Cobalt in PDB 3b5s: Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification at the Active Site

The structure of Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification at the Active Site, PDB code: 3b5s 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)	40.49 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.500, 93.500, 133.420, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 24.1

The binding sites of Cobalt atom in the Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification at the Active Site (pdb code 3b5s). 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 Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification at the Active Site, PDB code: 3b5s:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification 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 Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:0.6 occ:1.00 CO B:NCO102 0.0 0.6 1.0 N5 B:NCO102 2.0 0.7 1.0 N4 B:NCO102 2.0 0.3 1.0 N2 B:NCO102 2.0 0.1 1.0 N3 B:NCO102 2.0 0.2 1.0 N1 B:NCO102 2.0 0.8 1.0 N6 B:NCO102 2.0 0.1 1.0 O1 A:SO4103 3.9 0.3 1.0 O6 B:G12 4.2 53.9 1.0 O6 B:G13 4.3 52.8 1.0 O2 A:SO4103 4.6 0.5 1.0 N7 B:G12 4.6 52.6 1.0 O6 B:G11 4.7 57.1 1.0 S A:SO4103 4.8 0.1 1.0 N4 A:C2 4.9 54.3 1.0 N7 B:G11 4.9 64.2 1.0

Cobalt binding site 2 out of 2 in the Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification 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 Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'- O-Methyl Modification at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Co101 b:92.8 occ:1.00 CO C:NCO101 0.0 92.8 1.0 N5 C:NCO101 2.0 92.2 1.0 N3 C:NCO101 2.0 93.1 1.0 N4 C:NCO101 2.0 90.4 1.0 N2 C:NCO101 2.0 93.3 1.0 N6 C:NCO101 2.0 92.2 1.0 N1 C:NCO101 2.1 92.1 1.0 OP2 B:A20 3.8 84.5 1.0 OP1 C:A40 3.9 68.7 1.0 OP2 C:U41 4.0 60.3 1.0 O6 B:G21 4.3 53.2 1.0 N7 B:G21 4.5 59.9 1.0 P C:A40 4.8 71.7 1.0 OP2 C:A40 4.9 63.6 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