Cobalt in PDB 3i2s: Crystal Structure of the Hairpin Ribozyme with A 2'Ome Substrate and N1-Deazaadenosine at Position A10

The structure of Crystal Structure of the Hairpin Ribozyme with A 2'Ome Substrate and N1-Deazaadenosine at Position A10, PDB code: 3i2s 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)	30.67 / 2.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.830, 92.830, 132.690, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 26.1

The binding sites of Cobalt atom in the Crystal Structure of the Hairpin Ribozyme with A 2'Ome Substrate and N1-Deazaadenosine at Position A10 (pdb code 3i2s). 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 A 2'Ome Substrate and N1-Deazaadenosine at Position A10, PDB code: 3i2s:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of the Hairpin Ribozyme with A 2'Ome Substrate and N1-Deazaadenosine at Position A10


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 A 2'Ome Substrate and N1-Deazaadenosine at Position A10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:76.6 occ:1.00 CO B:NCO101 0.0 76.6 1.0 N5 B:NCO101 2.0 76.8 1.0 N4 B:NCO101 2.0 77.9 1.0 N3 B:NCO101 2.0 77.7 1.0 N2 B:NCO101 2.0 76.6 1.0 N6 B:NCO101 2.0 82.9 1.0 N1 B:NCO101 2.0 78.3 1.0 OP1 C:A40 3.5 81.7 1.0 OP2 B:A20 3.7 80.5 1.0 N7 B:G21 3.8 62.8 1.0 O6 B:G21 3.9 66.1 1.0 N7 B:A20 4.3 64.6 1.0 OP2 C:U41 4.5 57.3 1.0 C5 B:G21 4.6 62.8 1.0 C6 B:G21 4.7 62.7 1.0 C8 B:A20 4.7 65.3 1.0 P C:A40 4.8 77.1 1.0 C8 B:G21 4.9 63.3 1.0 P B:A20 4.9 81.1 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the Hairpin Ribozyme with A 2'Ome Substrate and N1-Deazaadenosine at Position A10


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 A 2'Ome Substrate and N1-Deazaadenosine at Position A10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:80.5 occ:1.00 CO B:NCO102 0.0 80.5 1.0 N5 B:NCO102 1.9 83.6 1.0 N4 B:NCO102 2.0 80.9 1.0 N3 B:NCO102 2.0 81.1 1.0 N2 B:NCO102 2.0 82.5 1.0 N1 B:NCO102 2.0 81.5 1.0 N6 B:NCO102 2.0 82.2 1.0 O6 B:G13 3.6 59.9 1.0 O4 A:U-5 3.9 88.9 0.5 O6 B:G12 4.0 55.0 1.0 N7 B:G12 4.4 58.1 1.0 O2 A:SO4103 4.4 82.1 0.5 N4 A:C-4 4.7 51.2 1.0 C6 B:G13 4.7 57.8 1.0 C6 B:G12 4.7 54.3 1.0 C5 B:G12 4.9 54.7 1.0 O3 A:SO4103 5.0 82.0 0.5

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