Cobalt in PDB 3b5f: Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage at the Active Site

The structure of Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage at the Active Site, PDB code: 3b5f 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)	38.32 / 2.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.490, 93.490, 133.820, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 25

The binding sites of Cobalt atom in the Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage at the Active Site (pdb code 3b5f). 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 the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage at the Active Site, PDB code: 3b5f:
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 the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage 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 the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:91.2 occ:1.00 CO B:NCO101 0.0 91.2 1.0 N5 B:NCO101 1.9 90.8 1.0 N4 B:NCO101 2.0 90.5 1.0 N3 B:NCO101 2.0 89.6 1.0 N2 B:NCO101 2.0 89.4 1.0 N6 B:NCO101 2.0 90.6 1.0 N1 B:NCO101 2.0 90.1 1.0 OP2 C:U41 3.8 69.4 1.0 OP1 C:A40 3.8 78.9 1.0 OP2 B:A20 4.0 87.3 1.0 O6 B:G21 4.1 70.1 1.0 N7 B:G21 4.3 68.6 1.0 OP2 C:A40 4.6 78.8 1.0 P C:A40 4.7 77.2 1.0 C6 B:G21 4.9 68.8 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of A Minimally Hinged Hairpin Ribozyme Incorporating the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage 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 the ADE38DAP Mutation and A 2',5' Phosphodiester Linkage at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:0.9 occ:1.00 CO B:NCO102 0.0 0.9 1.0 N5 B:NCO102 2.0 0.1 1.0 N4 B:NCO102 2.0 0.5 1.0 N3 B:NCO102 2.0 0.4 1.0 N6 B:NCO102 2.0 0.6 1.0 N2 B:NCO102 2.0 0.4 1.0 N1 B:NCO102 2.0 0.8 1.0 O6 B:G12 4.1 65.9 1.0 N7 B:G12 4.4 64.4 1.0 N7 B:G11 4.6 65.8 1.0 O6 B:G13 4.6 65.9 1.0 O6 B:G11 4.8 64.7 1.0 C6 B:G12 5.0 64.6 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