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Table 2 Structural, experimental dissociation and calculated HINT score data for the 39 protein-DNA complexes.

From: Energetics of the protein-DNA-water interaction

     

HINT scores for protein-DNA complexes

PDB code (Resolution, Ã…)

Total water count

pK d (M)

K d ref

ΔG° (kcal mol -1 )

H protein-DNA

H P-D-W a(water count)

H P-D-W (R > 0)b(water count)

H P-D-W (R≥4)c(water count)

1a3q (2.10)

785

10.82

[79]

-14.71

11257

22843 (39)

19954 (28)

12461 (2)

1aay (1.60)

148

9.90

[114]

-13.46

14166

36884 (47)

36300 (43)

20454 (11)

1azp (1.60)

132

6.81

[115]

-9.26

4045

9182 (16)

8400 (12)

5225 (4)

1bl0 (2.30)

144

7.70

[116]

-10.46

4742

6513 (15)

6294 (12)

5143 (4)

1by4 (2.10)d

120

6.46

[83]

-8.78

6328

17213 (24)

14606 (19)

10407 (7)

1c9b (2.65)d

101

7.35

[117]

-9.99

7122

14402 (20)

13101 (14)

7355 (1)

1cez (2.40)

471

6.33

[118]

-8.60

2697

8969 (17)

8125 (12)

4807 (4)

1cit (2.70)

38

9.00

[119]

-12.23

8239

12266 (9)

12347 (8)

9973 (4)

1du0 (2.00)

103

9.72

[120]

-13.21

9793

15802 (37)

16295 (24)

12380 (5)

1dux (2.10)

129

10.07

[121]

-13.69

8837

18746 (24)

18768 (20)

13227 (7)

1f4k (2.50)

96

10.70

[89]

-14.54

10836

18458 (20)

17928 (18)

14753 (8)

1g9y (2.05)

435

10.00

[105]

-13.59

2991

37385 (102)

33546 (83)

16470 (30)

1g9z (1.80)

857

8.70

[122]

-11.83

-747

32408 (117)

31561 (93)

10064 (25)

1h88 (2.80)

25

7.45

[91]

-10.13

7335

8677 (3)

8436 (2)

7335 (0)

1hcr (1.80)

16

7.47

[96]

-10.15

5553

6173 (4)

6173 (4)

5553 (0)

1i3j (2.20)

185

8.02

[123]

-10.90

11217

21035 (37)

21381 (30)

13263 (6)

1ig7 (2.20)

153

8.70

[124]

-11.83

7656

19284 (34)

10839 (27)

10839 (6)

1jk1 (1.90)

136

10.59

[95]

-14.39

14098

38199 (53)

35286 (40)

18768 (7)

1jk2 (1.65)

145

10.37

[95]

-14.09

14283

35196 (51)

33716 (42)

19239 (7)

1jko (2.24)

13

7.03

[96]

-9.55

7571

7731 (1)

7731 (1)

7732 (1)

1jkr (2.28)

2

6.08

[96]

-8.27

6787

6787 (0)

6787 (0)

6787 (0)

1le8 (2.30)

102

6.66

[97]

-9.05

8571

12904 (26)

12679 (18)

8990 (2)

1lmb (1.80)

140

9.00

[98]

-12.23

8191

19046 (37)

16445 (31)

10154 (6)

1mhd (2.80)

24

6.93

[99]

-9.42

1607

1660 (2)

1660 (2)

1629 (1)

1pnr (2.70)

92

8.47

[125]

-11.51

11760

14090 (6)

14090 (6)

11760 (0)

1pue (2.10)d

61

6.85

[126]

-9.30

5823

11403(18)

10461 (14)

6659 (1)

1qpz (2.50)

184

8.59

[102]

-11.67

12015

16625 (12)

16877 (12)

13527 (4)

1skn (2.50)

28

9.00

[103]

-12.23

9158

10976 (6)

10976 (6)

9618 (2)

1t2t (2.50)

72

8.28

[104]

-11.25

12893

16500 (13)

15693 (7)

14360 (4)

1t9i (1.60)

656

8.74

[105]

-11.89

6895

49015 (122)

43140 (98)

18371 (31)

1t9j (2.00)

189

9.22

[105]

-12.54

-449

27873 (81)

24965 (70)

8215 (22)

1tc3 (2.45)

49

7.10

[127]

-9.65

10246

13475 (9)

13390 (6)

10720 (1)

1tro (1.90)

572

9.30

[128]

-12.64

5739

22606 (60)

22434 (46)

10568 (12)

1u0c (2.50)

90

8.23

[108]

-11.19

-2591

12569 (37)

7561 (30)

3622 (14)

1yrn (2.50)

58

10.00

[129]

-13.59

14429

22584 (25)

22846 (24)

17871 (9)

1ytb (1.80)

513

8.40

[130]

-10.06

9035

16607 (32)

17529 (23)

9996 (1)

2bop (1.70)

121

9.40

[131]

-12.77

13400

22452 (33)

22254 (24)

14692 (2)

2hdd (1.90)

183

11.06

[120]

-15.03

14613

31840 (46)

30951 (39)

18688 (9)

9ant (2.40)

26

8.80

[132]

-11.96

9192

12971 (9)

13049 (8)

11711 (5)

  1. aHP-D-W = Hprotein-DNA + Hprotein-water + HDNA-water. Only the contributions of water molecules in a 4 Ã… range at the protein-DNA interface are considered.
  2. bOnly waters with nonzero Ranks with respect to both protein and DNA are included in HP-D-W.
  3. cOnly waters with nonzero Ranks with respect to both protein and DNA and total Rank ≥ 4 are included in HP-D-W.
  4. dThe PDB files report the structures as two equivalent protein-DNA complexes. The second complexes were removed and only waters surrounding the first in a 8 Ã… sphere were considered.
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BMC Structural Biology

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