Cobalt in PDB 3gs5: An All-Rna Hairpin Ribozyme A38N1DA Variant with A Product Mimic Substrate Strand

The structure of An All-Rna Hairpin Ribozyme A38N1DA Variant with A Product Mimic Substrate Strand, PDB code: 3gs5 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)	27.85 / 2.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.830, 93.830, 132.090, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 24.3

The binding sites of Cobalt atom in the An All-Rna Hairpin Ribozyme A38N1DA Variant with A Product Mimic Substrate Strand (pdb code 3gs5). 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 A38N1DA Variant with A Product Mimic Substrate Strand, PDB code: 3gs5:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the An All-Rna Hairpin Ribozyme A38N1DA Variant with A Product 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 A38N1DA Variant with A Product Mimic Substrate Strand within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1 b:0.1 occ:1.00 CO C:NCO1 0.0 0.1 1.0 N4 C:NCO1 2.0 0.8 1.0 N5 C:NCO1 2.0 1.0 1.0 N3 C:NCO1 2.0 0.1 1.0 N2 C:NCO1 2.0 1.0 1.0 N1 C:NCO1 2.0 0.7 1.0 N6 C:NCO1 2.0 0.2 1.0 OP1 C:A53 3.7 80.1 1.0 OP2 C:U54 3.9 62.1 1.0 OP2 C:A32 3.9 86.9 1.0 N7 C:G33 4.1 65.2 1.0 O6 C:G33 4.1 69.0 1.0 P C:A53 4.7 82.1 1.0 C5 C:G33 4.8 65.3 1.0 C6 C:G33 4.8 65.0 1.0 OP2 C:A53 4.9 80.0 1.0 N7 C:A32 4.9 61.3 1.0

Cobalt binding site 2 out of 2 in the An All-Rna Hairpin Ribozyme A38N1DA Variant with A Product 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 A38N1DA Variant with A Product Mimic Substrate Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Co27 b:0.6 occ:1.00 CO A:NCO27 0.0 0.6 1.0 N5 A:NCO27 2.0 0.5 1.0 N4 A:NCO27 2.0 0.4 1.0 N3 A:NCO27 2.0 0.6 1.0 N2 A:NCO27 2.0 0.1 1.0 N6 A:NCO27 2.0 0.1 1.0 N1 A:NCO27 2.0 0.1 1.0 O6 A:G24 4.1 61.9 1.0 O2 A:SO428 4.3 0.7 1.0 O6 A:G25 4.4 62.9 1.0 N7 A:G24 4.6 59.1 1.0 O6 A:G23 4.8 61.3 1.0 N7 A:G23 4.9 59.1 1.0 O1 A:SO428 4.9 0.8 1.0 C6 A:G24 5.0 58.1 1.0 O3 A:SO428 5.0 0.5 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