Cobalt in PDB 3i2u: Crystal Structure of the Haiprin Ribozyme with A 2',5'- Linked Substrate and N1-Deazaadenosine at Position A10

The structure of Crystal Structure of the Haiprin Ribozyme with A 2',5'- Linked Substrate and N1-Deazaadenosine at Position A10, PDB code: 3i2u 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)	39.00 / 2.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.120, 94.120, 134.500, 90.00, 90.00, 120.00
R / Rfree (%)	24.4 / 26.6

The binding sites of Cobalt atom in the Crystal Structure of the Haiprin Ribozyme with A 2',5'- Linked Substrate and N1-Deazaadenosine at Position A10 (pdb code 3i2u). 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 Haiprin Ribozyme with A 2',5'- Linked Substrate and N1-Deazaadenosine at Position A10, PDB code: 3i2u:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of the Haiprin Ribozyme with A 2',5'- Linked 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 Haiprin Ribozyme with A 2',5'- Linked Substrate and N1-Deazaadenosine at Position A10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:84.9 occ:1.00 CO B:NCO101 0.0 84.9 1.0 N5 B:NCO101 2.0 83.7 1.0 N4 B:NCO101 2.0 84.7 1.0 N3 B:NCO101 2.0 84.2 1.0 N2 B:NCO101 2.0 84.1 1.0 N6 B:NCO101 2.0 84.2 1.0 N1 B:NCO101 2.0 84.3 1.0 OP2 C:U41 3.9 55.3 1.0 OP1 C:A40 4.1 64.4 1.0 OP2 B:A20 4.2 82.7 1.0 O6 B:G21 4.3 52.3 1.0 N7 B:G21 4.4 55.3 1.0 O5' C:A40 4.8 71.4 1.0 P C:A40 5.0 73.5 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the Haiprin Ribozyme with A 2',5'- Linked 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 Haiprin Ribozyme with A 2',5'- Linked Substrate and N1-Deazaadenosine at Position A10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:86.8 occ:1.00 CO B:NCO102 0.0 86.8 1.0 N4 B:NCO102 2.0 86.1 1.0 N5 B:NCO102 2.0 86.3 1.0 N3 B:NCO102 2.0 86.2 1.0 N2 B:NCO102 2.0 86.5 1.0 N6 B:NCO102 2.0 86.1 1.0 N1 B:NCO102 2.0 86.2 1.0 O6 B:G12 3.9 50.0 1.0 O6 B:G13 4.1 49.0 1.0 O2 A:SO4103 4.2 64.7 0.3 N7 B:G12 4.4 48.8 1.0 O4 A:SO4103 4.5 64.4 0.3 C6 B:G12 4.7 47.3 1.0 O6 B:G11 4.8 53.6 1.0 S A:SO4103 4.8 64.7 0.3 N7 B:G11 4.8 52.6 1.0 N4 A:C2 4.8 44.6 1.0 O3 A:SO4103 4.9 65.7 0.3 C5 B:G12 4.9 46.6 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