Cobalt in PDB 3bbm: Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site

The structure of Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site, PDB code: 3bbm 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)	29.97 / 2.65
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.650, 93.650, 133.500, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 21.7

The binding sites of Cobalt atom in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site (pdb code 3bbm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site, PDB code: 3bbm:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at 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 A38C and 2'O-Me Modification at 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 N5 B:NCO32 1.9 0.6 1.0 N4 B:NCO32 2.0 0.2 1.0 N3 B:NCO32 2.0 0.2 1.0 N2 B:NCO32 2.0 1.0 1.0 N1 B:NCO32 2.0 0.6 1.0 N6 B:NCO32 2.0 0.6 1.0 O2 A:SO414 4.0 0.7 1.0 O6 B:G13 4.5 67.4 1.0 O6 B:G12 4.5 68.6 1.0 O4 A:SO414 4.7 0.4 1.0 S A:SO414 4.8 1.0 1.0 N7 B:G12 4.9 66.4 1.0

Cobalt binding site 2 out of 3 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at 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 A38C and 2'O-Me Modification at Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1 b:1.0 occ:1.00 CO C:NCO1 0.0 1.0 1.0 N5 C:NCO1 2.0 0.3 1.0 N4 C:NCO1 2.0 0.3 1.0 N3 C:NCO1 2.0 0.1 1.0 N2 C:NCO1 2.0 0.6 1.0 N6 C:NCO1 2.0 0.9 1.0 N1 C:NCO1 2.0 99.3 1.0 OP2 C:U41 3.8 70.5 1.0 OP1 C:A40 3.9 80.9 1.0 OP2 B:A20 4.1 0.1 1.0 O6 B:G21 4.2 78.8 1.0 N7 B:G21 4.3 78.1 1.0 P C:A40 4.7 85.8 1.0 OP2 C:A40 4.8 85.2 1.0 O5' C:A40 5.0 83.6 1.0 C6 B:G21 5.0 77.6 1.0

Cobalt binding site 3 out of 3 in the Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Minimally Junctioned Hairpin Ribozyme Incorporates A38C and 2'O-Me Modification at Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Co3 b:0.9 occ:1.00 CO C:NCO3 0.0 0.9 1.0 N4 C:NCO3 2.0 0.6 1.0 N5 C:NCO3 2.0 0.8 1.0 N2 C:NCO3 2.0 0.4 1.0 N3 C:NCO3 2.0 0.5 1.0 N1 C:NCO3 2.0 0.8 1.0 N6 C:NCO3 2.0 0.2 1.0 N7 C:G36 4.1 71.8 1.0 O6 C:G36 4.2 72.2 1.0 O2' C:C38 4.3 70.3 1.0 O6 A:G6 4.5 62.0 1.0 N4 B:C25 4.7 63.1 1.0 OP2 B:A23 4.7 78.4 1.0 C5 C:G36 4.7 70.0 1.0 C6 C:G36 4.7 70.4 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