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Table 7 Curvature data for bound DNA duplexes of length ≥ 18 basepairs, excluding terminal basepairs, for the HTH-bound DNA dataset.

From: Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

PDB ID

LENGTH

Succ. Bend. Ang. (°)

End-to-end (°) Bend. Ang.

d/l local

R.O.C.(Ã…)

RMSD (Ã…)

Geometry Assigned

Out-of-Plane (°) Bend. Ang.

  

AVG.

S.D.

MAX.

   

Cfit

Lfit

Cfit/Lfit

  
    

Value

Position

        

1KX5

30

15.1

10.5

51.9

A10A11A12

126.7

0.77

37.9

0.6

20.0

0.03

C

0.1

1J59

28

25.3

16.2

66.5

T9G10A11

98.5

0.85

47.2

0.7

21.4

0.03

C

-41.9

1RUN

28

30.4

17.1

71.1

T9G10A11

109.7

0.85

47.8

0.6

22.2

0.03

C

-50.6

1CGP

26

19.1

18.9

65.9

G7T8G9

72.4

0.86

48.2

0.8

17.9

0.04

C

-51.1

1BL0

20

10.5

6.1

25.0

A6G7C8

38.8

0.94

47.0

0.7

3.6

0.19

C

-68.9

1HLV

19

10.0

7.6

30.1

G15G16G17

39.3

0.95

54.6

0.6

3.3

0.18

C

-129.0

1APL

18

11.8

7.3

33.0

A16C17G18

3.7

0.99

NA

4.9

0.9

5.44

L

NA

1K78

23

9.1

3.2

15.6

T19G20G21

15.9

1.00

NA

2.4

1.0

2.40

L

NA

4CRX

32

11.8

12.2

56.5

A17T18G19

76.3

0.82

NA

3.4

9.1

0.37

U

NA

1GDT

32

15.4

13.0

60.3

T14T15A16

40.2

0.87

NA

1.6

14.5

0.11

U

NA

1MNM

23

11.8

7.8

26.8

G13A14A15

58.7

0.89

NA

1.7

5.4

0.31

U

NA

1JE8

18

23.0

13.0

49.6

T2A3C4

56.9

0.93

NA

1.1

5.0

0.22

U

NA

1DDN

23

8.8

4.4

19.1

T13T14A15

36.0

0.95

NA

7.7

2.5

3.08

U

NA

1L3L

18

9.0

5.9

19.7

C14A15C16

32.5

0.96

NA

1.5

1.6

0.94

U

NA

1U78

23

10.6

12.3

51.1

T10A11G12

41.3

0.97

NA

1.4

19.6

0.07

U

NA

1Z9C

24

10.0

5.9

23.9

T11A12T13

3.4

0.97

NA

6.1

2.0

3.05

U

NA

1H88

23

7.4

4.5

16.8

C8A9A10

12.3

0.98

NA

1.6

7.8

0.21

U

NA

1D5Y

18

8.9

5.7

21.6

C15A16A17

10.6

0.98

NA

2.6

2.0

1.30

U

NA

1K61

18

8.8

6.1

22.3

T4A5A6

6.6

0.99

NA

1.3

7.1

0.18

U

NA

1DU0

18

6.3

4.0

15.2

C15C16T17

10.1

0.99

NA

0.6

2.9

0.21

U

NA

1RIO

25

14.8

8.7

34.1

C8C9G10

16.1

0.99

NA

0.6

2.7

0.22

U

NA

6PAX

22

11.8

7.1

25.6

A8C9G10

20.4

0.99

NA

0.6

2.1

0.29

U

NA

2HDD

18

10.7

5.4

23.3

T12C13C14

22.9

0.99

NA

1.2

1.8

0.67

U

NA

1HDD

18

10.9

4.1

19.9

G3C4C5

1.9

0.99

NA

2.6

1.4

1.86

U

NA

3HDD

18

6.5

3.7

14.4

G8T9A10

8.3

0.99

NA

3.0

1.4

2.14

U

NA

1JT0

26

10.4

5.9

22.1

A23T24A25

29.8

0.99

NA

9.1

1.1

8.27

U

NA

1F4K

19

7.9

5.1

20.2

T3G4A5

24.8

1.00

NA

0.8

2.4

0.33

U

NA

1MDM

23

9.2

4.7

20.8

A6G7A8

15.6

1.00

NA

1.7

1.1

1.55

U

NA

1HF0

20

10.5

7.3

30.7

T6G7A8

28.6

1.01

NA

1.4

0.9

1.56

U

NA

  1. The calculation of successive bending angles, end-to-end bending angle, d/l local , Radius of Curvature (ROC), RMSD for circle fit (Cfit) and line fit (Lfit) and torsion angle for out-of-plane component of bending have been described in the 'Methods' section. 'MAX.' denotes the position and value of the maximum successive bending angle within the particular structure. The criteria used to assign DNA molecule geometry as curved (C), linear (L) or unassigned (U) have also been described in the 'Methods' section. The radius of curvature (ROC) and out-of-plane component of bending are reported only when a DNA molecule's geometry is assigned as curved.
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BMC Structural Biology

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