Cobalt in PDB 4g6s: Minimal Hairpin Ribozyme in the Transition State with A38P Variation

The structure of Minimal Hairpin Ribozyme in the Transition State with A38P Variation, PDB code: 4g6s was solved by J.A.Liberman, J.L.Jenkins, J.Krucinska, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.10 / 2.84
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.966, 93.966, 134.171, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.2

The binding sites of Cobalt atom in the Minimal Hairpin Ribozyme in the Transition State with A38P Variation (pdb code 4g6s). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Minimal Hairpin Ribozyme in the Transition State with A38P Variation, PDB code: 4g6s:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Minimal Hairpin Ribozyme in the Transition State with A38P Variation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Minimal Hairpin Ribozyme in the Transition State with A38P Variation within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:0.9 occ:1.00 CO B:NCO101 0.0 0.9 1.0 N6 B:NCO101 2.0 94.8 1.0 N1 B:NCO101 2.0 85.3 1.0 N5 B:NCO101 2.0 95.9 1.0 N3 B:NCO101 2.0 96.4 1.0 N2 B:NCO101 2.0 89.4 1.0 N4 B:NCO101 2.0 87.7 1.0 OP2 C:U41 3.9 82.0 1.0 OP1 C:A40 4.0 94.5 1.0 N7 B:G21 4.1 85.0 1.0 OP2 B:A20 4.2 0.0 1.0 O6 B:G21 4.2 86.2 1.0 OP2 C:A40 4.6 90.2 1.0 P C:A40 4.7 96.5 1.0 N7 B:A20 4.8 85.6 1.0 C5 B:G21 4.9 84.9 1.0 C6 B:G21 4.9 82.8 1.0

Cobalt binding site 2 out of 2 in the Minimal Hairpin Ribozyme in the Transition State with A38P Variation


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Minimal Hairpin Ribozyme in the Transition State with A38P Variation within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:0.5 occ:0.63 CO B:NCO102 0.0 0.5 0.6 N6 B:NCO102 2.0 75.6 0.6 N2 B:NCO102 2.0 78.1 0.6 N4 B:NCO102 2.0 96.0 0.6 N5 B:NCO102 2.0 89.6 0.6 N1 B:NCO102 2.0 82.5 0.6 N3 B:NCO102 2.0 85.7 0.6 O2 A:SO4201 4.0 82.6 0.6 O6 B:G12 4.0 75.5 1.0 O6 B:G13 4.3 73.6 1.0 N7 B:G12 4.6 75.0 1.0 C6 B:G12 4.9 72.3 1.0 N4 A:C2 5.0 69.3 1.0

J.A.Liberman, M.Guo, J.L.Jenkins, J.Krucinska, Y.Chen, P.R.Carey, J.E.Wedekind. A Transition-State Interaction Shifts Nucleobase Ionization Toward Neutrality to Facilitate Small Ribozyme Catalysis. J.Am.Chem.Soc. V. 134 16933 2012.
ISSN: ISSN 0002-7863
PubMed: 22989273
DOI: 10.1021/JA3070528