Cobalt in PDB 1zfx: The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site

The structure of The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site, PDB code: 1zfx was solved by J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.68 / 2.38
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.350, 93.350, 123.560, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 25.7

The binding sites of Cobalt atom in the The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site (pdb code 1zfx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site, PDB code: 1zfx:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:74.9 occ:1.00 CO B:NCO102 0.0 74.9 1.0 N4 B:NCO102 2.0 75.5 1.0 N5 B:NCO102 2.0 76.5 1.0 N3 B:NCO102 2.0 73.7 1.0 N2 B:NCO102 2.0 73.7 1.0 N6 B:NCO102 2.0 75.5 1.0 N1 B:NCO102 2.0 74.6 1.0 O6 B:G12 4.1 53.5 1.0 O6 B:G13 4.1 53.4 1.0 N7 B:G12 4.2 50.8 1.0 O B:HOH105 4.3 76.6 1.0 O4 A:SO4103 4.3 0.7 0.5 C6 B:G12 4.8 51.9 1.0 C5 B:G12 4.8 49.5 1.0 N7 B:G13 4.8 49.5 1.0

Cobalt binding site 2 out of 2 in the The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Structure of A Minimal All-Rna Hairpin Ribozyme with the Mutant G8U at the Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Co101 b:51.1 occ:1.00 CO D:NCO101 0.0 51.1 1.0 N4 D:NCO101 2.0 62.6 1.0 N5 D:NCO101 2.0 58.3 1.0 N3 D:NCO101 2.0 61.8 1.0 N2 D:NCO101 2.0 59.3 1.0 N6 D:NCO101 2.0 59.2 1.0 N1 D:NCO101 2.0 58.7 1.0 OP1 D:A40 3.4 64.5 1.0 OP2 D:U41 3.8 58.3 1.0 OP2 C:A20 3.8 77.2 1.0 O6 C:G21 4.2 60.3 1.0 N7 C:G21 4.3 59.4 1.0 P D:A40 4.4 64.8 1.0 OP2 D:A40 4.5 63.1 1.0 O5' D:A40 4.9 66.6 1.0 C6 C:G21 5.0 56.0 1.0

J.Salter, J.Krucinska, S.Alam, V.Grum-Tokars, J.E.Wedekind. Water in the Active Site of An All-Rna Hairpin Ribozyme and Effects of GUA8 Base Variants on the Geometry of Phosphoryl Transfer. Biochemistry V. 45 686 2006.
ISSN: ISSN 0006-2960
PubMed: 16411744
DOI: 10.1021/BI051887K