Cobalt in PDB 3bbk: Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site

The structure of Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site, PDB code: 3bbk 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)	30.00 / 2.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.520, 93.520, 133.970, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.1

The binding sites of Cobalt atom in the Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site (pdb code 3bbk). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site, PDB code: 3bbk:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:99.8 occ:1.00 CO B:NCO101 0.0 99.8 1.0 N5 B:NCO101 1.9 92.4 1.0 N4 B:NCO101 2.0 94.8 1.0 N3 B:NCO101 2.0 93.9 1.0 N2 B:NCO101 2.0 93.4 1.0 N6 B:NCO101 2.0 93.9 1.0 N1 B:NCO101 2.0 92.2 1.0 OP2 C:U41 3.9 75.5 1.0 OP2 B:A20 4.1 96.3 1.0 O6 B:G21 4.1 76.0 1.0 OP1 C:A40 4.2 85.6 1.0 N7 B:G21 4.2 76.3 1.0 OP2 C:A40 4.2 81.4 1.0 P C:A40 4.6 86.6 1.0 C6 B:G21 4.9 72.6 1.0 C5 B:G21 4.9 74.4 1.0

Cobalt binding site 2 out of 3 in the Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:0.7 occ:1.00 CO B:NCO102 0.0 0.7 1.0 N5 B:NCO102 2.0 0.7 1.0 N4 B:NCO102 2.0 0.9 1.0 N3 B:NCO102 2.0 0.3 1.0 N2 B:NCO102 2.0 0.5 1.0 N6 B:NCO102 2.0 0.6 1.0 N1 B:NCO102 2.0 1.0 1.0 O6 B:G13 4.2 73.8 1.0 O6 B:G12 4.3 66.8 1.0 N7 B:G12 4.4 65.7 1.0 N7 B:G11 4.8 74.6 1.0 O1 A:SO4104 4.9 0.1 1.0 O6 B:G11 5.0 75.3 1.0 O3 A:SO4104 5.0 0.0 1.0

Cobalt binding site 3 out of 3 in the Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Miminally Junctioned Hairpin Ribozyme Incorporates A38C and 2'5'- Phosphodiester Linkage Within Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Co103 b:0.8 occ:1.00 CO C:NCO103 0.0 0.8 1.0 N4 C:NCO103 1.9 0.4 1.0 N5 C:NCO103 2.0 0.6 1.0 N3 C:NCO103 2.0 0.3 1.0 N2 C:NCO103 2.0 0.7 1.0 N6 C:NCO103 2.0 0.1 1.0 N1 C:NCO103 2.0 1.0 1.0 N7 C:G36 4.2 76.6 1.0 O2' C:C38 4.2 77.1 1.0 OP2 B:A23 4.3 77.3 1.0 O6 A:G6 4.3 63.5 1.0 O6 C:G36 4.3 70.0 1.0 C5 C:G36 4.7 74.0 1.0 C6 C:G36 4.8 72.3 1.0 N4 B:C25 4.8 65.3 1.0 C8 C:G36 5.0 76.8 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