCTG--TCAGATG- |
7ich | A | " | " | 2.9 | CATCTG--TCAGATG- |
7ici | A | " | " | 2.8 | CATCTG--TCAGATG- |
7ick | A | " | " | 2.9 | CATCTG--TCAGATG- |
7icm | A | " | " | 3.0 | CATCTG--TCAGATG- |
7icn | A | " | " | 2.8 | CATCTG--TCAGATG- |
7icp | A | " | " | 3.0 | CATCTG--TCAGATG- |
7icq | A | " | " | 2.9 | CATCTG--TCAGATG- |
7icr | A | " | " | 3.0 | CATCTG--TCAGATG- |
7ics | A | " | " | 2.8 | CATCTG--TCAGATG- |
7ict | A | " | " | 2.8 | CATCTG--TCAGATG- |
7icv | A | " | " | 2.8 | CATCTG---CAGATG- |
8ica | A | " | " | 3.0 | CATTAGAATCTAATG- |
8icc | A | " | " | 2.8 | CATTAGAATCTAATGA |
8icf | A | " | " | 2.9 | CATTAGAATCTAATG- |
8ici | A | " | " | 2.8 | CATTAGAATCTAATGA |
8ick | A | " | " | 2.7 | CATTAGAATCTAATG- |
8icm | A | " | " | 2.9 | CATTAGAATCTAATGA |
8icn | A | " | " | 2.8 | CATTAGAATCTAATG- |
8ico | A | " | " | 2.7 | CATTAGAATCTAATGA |
8icp | A | " | " | 2.9 | CATTAGAATCTAATG- |
8icq | A | " | " | 3.0 | CATTAGAATCTAATGA |
8icr | A | " | " | 2.9 | CATTAGAATCTAATGA |
8ics | A | " | " | 2.9 | CATTAGAATCTAATGA |
8icu | A | " | " | 3.0 | CATTAGAATCTAATG- |
8icx | A | " | " | 3.0 | CATTAGAATCTAATG- |
9ica | A | " | " | 3.0 | CATTAGAA-CTAATG- |
9icf | A | " | " | 3.0 | CATTAGAT-CTAATG- |
9icg | A | " | " | 3.0 | CATTAGAT-CTAATG- |
9ich | A | " | " | 2.9 | CATTAGAT-CTAATG- |
9ick | A | " | " | 2.7 | CATTAGAT-CTAATG- |
9icl | A | " | " | 2.8 | CATTAGAT-CTAATG- |
9icm | A | " | " | 2.9 | CATTAGAT-CTAATG- |
9icn | A | " | " | 3.0 | CATTAGAATCTAATG- |
9ico | A | " | " | 2.9 | CATTAGAATCTAATG- |
9icq | A | " | " | 2.9 | CATTAGAATCTAATG- |
9icr | A | " | " | 3.0 | CATTAGAA-CTAATG- |
9ics | A | " | " | 2.9 | CATTAGAT-CTAATG- |
9ict | A | " | " | 3.0 | CATTAGAT-CTAATG- |
9icu | A | " | " | 2.9 | CATTAGAATCTAATG- |
9icv | A | " | " | 2.7 | CATTAGAATCTAATG- |
9icw | A | " | " | 2.6 | CATTAGAATCTAATG- |
9icx | A | " | " | 2.6 | CATTAGAATCTAATG- |
9icy | A | " | " | 3.0 | CATTAGAATCTAATG- |
2bpf | A | " | R. norvegicus | 2.9 | GGGCGCCGCGGCGCC- |
 |  |  |  |  | * * * |
48. DNA polymerase I | Â | Â | Â | Â | Â |
2bdp* | A | DNA polymerase I | B. stearothermophilus | 1.8 | --GCATGATGCAGCATCATGC--- |
4bdp | A | DNA polymerase I | B. stearothermophilus | 1.8 | --GCATGATGCAGCATCATGC--- |
1qsy | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCAGGGCGCCGTGGT |
1qss | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCAGGGCGCCGTGGT |
2ktq | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCGGGCGCCGTAATC |
3ktq | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCGGGCGCCGTAATC |
4ktq | A | DNA polymerase I | T. aquaticus | 2.5 | GACCACGGCGCGGGCGCCGTAATC |
1tau | A | DNA polymerase I | T. aquaticus | 3.0 | -GCCATGCGGCAGTCGC------- |
1d8y | A | DNA polymerase I | E. coli | 2.08 | TTTTTTTTTTTTTTTTT |
 |  |  |  |  | ** * ** * |
49. DNA polymerase T7 | Â | Â | Â | Â | Â |
1t7p* | A | DNA polymerase | Bacteriophage | 2.2 | GCCAGTGCCAACCTTGGCACTGGC |
1clq | A | DNA polymerase | Bacteriophage | 2.7 | GCGGAACTACTAGTAGTTCCGAG |
 |  |  |  |  | ** * * ** |
50. HIV reverse transcriptase | Â | Â | Â | Â | Â |
1hmi* | A,B | HIV reverse transcriptase | HIV type 1 | 2.8 | ATGGCGCCCGAACAGGAC |
2hmi | A,B | HIV reverse transcriptase | HIV type 1 | 2.8 | ATGGCGCCCGAACAGGAC |
51. Uracil-DNA glycosylase | Â | Â | Â | Â | Â |
1ssp* | E | Uracil-DNA glycosylase | H. sapiens | 1.9 | CTGTATCTTAAAGATAACAG |
2ssp | E | Uracil-DNA glycosylase | H. sapiens | 2.25 | CTGTATCTTAAAGATAACAG |
4skn | A | Uracil-DNA glycosylase | H. sapiens | 2.9 | TGGGGGCTTAAAGCCGCCC- |
 |  |  |  |  | * ******* * |
52. 3-Methyladenine DNA glycosylase | Â | Â | Â | Â | Â |
1bnk* | A | 3-Methyladenine DNA glycosylase H. | H. sapiens | 2.7 | GACATGTTGCCTGGCAATCATGTCA |
53. Homing endonuclease | Â | Â | Â | Â | Â |
1a73* | A,B, | Intron-encoded | P. polycephalum | 1.8 | -TTGACTCTCTTAAGCGAGTCA |
 |  | Endonuclease I-Ppoi |  |  |  |
1a74 | A,B, | Intron-encoded | P. polycephalum | 2.2 | -TTGACTCTCTTAAGCGAGTCA |
 |  | Endonuclease I-Ppoi |  |  |  |
1cyq | A,B, | Intron-encoded | P. polycephalum | 1.93 | -TTGACTCTCTTAAGCGAGTCA |
 |  | Endonuclease I-Ppoi |  |  |  |
1ipp | A,B, | Intron-encoded | P. polycephalum | 2.2 | -TTGACTCTCTTAAGCGAGTCA |
 |  | Endonuclease I-Ppoi |  |  |  |
1bp7 | A,B,C,D | Homing endlonuclease | C. reinhardtii | 3.0 | GCAAAACGTCGTGAGACAGTTCG |
 |  | I-CreI |  |  |  |
 |  |  |  |  | * ** * ** *** |
54. Topoisomerase I | Â | Â | Â | Â | Â |
1a31* | A | Topoisomerase I | H. sapiens | 2.1 | AAAAAGACCCTGAAAAACCCCT |
1a35 | A | Topoisomerase I | H. sapiens | 2.5 | AAAAAGACCCTGAAAAACCCCT |
1a36 | A | Topoisomerase I | H. sapiens | 2.8 | AAAAAGACTTAGAAAAATTTTT |