Cobalt in PDB 3gs8: An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand

The structure of An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand, PDB code: 3gs8 was solved by R.C.Spitale, R.Volpini, M.G.Heller, J.Krucinska, G.Cristalli, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.37 / 2.85
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.820, 93.820, 134.760, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 25.4

The binding sites of Cobalt atom in the An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand (pdb code 3gs8). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand, PDB code: 3gs8:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1 b:0.0 occ:1.00 CO C:NCO1 0.0 0.0 1.0 N4 C:NCO1 2.0 0.9 1.0 N5 C:NCO1 2.0 1.0 1.0 N3 C:NCO1 2.0 0.6 1.0 N2 C:NCO1 2.0 1.0 1.0 N6 C:NCO1 2.0 0.0 1.0 N1 C:NCO1 2.0 0.0 1.0 N7 C:G21 3.7 93.9 1.0 OP1 D:A40 3.9 96.2 1.0 OP2 D:U41 4.0 78.1 1.0 OP2 C:A20 4.1 0.7 1.0 O6 C:G21 4.3 94.8 1.0 C5 C:G21 4.6 91.5 1.0 N7 C:A20 4.7 88.3 1.0 P D:A40 4.7 99.8 1.0 C8 C:G21 4.7 94.1 1.0 OP2 D:A40 4.7 94.8 1.0 C6 C:G21 4.8 90.7 1.0

Cobalt binding site 2 out of 2 in the An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of An All-Rna Hairpin Ribozyme A38N1DA38 Variant with A Transition-State Mimic Substrate Strand within 5.0Å range: probe atom residue distance (Å) B Occ B:Co15 b:0.0 occ:1.00 CO B:NCO15 0.0 0.0 1.0 N5 B:NCO15 2.0 0.0 1.0 N4 B:NCO15 2.0 0.6 1.0 N3 B:NCO15 2.0 0.5 1.0 N2 B:NCO15 2.0 0.0 1.0 N6 B:NCO15 2.0 0.5 1.0 N1 B:NCO15 2.0 0.6 1.0 O4 A:SO415 4.1 0.7 0.5 O6 B:G13 4.2 81.0 1.0 O3 A:SO415 4.3 0.9 0.5 O6 B:G12 4.4 86.8 1.0 N7 B:G12 4.8 83.3 1.0 S A:SO415 4.9 0.1 0.5 N4 A:C2 4.9 85.3 1.0

R.C.Spitale, R.Volpini, M.G.Heller, J.Krucinska, G.Cristalli, J.E.Wedekind. Identification of An Imino Group Indispensable For Cleavage By A Small Ribozyme. J.Am.Chem.Soc. V. 131 6093 2009.
ISSN: ISSN 0002-7863
PubMed: 19354216
DOI: 10.1021/JA900450H