Cobalt in PDB 3i2r: Crystal Structure of the Hairpin Ribozyme with A 2',5'- Linked Substrate with N1-Deazaadenosine at Position A9

The structure of Crystal Structure of the Hairpin Ribozyme with A 2',5'- Linked Substrate with N1-Deazaadenosine at Position A9, PDB code: 3i2r 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)	38.77 / 2.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.650, 93.650, 132.240, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 27.3

The binding sites of Cobalt atom in the Crystal Structure of the Hairpin Ribozyme with A 2',5'- Linked Substrate with N1-Deazaadenosine at Position A9 (pdb code 3i2r). 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',5'- Linked Substrate with N1-Deazaadenosine at Position A9, PDB code: 3i2r:
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',5'- Linked Substrate with 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 A 2',5'- Linked Substrate with N1-Deazaadenosine at Position A9 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co101 b:87.5 occ:1.00 CO C:NCO101 0.0 87.5 1.0 N5 C:NCO101 2.0 83.1 1.0 N4 C:NCO101 2.0 87.7 1.0 N3 C:NCO101 2.0 84.5 1.0 N2 C:NCO101 2.0 85.5 1.0 N6 C:NCO101 2.0 85.7 1.0 N1 C:NCO101 2.0 84.7 1.0 OP2 C:U41 3.7 58.7 1.0 OP1 C:A40 3.8 71.1 1.0 OP2 B:A20 4.3 80.4 1.0 N7 B:G21 4.4 55.8 1.0 O6 B:G21 4.4 58.1 1.0 P C:A40 4.8 68.8 1.0 O5' C:A40 4.8 66.9 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the Hairpin Ribozyme with A 2',5'- Linked Substrate with 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 A 2',5'- Linked Substrate with N1-Deazaadenosine at Position A9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:79.1 occ:0.50 CO B:NCO101 0.0 79.1 0.5 N5 B:NCO101 2.0 79.3 0.5 N4 B:NCO101 2.0 78.7 0.5 N3 B:NCO101 2.0 79.0 0.5 N2 B:NCO101 2.0 79.3 0.5 N6 B:NCO101 2.0 78.7 0.5 N1 B:NCO101 2.0 79.0 0.5 O2 A:SO4102 3.8 56.8 0.3 O6 B:G12 4.1 55.1 1.0 O6 B:G13 4.3 55.5 1.0 O3 A:SO4102 4.3 57.4 0.3 N7 B:G12 4.6 54.1 1.0 S A:SO4102 4.7 57.6 0.3 N4 A:C2 4.7 44.8 1.0 O6 B:G11 5.0 56.8 1.0 C6 B:G12 5.0 53.2 1.0 N7 B:G11 5.0 56.1 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