Cobalt in PDB 3b58: Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site

The structure of Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site, PDB code: 3b58 was solved by C.Macelrevey, J.Krucinska, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.80 / 2.65
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.370, 93.370, 132.270, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 26.2

The binding sites of Cobalt atom in the Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site (pdb code 3b58). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site, PDB code: 3b58:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co32 b:0.9 occ:1.00 CO B:NCO32 0.0 0.9 1.0 N4 B:NCO32 2.0 0.6 1.0 N5 B:NCO32 2.0 0.0 1.0 N3 B:NCO32 2.0 0.4 1.0 N2 B:NCO32 2.0 0.8 1.0 N6 B:NCO32 2.0 0.2 1.0 N1 B:NCO32 2.0 0.9 1.0 O6 B:G13 4.1 62.0 1.0 O6 B:G12 4.2 57.4 1.0 N7 B:G12 4.3 60.9 1.0 O2 A:SO414 4.3 0.8 1.0 N4 A:C2 4.9 54.7 1.0 C6 B:G12 4.9 57.9 1.0

Cobalt binding site 2 out of 2 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and A 2',5'-Phosphodiester Linkage at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1 b:0.8 occ:1.00 CO C:NCO1 0.0 0.8 1.0 N4 C:NCO1 2.0 0.3 1.0 N5 C:NCO1 2.0 0.9 1.0 N3 C:NCO1 2.0 0.4 1.0 N2 C:NCO1 2.0 0.9 1.0 N6 C:NCO1 2.0 0.8 1.0 N1 C:NCO1 2.0 0.0 1.0 OP1 C:A40 3.9 0.3 1.0 OP2 C:U41 4.0 71.7 1.0 N7 B:G21 4.1 70.6 1.0 OP2 B:A20 4.2 90.6 1.0 O6 B:G21 4.5 70.2 1.0 P C:A40 4.7 0.9 1.0 OP2 C:A40 4.8 0.3 1.0

C.Macelrevey, J.D.Salter, J.Krucinska, J.E.Wedekind. Structural Effects of Nucleobase Variations at Key Active Site Residue ADE38 in the Hairpin Ribozyme. Rna V. 14 1600 2008.
ISSN: ISSN 1355-8382
PubMed: 18596253
DOI: 10.1261/RNA.1055308