BIOINORGANIC CHEMISTRY A Short Course Second Edition

MAGNESIUM AND CATALYTIC RNA 295

TABLE 6.6 Inline Fitness Data for Hammerhead Ribozyme Crystal

Structures

a

PDB Accession Number

O2

′ (C

) – P (A 17

1.1

) –

O5

′ (A

1.1

) Angle ( ° )

O2

′ (C

17

) – P

(A

1.1

) ( Å )

O5

′ (A

1.1

) – P

(A

1.1

) ( Å )

O2

′ (C

) – O5 17

′

(A

1.1

) ( Å )

Inline Fitness

Reference/Year

299D

56.9

3.46

1.59

2.91

39 /1996

300D

60.0

3.51

1.59

3.04

39 /1996

301D

74.9

4.08

1.59

3.98

39 /1996

379D with P modeled

into the structure

111

2.51

1.59

3.42

0.84

58 /2003 Table 2

b

488D uncleaved

99.4

4.37

1.59

4.89

52 /2000

488D cleaved

1.7

52 /2000

1NYI

59.5

3.60

1.59

3.11

0.06

58 /2003 Table 2

b

1Q29

135

2.24

1.60

3.56

1.6

58 /2003 Table 2

b

Ideal “ Inline Fitness ”

180

3.00

1.59

4.59

1.0

58 /2003 Table 2

b

299D A

• G 9

noncleaving 8

site

170

2.66

1.59

4.23

1.3

58 /2003 Table 2

b

53 /2001

Hairpin ribozyme

ligation site

172

2.70

1.59

4.28

1.3

58 /2003 Table 2

b

a Some data are from Table 2 of reference 58. b Note that distance parameter labels in lines 1,

d (O2

′ – P), and 2,

d (O5

′ – P), are labeled incorrectly in Table 2 of reference 58.