Cobalt in PDB 3b5a: Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome Modification at the Active Site

The structure of Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome Modification at the Active Site, PDB code: 3b5a 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)	38.13 / 2.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.560, 93.560, 131.660, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 23.8

The binding sites of Cobalt atom in the Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome Modification at the Active Site (pdb code 3b5a). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome Modification at the Active Site, PDB code: 3b5a:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome 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 Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome Modification at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:96.7 occ:1.00 CO B:NCO101 0.0 96.7 1.0 N5 B:NCO101 2.0 94.1 1.0 N4 B:NCO101 2.0 93.8 1.0 N3 B:NCO101 2.0 93.5 1.0 N2 B:NCO101 2.0 93.5 1.0 N6 B:NCO101 2.0 94.3 1.0 N1 B:NCO101 2.0 93.2 1.0 OP2 C:A40 4.0 83.3 1.0 OP2 C:U41 4.0 62.4 1.0 OP2 B:A20 4.0 83.2 1.0 O6 B:G21 4.2 59.6 1.0 N7 B:G21 4.3 62.8 1.0 OP1 C:A40 4.4 80.5 1.0 P C:A40 4.7 82.9 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome 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 Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating A38G Mutation with A 2'Ome Modification at the 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 0.8 1.0 N4 B:NCO102 2.0 1.0 1.0 N3 B:NCO102 2.0 0.7 1.0 N6 B:NCO102 2.0 0.9 1.0 N2 B:NCO102 2.0 0.0 1.0 N1 B:NCO102 2.0 0.3 1.0 O6 B:G12 4.2 51.3 1.0 O1 A:SO4103 4.4 0.8 1.0 O6 B:G13 4.4 53.5 1.0 N7 B:G12 4.6 52.7 1.0 O2 A:SO4103 4.9 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