Cobalt in PDB 379d: The Structural Basis of Hammerhead Ribozyme Self-Cleavage

The structure of The Structural Basis of Hammerhead Ribozyme Self-Cleavage, PDB code: 379d was solved by J.B.Murray, D.P.Terwey, L.Maloney, A.Karpeisky, N.Usman, L.Beigelman, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 3.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.100, 65.100, 138.700, 90.00, 90.00, 120.00
R / Rfree (%)	23 / n/a

The binding sites of Cobalt atom in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage (pdb code 379d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage, PDB code: 379d:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1 b:51.7 occ:1.18 O6 A:G22 4.0 42.1 1.0 N7 A:G22 4.1 35.8 1.0 O6 A:G23 4.4 36.6 1.0 C6 A:G22 4.7 33.3 1.0 C5 A:G22 4.8 36.8 1.0

Cobalt binding site 2 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2 b:65.3 occ:1.19 N7 A:G50 2.2 22.5 1.0 C5 A:G50 3.1 25.5 1.0 O6 A:G50 3.1 29.9 1.0 C8 A:G50 3.3 17.9 1.0 C6 A:G50 3.4 27.3 1.0 O2' A:U40 4.0 36.9 1.0 OP1 A:G50 4.2 45.2 1.0 N6 A:A60 4.3 37.6 1.0 C4 A:G50 4.3 23.8 1.0 N9 A:G50 4.4 24.5 1.0 N1 A:G50 4.8 22.1 1.0

Cobalt binding site 3 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Co3 b:49.2 occ:1.07 O6 B:G164 2.2 10.2 1.0 N7 B:G164 2.4 14.1 1.0 C6 B:G164 2.7 13.2 1.0 C5 B:G164 2.8 12.7 1.0 C8 B:G164 3.6 11.2 1.0 OP2 B:A34 4.0 20.9 1.0 N1 B:G164 4.1 14.4 1.0 C4 B:G164 4.1 12.8 1.0 N9 B:G164 4.5 12.5 1.0 OP2 B:G164 4.8 29.0 1.0

Cobalt binding site 4 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Co4 b:71.4 occ:0.98 N3 B:G164 2.2 12.6 1.0 C2' B:G164 2.6 18.1 1.0 C1' B:G164 2.6 16.0 1.0 O2' B:G164 2.8 19.7 1.0 C4 B:G164 2.9 12.8 1.0 N9 B:G164 3.0 12.5 1.0 C2 B:G164 3.3 13.6 1.0 C8 B:A163 3.5 24.4 1.0 O4' B:A163 3.5 17.1 1.0 N9 B:A163 3.6 21.7 1.0 N2 B:G164 3.7 7.2 1.0 C1' B:A163 3.8 18.3 1.0 O4' B:G164 3.9 17.1 1.0 C3' B:G164 4.0 21.0 1.0 N7 B:A163 4.1 33.6 1.0 N2 B:G31 4.2 45.3 1.0 C5 B:G164 4.2 12.7 1.0 C4 B:A163 4.3 26.1 1.0 C8 B:G164 4.4 11.2 1.0 N1 B:G164 4.5 14.4 1.0 C5 B:A163 4.5 31.4 1.0 N7 B:A34 4.6 19.6 1.0 C4' B:G164 4.6 18.8 1.0 N3 B:G31 4.7 44.0 1.0 C2 B:G31 4.8 44.6 1.0 O3' B:G164 4.8 27.8 1.0 C4' B:A163 4.9 17.5 1.0 C5 B:A34 5.0 23.5 1.0 O5' B:A163 5.0 15.5 1.0 C6 B:G164 5.0 13.2 1.0 N7 B:G164 5.0 14.1 1.0

Cobalt binding site 5 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Co5 b:27.8 occ:1.01 N7 B:A11 2.6 29.4 1.0 C8 B:A11 2.9 19.2 1.0 C5' B:C170 3.4 40.7 1.0 O3' B:C170 3.5 44.3 1.0 C3' B:C170 3.8 45.9 1.0 C5 B:A11 4.0 29.2 1.0 C4' B:C170 4.1 44.8 1.0 N9 B:A11 4.2 17.2 1.0 O5' B:C170 4.5 38.7 1.0 O5' B:A11 4.7 19.5 1.0 C4 B:A11 4.8 26.1 1.0 C6 B:A11 4.9 28.2 1.0 N6 B:A11 4.9 23.4 1.0 O4' B:A11 4.9 26.8 1.0

Cobalt binding site 6 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Co6 b:51.4 occ:0.97 N7 A:G25 1.9 55.3 1.0 O6 A:G25 2.7 59.6 1.0 C5 A:G25 2.7 56.8 1.0 C6 A:G25 3.0 55.6 1.0 C8 A:G25 3.1 53.2 1.0 C4 A:G25 4.0 59.0 1.0 N9 A:G25 4.2 56.0 1.0 N1 A:G25 4.4 54.5 1.0 O4 A:U24 4.5 7.8 1.0

Cobalt binding site 7 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ B:Co7 b:53.6 occ:0.96 O6 B:G162 2.1 2.0 1.0 N7 B:G162 2.6 22.8 1.0 C6 B:G162 2.7 21.1 1.0 C5 B:G162 2.9 20.7 1.0 OP2 B:G162 3.5 17.2 1.0 C8 B:G162 3.8 18.2 1.0 N1 B:G162 4.1 18.7 1.0 C4 B:G162 4.3 16.9 1.0 N9 B:G162 4.7 26.6 1.0 N7 B:A163 4.7 33.6 1.0 P B:G162 4.9 20.9 1.0 C5 B:A163 4.9 31.4 1.0

Cobalt binding site 8 out of 8 in the The Structural Basis of Hammerhead Ribozyme Self-Cleavage


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of The Structural Basis of Hammerhead Ribozyme Self-Cleavage within 5.0Å range: probe atom residue distance (Å) B Occ A:Co8 b:63.9 occ:1.05 N7 A:G101 2.0 37.2 1.0 O6 A:G101 2.2 50.3 1.0 C5 A:G101 2.4 43.8 1.0 OP2 A:A90 2.5 71.6 1.0 C6 A:G101 2.5 46.6 1.0 C8 A:G101 3.2 40.9 1.0 P A:A90 3.6 71.0 1.0 O5' A:A90 3.6 65.4 1.0 C4 A:G101 3.8 44.8 1.0 O2' A:G80 3.8 51.5 1.0 N1 A:G101 3.9 43.1 1.0 OP2 A:G101 4.1 54.5 1.0 N9 A:G101 4.1 45.3 1.0 OP1 A:A90 4.3 73.5 1.0 N2 B:G120 4.3 40.8 1.0 C2' A:G80 4.5 50.4 1.0 C5' A:A90 4.6 62.5 1.0 C2 A:G101 4.9 42.0 1.0 N7 A:G102 4.9 33.9 1.0 N3 A:G101 4.9 44.4 1.0 O3' A:G80 5.0 61.2 1.0

J.B.Murray, D.P.Terwey, L.Maloney, A.Karpeisky, N.Usman, L.Beigelman, W.G.Scott. The Structural Basis of Hammerhead Ribozyme Self-Cleavage. Cell(Cambridge,Mass.) V. 92 665 1998.
ISSN: ISSN 0092-8674
PubMed: 9506521
DOI: 10.1016/S0092-8674(00)81134-4