Table 1 Classification data for the 39 protein-DNA complexes used in this study.

1a3q

NF kB p52

Transcr. regulator

Rel homology region

other

Mixed ^b

[79]

1aay

Zif268 zinc finger

Transcr. regulator

ββα-zinc finger

Zinc coordinating group

3.30.160.60

[80]

1azp

Sac7D

DNA binding

Hyperthermophyle DNA-BP

β-sheet group

2.40.50.40

[81]

1bl0

MarA

Transcr. regulator

AraC transcriptional activator

Helix-turn-helix

1.10.10.60

[82]

1by4

Retinoic acid receptor rxr-alpha

Transcr. regulator

Nuclear receptor

Zinc coordinating group

3.30.50.10

[83]

1c9b

TF IIB

Transcr. initiator

TF IIB

Helix-turn-helix

1.10.472.10

[84]

1cez

T7 RNA polymerase

Enzyme

T7 RNA polymerase

DNA/RNA polymerases

Mixed ^b

[85]

1cit

Orphan nuclear receptor NGFI-B

Transcr. regulator

Nuclear receptor

Zinc coordinating group

3.30.50.10

[86]

1du0

Engrailed homeodomain (q50a)

Transcr. regulator

Homeodomain

Helix-turn-helix

1.10.10.60

[87]

1dux

Elk-1

Transcr. regulator

Ets domain

Winged HTH

1.10.10.10

[88]

1f4k

Replication terminator protein

DNA binding

Replication terminator protein

Winged HTH

1.10.10.10

[89]

1g9y ^a

Homing endonuclease I-CreI

Enzyme

Homing endonuclease

Homing endonuclease-like

3.10.28.10

[90]

1g9z ^a

Homing endonuclease I-CreI

Enzyme

Homing endonuclease

Homing endonuclease-like

3.10.28.10

[90]

1h88

Myb proto-oncogene protein

Transcr. regulator

Homeodomain

Helix-turn-helix

1.10.10.60

[91]

1hcr

Hin-recombinase

Enzyme

Hin-recombinase

Helix-turn-helix

1.10.10.60

[92]

1i3j

Homing endonuclease I-TevI

Enzyme

DNA-binding domain of intro endonuclease

DNA-binding domain of intro endonuclease

3.30.60.40

[93]

1ig7

Homeotic protein Msx-1

Transcr. regulator

Homeodomain

Helix-turn-helix

1.10.10.60

[94]

1jk1

Zif268 d20a mutant

Transcr. factor

ββα-zinc finger

Zinc coordinating group

3.30.160.60

[95]

1jk2

Zif268 d20a mutant

Transcr. factor

ββα-zinc finger

Zinc coordinating group

3.30.160.60

[95]

1jko

Hin recombinase

Enzyme

Homeodomain

Helix-turn-helix

1.10.10.60

[96]

1jkr

Hin recombinase

Enzyme

Homeodomain

Helix-turn-helix

1.10.10.60

[96]

1le8

3A Mating-type protein a-1

Transcr. regulator

Homeodomain

Helix-turn-helix

1.10.10.60

[97]

1lmb

Lambda repressor

Transcr. regulator

Repressor

Helix-turn-helix

1.10.260.40

[98]

1mhd

Smad3

Transcr. regulator

Smad Mh1 Domain

Smad Mh1 Domain

3.90.520.10

[99]

1pnr

Purine repressor

Transcr. regulator

LacI repressor

Helix-turn-helix

1.10.260.40

[100]

1pue

TF PU.1

Transcr. factor

Ets domain

Winged HTH

1.10.10.10

[101]

1qpz

Purine repressor

Transcr. regulator

LacI repressor

Helix-turn-helix

1.10.260.40

[102]

1skn

Transcription factor skn-1

Transcr. factor

Transcription factor skn-1

Other α-helix group

1.10.880.10

[103]

1t2t

Homing endonuclease I-TevI

Enzyme

DNA-binding domain of intro endonuclease

DNA-binding domain of intro endonuclease

3.30.60.40

[104]

1t9i ^a

Homing endonuclease I-CreI (d20n)

Enzyme

DNA-binding domain of intro endonuclease

DNA-binding domain of intro endonuclease

3.10.28.10

[105]

1t9j ^a

Homing endonuclease I-CreI (q47e)

Enzyme

DNA-binding domain of intro endonuclease

DNA-binding domain of intro endonuclease

3.10.28.10

[105]

1tc3

Transposase Tc3a1-65

Enzyme

Transposase

Helix-turn-helix

1.10.10.60

[106]

1tro

Tryptophane repressor

Transcr. regulator

Tryptophane repressor

Helix-turn-helix

1.10.1270.10

[107]

1u0c ^a

Homing endonuclease I-CreI (y33c)

Enzyme

DNA-binding domain of intro endonuclease

DNA-binding domain of intro endonuclease

3.10.28.10

[108]

1yrn

Mating-type protein a-1

Transcr. regulator

Homeodomain

Helix-turn-helix

1.10.10.60

[109]

1ytb

TATA box binding protein

Transcr. initiator

TATA box binding protein

β-sheet group

3.30.310.10

[110]

2bop

Bovine papillomavirus-I E2

Transcr. regulator

bovine papillomavirus-I E2

Other α-helix group

3.30.70.330

[111]

2hdd

Engrailed homeodomain (q50k)

Transcr. regulator

Homeodomain

Helix-turn-helix

1.10.10.60

[112]

9ant

Antennapedia protein

Transcr. regulator

Homeodomain

Helix-turn-helix

1.10.10.60

[113]