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Table 2 List of the 240 structures of protein-DNA complexes in the dataset.

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

     

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 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

     

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

  1. 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 (‡).