Table 2

List of the 240 structures of protein-DNA complexes in the dataset.
PDB code
 DNA-binding subunits
 Protein name
 Species
 Resolution /Å
 DNA sequence
I. Helix-turn-helix group




1. Cro and Repressor family




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




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




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 FokI 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




1ign*
 A,B
 RAP1
 S. cerevisiae
 2.25
 CCGCACACCCACACACCAG
8. Prd paired domain family




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




1trr*
 A,B,D,E,
 Trp repressor
 E. coli
 2.4
 AGCGTACTAGTACGCT

G,H,J,K



11. Diptheria Tox repressor family




1ddn*
 A,B,C,D
 Diptheria Tox repressor
 E. coli
 3.0
 ATATAATTAGGATAGCTTTACCTAATTATTTTA
12. Transcription factor IIB




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




13. Interferon regulatory factor




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




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




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




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




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




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




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:




1zme*
 C,D
 Proline utilization
 S. cerevisiae
 2.5
 -ACGGGAAGCCAACTCCG-
1d66
 A,B
 GAL4
 S. cerevisiae
 2.7
 CCGGAGGACAGTCCTCCGG





********
III. Zipper-type group




21. Leucine zipper family




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




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





*********
IV. Other a-helix group




23. Papillomavirus-1 E2 family




2bop*†
 A,C
 Papillomavirus-1 E2
 Bovine
 1.7
 CCGACCGACGTCGGTCG



papillomavirus

24. Histone family




1aoi*
 A,B,C,D,E,F,G,H
 Histone
 X. laevis
 2.8
 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTC





CATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGG





AGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT
25. EBNA1 nuclear protein family




1b3t*
 A,B
 Ebna-1
 H. herpesvirus 4
 2.2
 GGGAAGCATAGCTTCCC
26. Skn-1 transcription factor




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




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




1mnm*
 A,B
 Pheromone transcription
 S. cerevisiae
 2.25
 GATTACCTAATAGGGAAATTTACACG


factor MCM-1


V. ß-sheet group




30. TATA box-binding family




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




1cma*
 A,B
 Met repressor
 E. coli
 2.8
 TTAGACGTCTAGACGTCTA
32. Tus replication terminator family




1ecr*
 A
 Tus replication terminator
 E. coli
 2.7
 TTAGTTACAACATACT
33. Integration host factor family




1ihf*
 A,B
 Integration host factor
 E. coli
 2.5
 CGGTGCAACAAATTGATAAGCAATGCTTTTTTGGC
34. Transcription factor T-domain




1xbr*
 A,B
 T-domain
 X. laevis
 2.5
 AATTTCACACCTAGGTGTGAAAATT
35. Hyperthermophile DNA-BP.




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




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




37. Rel homology region family




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




1bf5*
 A
 Stat-1
 H. sapiens
 2.9
 ACAGTTTCCCGTAAATGC
VIII. Enzyme group




39. Methyltransferase family




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




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




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




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




3bam*
 A,B
 Endonuclease BamHI
 B. amyloliquefaciens
 1.8
 TATGGATCCATATATG
1bhm
 A,B
 Endonuclease BamHI
 B. amyloliquefaciens
 2.2
 TATGGATCCATA----





************
44. Endonuclease V family




1vas*
 A
 Endonuclease V
 Phage T4
 2.75
 ATCGCGTTGCGCTTAGCGCAACGCCGA
45. Dnase I family




2dnj*
 A
 Deoxyribonuclease I
 B. taurus
 2.0
 GCGATCGCGCGATC--
1dnk
 A
 Deoxyribonuclease I
 B. taurus
 2.3
 GGTATACGGCTATACC





******
46. DNA mismatch endonuclease




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




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




1t7p*
 A
 DNA polymerase
 Bacteriophage
 2.2
 GCCAGTGCCAACCTTGGCACTGGC
1clq
 A
 DNA polymerase
 Bacteriophage
 2.7
 GCGGAACTACTAGTAGTTCCGAG





******
50. HIV reverse transcriptase




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




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




1bnk*
 A
 3-Methyladenine DNA glycosylase H.
H. sapiens
 2.7
 GACATGTTGCCTGGCAATCATGTCA
53. Homing endonuclease




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




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

Each entry is provided with the four-digit PDB code, the name, the source, resolution and the aligned sequences of DNA to which the protein is bound in the crystal structure. Protein DNA-binding domains are identified by a single letter identifying the protein chain in the PDB file. Where more than one DNA-binding domain is contained in a single subunit, the chain is split into the individual domains. For these, the domains are labeled with the chain ID and a number and the PDB file residue numbers of the domain are given in brackets. The PDB entries are classified into 'groups' and 'families' according to the structure of the protein contained in the complex. The representative for each family, defined as the structure with the highest resolution is marked with an asterisk (*). The CAP family is an exception; the highest-resolution entry, 2cgp, contains only part of the dimer and so PDB code 1ber is used as the representative. The full coordinate files for homodimeric PDB entries that contain only half the structure were obtained from the NDB and are marked by a dagger (†). Enzyme families whose structures also qualified for another protein group are listed in all that are applicable and are marked by a double dagger (‡).

Luscombe et al. Genome Biology 2000 1:reviews001.1   doi:10.1186/gb-2000-1-1-reviews001