Cobalt in PDB 1q29: Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment

The structure of Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment, PDB code: 1q29 was solved by C.M.Dunham, J.B.Murray, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 3.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.689, 66.689, 140.528, 90.00, 90.00, 120.00
R / Rfree (%)	24.2 / 27.9

The binding sites of Cobalt atom in the Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment (pdb code 1q29). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment, PDB code: 1q29:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1 b:0.1 occ:1.00 O6 A:G14 3.4 78.0 1.0 N7 A:G14 4.3 79.7 1.0 C6 A:G14 4.4 79.0 1.0 O6 A:G13 4.5 81.4 1.0 C5 A:G14 4.7 79.0 1.0

Cobalt binding site 2 out of 5 in the Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2 b:82.3 occ:1.00 N7 A:G18 2.6 74.4 1.0 C8 A:G18 3.1 73.9 1.0 C5 A:G18 3.8 75.4 1.0 O6 A:G18 4.3 76.2 1.0 OP1 A:G18 4.4 77.1 1.0 N9 A:G18 4.4 74.3 1.0 O3' A:U17 4.5 76.6 1.0 O2' A:U17 4.5 77.3 1.0 C6 A:G18 4.5 75.9 1.0 C4 A:G18 4.8 75.5 1.0 N6 A:A19 4.9 72.8 1.0 P A:G18 4.9 77.2 1.0

Cobalt binding site 3 out of 5 in the Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment within 5.0Å range: probe atom residue distance (Å) B Occ A:Co5 b:71.4 occ:1.00 OP2 A:A22 2.3 85.2 1.0 N7 A:G23 2.3 86.2 1.0 O6 A:G23 3.1 84.8 1.0 C5 A:G23 3.2 85.6 1.0 C8 A:G23 3.4 86.3 1.0 C6 A:G23 3.5 85.0 1.0 P A:A22 3.7 85.0 1.0 OP2 A:G23 4.1 85.3 1.0 O5' A:A22 4.3 83.7 1.0 O2' A:G21 4.4 81.8 1.0 C4 A:G23 4.5 85.2 1.0 OP1 A:A22 4.5 84.5 1.0 N9 A:G23 4.6 85.6 1.0 N7 A:G24 4.6 82.0 1.0 N2 B:G105 4.6 82.4 1.0 O3' A:G21 4.8 83.4 1.0 N1 A:G23 4.9 84.5 1.0

Cobalt binding site 4 out of 5 in the Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment within 5.0Å range: probe atom residue distance (Å) B Occ B:Co3 b:76.7 occ:1.00 N7 B:G116 2.6 71.8 1.0 C8 B:G116 3.2 71.4 1.0 C5 B:G116 3.8 72.2 1.0 O6 B:G116 4.4 72.0 1.0 OP2 B:A115 4.4 71.0 1.0 C6 B:G116 4.5 73.7 1.0 N9 B:G116 4.5 70.9 1.0 C4 B:G116 4.8 71.1 1.0

Cobalt binding site 5 out of 5 in the Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Hammerhead Ribozyme with 5'-5' G-G Linkage: Conformational Change Experiment within 5.0Å range: probe atom residue distance (Å) B Occ B:Co4 b:78.2 occ:1.00 N7 B:G118 2.0 71.1 1.0 C8 B:G118 3.0 70.9 1.0 C5 B:G118 3.0 70.7 1.0 O6 B:G118 3.4 69.1 1.0 C6 B:G118 3.5 69.6 1.0 N9 B:G118 4.2 72.6 1.0 C4 B:G118 4.2 71.2 1.0 OP2 B:G118 4.3 68.1 1.0 C5 B:A117 4.5 67.5 1.0 C6 B:A117 4.6 64.6 1.0 N7 B:A117 4.6 67.6 1.0 N6 B:A117 4.7 63.4 1.0 C4 B:A117 4.9 68.3 1.0 N1 B:G118 4.9 69.4 1.0

C.M.Dunham, J.B.Murray, W.G.Scott. A Helical Twist-Induced Conformational Switch Activates Cleavage in the Hammerhead Ribozyme. J.Mol.Biol. V. 332 327 2003.
ISSN: ISSN 0022-2836
PubMed: 12948485
DOI: 10.1016/S0022-2836(03)00843-X