Cobalt in PDB 3i2q: Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9

The structure of Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9, PDB code: 3i2q was solved by J.E.Wedekind, R.C.Spitale, J.Krucinska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.42 / 2.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.350, 93.350, 131.450, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 22.7

The binding sites of Cobalt atom in the Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9 (pdb code 3i2q). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9, PDB code: 3i2q:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:67.0 occ:0.75 CO B:NCO101 0.0 67.0 0.8 N5 B:NCO101 2.0 66.7 0.8 N4 B:NCO101 2.0 66.1 0.8 N3 B:NCO101 2.0 65.8 0.8 N2 B:NCO101 2.0 66.2 0.8 N6 B:NCO101 2.0 66.3 0.8 N1 B:NCO101 2.0 65.4 0.8 OP1 C:A40 3.5 83.1 1.0 OP2 B:A20 3.9 84.2 1.0 OP2 C:U41 4.1 61.3 1.0 O6 B:G21 4.1 64.1 1.0 N7 B:G21 4.3 61.0 1.0 P C:A40 4.7 77.7 1.0 C6 B:G21 4.9 61.6 1.0 N7 B:A20 4.9 61.1 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Hairpin Ribozyme with 2'Ome Substrate Strand and N1-Deazaadenosine at Position A9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:70.4 occ:0.25 CO B:NCO101 0.0 70.4 0.2 N4 B:NCO101 2.0 69.4 0.2 N5 B:NCO101 2.0 69.4 0.2 N3 B:NCO101 2.0 69.3 0.2 N2 B:NCO101 2.0 69.2 0.2 N6 B:NCO101 2.0 69.3 0.2 N1 B:NCO101 2.0 70.3 0.2 O6 B:G12 3.9 54.6 1.0 O6 B:G13 4.0 58.4 1.0 N7 B:G12 4.3 54.5 1.0 C6 B:G12 4.7 52.6 1.0 N4 A:C-4 4.8 50.7 1.0 C5 B:G12 4.8 52.5 1.0 O6 B:G11 4.9 59.2 1.0 O3 A:SO4102 4.9 89.8 0.3 O2 A:SO4102 4.9 89.8 0.3 C6 B:G13 5.0 55.0 1.0

R.C.Spitale, R.Volpini, M.V.Mungillo, J.Krucinska, G.Cristalli, J.E.Wedekind. Single-Atom Imino Substitutions at A9 and A10 Reveal Distinct Effects on the Fold and Function of the Hairpin Ribozyme Catalytic Core. Biochemistry V. 48 7777 2009.
ISSN: ISSN 0006-2960
PubMed: 19634899
DOI: 10.1021/BI9011622