BIOINORGANIC CHEMISTRY A Short Course Second Edition

MAGNESIUM AND CATALYTIC RNA 267

TABLE 6.3 Description of Hammerhead Crystal Structures

PDB ID Description Metal Ions (Locations)

Resolution/

pH

Reference/

Year

1HMH RNA – DNA
construct

2.60 14 /1994

1MME RNA – RNA 2 ′ -
OCH 3 at
cleavage site

Mg 2+ (near G 2.2 , G 2.3 , near

cleavage site – CUGA loop,

bonds topro - R - oxygen A 9 ,

N 7 of G 10.1 )

3.10 35 /1995

299D Freeze - trapped
RNA – RNA

No metals 3.00/6.0 39 /1996

300D Freeze - trapped
RNA – RNA

6 Mn 2+ (Mn 2+ – pro - R - oxygen

A 9 = 2.3 Å , Mn 2+ – N 7 G 10.1

= 2.2 Å , Mn 2+ – N 7 G 5.0 =

3.1 Å , Mn 2+ – O 6 G 5.0 =

4.3 Å )

3.00/5.0 39 /1996

301D Freeze - trapped
RNA – RNA

5 Mg 2+ (Mg 2+ – pro - R p - oxygen

A1.1 = 2.4 Å , Mg 2+ – N 2 G 5.0

= 3.8 Å , Mg 2+ – N 1 G 5.0 =

3.9 Å , Mg 2+ within 7 – 11 Å

of A 9.0 – G 10.1 )

3.00/8.5 39 /1996

359D RNA – RNA 5 Tb 3+ (Tb 3+ – N 2 G 5.0 = 3.9 Å ,
Tb3+ – N 1 G 5.0 = 3.8 Å , Tb 3+ –
O 6 G 5.0 = 4.7 Å )

2.90/6.0 43 /1998

379D RNA – RNA talo -
5 ′ - C – CH 3 at A 1.1

8 Co 2+ (Co 2+ - pro - R p - oxygen

A 9 = 2.5 Å , Co 2+ – N 7 G 10.1 =

2.0 Å , Co 2+ – N 7 G 5.0 = 2.2 Å ,

Co2+ – N 7 A 1.1 = 2.6 Å Co 2+ –

O 6 G 16.2 = 2.1 Å , Co 2+ – N 7

G16.4 = 2.6 Å )

3.1/8.5 44 /1998

488D Lattice trapped
RNA – RNA
ribozyme – product

8 Cd 2+ (Cd 2+ – pro - R - oxygen

A 9 = 2.2 Å , Cd 2+ – N 7 G 10.1 =

2.0 Å , Cd 2+ – N 7 G 5.0 = 2.0 Å ,

Cd2+ ions near A 6.0 , G 2.3 ,

U2.4 , G 2.5 )

3.1/8.5 52 /2000

1NYI RNA – RNA, base
pair tether stem
I to stem II

4 Co 2+ (Co 2+ – N 2 G 5.0 = 3.5 Å ,

Co2+ – N 1 G 5.0 = 3.6 Å , Co 2+ –

O 6 G 5.0 = 4.7 Å , Co 2+ – O2 ′

U16.1 = 1.8 Å , Co 2+ – pro - R p

oxygen C 17.0 = 3.9 Å )

2.85/6.0 58 /2003

1Q29 RNA – RNA, base
pair tether stem
I to stem II

5 Co 2+ (Co 2+ - pro - R oxygen

A 9 = 2.3 Å , Co 2+ – N 7 G 10.1 =

2.3 Å , Co 2+ – N 7 G 5.0 = 2.6 Å ,

Co2+ – O 6 G 5.0 = 4.3 Å ,

Co2+ – N 7 G 16.2 = 2.0 Å )

2.99/8.5 58 /2003