Cobalt in PDB 3bbi: Minimally Junctioned Hairpin Ribozyme Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near Active Site

The structure of Minimally Junctioned Hairpin Ribozyme Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near Active Site, PDB code: 3bbi 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)	23.08 / 2.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.250, 93.250, 132.830, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 23.8

The binding sites of Cobalt atom in the Minimally Junctioned Hairpin Ribozyme Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near Active Site (pdb code 3bbi). 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 Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near Active Site, PDB code: 3bbi:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Minimally Junctioned Hairpin Ribozyme Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near 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 Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:0.8 occ:1.00 CO B:NCO102 0.0 0.8 1.0 N5 B:NCO102 2.0 0.7 1.0 N4 B:NCO102 2.0 0.7 1.0 N3 B:NCO102 2.0 0.6 1.0 N2 B:NCO102 2.0 0.6 1.0 N1 B:NCO102 2.0 0.7 1.0 N6 B:NCO102 2.0 0.7 1.0 O6 B:G12 4.2 49.3 1.0 O3 A:SO4103 4.3 0.6 1.0 O6 B:G11 4.3 53.0 1.0 O2 A:SO4103 4.4 0.1 1.0 N7 B:G11 4.4 57.9 1.0 O1 A:SO4103 4.6 0.7 1.0 S A:SO4103 4.7 0.8 1.0 N7 B:G12 4.8 48.9 1.0 C6 B:G11 4.9 54.8 1.0 C5 B:G11 4.9 55.3 1.0

Cobalt binding site 2 out of 2 in the Minimally Junctioned Hairpin Ribozyme Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near 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 Incorporating A38(2AP) and A-1 2'-O-Me Modifications Near Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Co101 b:0.2 occ:1.00 CO C:NCO101 0.0 0.2 1.0 N5 C:NCO101 2.0 95.8 1.0 N4 C:NCO101 2.0 96.2 1.0 N3 C:NCO101 2.0 96.0 1.0 N2 C:NCO101 2.0 95.2 1.0 N6 C:NCO101 2.0 95.7 1.0 N1 C:NCO101 2.0 94.2 1.0 OP1 C:A40 3.8 66.1 1.0 OP2 B:A20 3.9 76.3 1.0 OP2 C:U41 4.0 58.9 1.0 O6 B:G21 4.2 59.7 1.0 N7 B:G21 4.3 60.1 1.0 P C:A40 4.7 68.0 1.0 OP2 C:A40 4.9 65.6 1.0 C6 B:G21 5.0 56.9 1.0 N7 B:A20 5.0 61.9 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