Cobalt in PDB 1nyi: Crosslinked Hammerhead Ribozyme Initial State

The structure of Crosslinked Hammerhead Ribozyme Initial State, PDB code: 1nyi 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)	19.76 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.639, 65.639, 137.475, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.2

The binding sites of Cobalt atom in the Crosslinked Hammerhead Ribozyme Initial State (pdb code 1nyi). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crosslinked Hammerhead Ribozyme Initial State, PDB code: 1nyi:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crosslinked Hammerhead Ribozyme Initial State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crosslinked Hammerhead Ribozyme Initial State within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2 b:72.8 occ:1.00 N2 A:G18 3.5 50.9 1.0 N1 A:G18 3.6 47.1 1.0 C2 A:G18 4.1 47.9 1.0 C6 A:G18 4.7 46.5 1.0 C2 A:A19 4.7 42.4 1.0 O6 A:G18 4.7 47.1 1.0 N1 A:A19 4.9 42.7 1.0

Cobalt binding site 2 out of 4 in the Crosslinked Hammerhead Ribozyme Initial State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crosslinked Hammerhead Ribozyme Initial State within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1 b:77.9 occ:1.00 N4 B:C122 3.7 34.2 1.0 C5 B:C122 4.2 36.0 1.0 C4 B:C122 4.4 36.2 1.0

Cobalt binding site 3 out of 4 in the Crosslinked Hammerhead Ribozyme Initial State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crosslinked Hammerhead Ribozyme Initial State within 5.0Å range:

Cobalt binding site 4 out of 4 in the Crosslinked Hammerhead Ribozyme Initial State


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crosslinked Hammerhead Ribozyme Initial State within 5.0Å range: probe atom residue distance (Å) B Occ B:Co4 b:86.7 occ:1.00 O2' B:U119 1.8 51.2 1.0 O4 A:U20 2.2 28.0 1.0 C2' B:U119 2.4 49.3 1.0 C6 B:U119 2.6 43.2 1.0 C4 A:U20 3.0 28.0 1.0 N1 B:U119 3.0 44.6 1.0 C5 A:U20 3.1 27.6 1.0 C1' B:U119 3.2 47.8 1.0 C5 B:U119 3.3 42.2 1.0 C3' B:U119 3.8 49.7 1.0 C2 B:U119 3.8 44.5 1.0 OP2 B:C120 3.9 47.3 1.0 O2' A:A19 4.2 36.9 1.0 C4 B:U119 4.2 41.2 1.0 N3 A:U20 4.2 28.4 1.0 N3 B:U119 4.3 43.1 1.0 O4' B:U119 4.4 49.4 1.0 C6 A:U20 4.4 26.5 1.0 O3' B:U119 4.5 49.4 1.0 O5' B:U119 4.5 47.6 1.0 O2 B:U119 4.6 46.4 1.0 C4' B:U119 4.7 50.0 1.0 P B:C120 4.8 47.8 1.0 OP2 B:U119 5.0 44.3 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