Cobalt in PDB 2d2k: Crystal Structure of A Minimal, Native (U39) All-Rna Hairpin Ribozyme

The structure of Crystal Structure of A Minimal, Native (U39) All-Rna Hairpin Ribozyme, PDB code: 2d2k was solved by S.Alam, V.Grum-Tokars, J.Krucinska, M.L.Kundracik, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.01 / 2.65
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.200, 93.200, 126.360, 90.00, 90.00, 120.00
R / Rfree (%)	24.7 / 27

The binding sites of Cobalt atom in the Crystal Structure of A Minimal, Native (U39) All-Rna Hairpin Ribozyme (pdb code 2d2k). 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 Minimal, Native (U39) All-Rna Hairpin Ribozyme, PDB code: 2d2k:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of A Minimal, Native (U39) All-Rna Hairpin Ribozyme


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 Minimal, Native (U39) All-Rna Hairpin Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:51.5 occ:1.00 CO B:NCO102 0.0 51.5 1.0 N5 B:NCO102 2.0 55.0 1.0 N4 B:NCO102 2.0 54.2 1.0 N3 B:NCO102 2.0 54.1 1.0 N2 B:NCO102 2.0 56.5 1.0 N1 B:NCO102 2.0 58.6 1.0 N6 B:NCO102 2.0 54.5 1.0 O2' B:A9 3.8 64.5 1.0 N3 B:A9 4.0 53.6 1.0 O3' C:A26 4.0 43.1 1.0 C4' C:A26 4.3 37.0 1.0 C2' B:A9 4.4 56.9 1.0 O2 A:U7 4.4 55.8 1.0 C1' B:A9 4.5 57.3 1.0 C5' C:A26 4.5 38.8 1.0 OP1 C:C27 4.6 40.0 1.0 O4' B:A10 4.6 43.1 1.0 C2 B:A9 4.7 51.2 1.0 C3' C:A26 4.8 37.7 1.0 C4 B:A9 4.9 55.2 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of A Minimal, Native (U39) All-Rna Hairpin Ribozyme


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 Minimal, Native (U39) All-Rna Hairpin Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Co101 b:82.9 occ:0.50 CO C:NCO101 0.0 82.9 0.5 N4 C:NCO101 2.0 83.1 0.5 N5 C:NCO101 2.0 82.6 0.5 N3 C:NCO101 2.0 83.4 0.5 N2 C:NCO101 2.0 83.8 0.5 N6 C:NCO101 2.0 84.3 0.5 N1 C:NCO101 2.0 84.2 0.5 OP1 D:A40 3.8 62.2 1.0 OP2 C:A20 3.8 74.0 1.0 OP2 D:U41 4.0 37.4 1.0 O6 C:G21 4.3 53.5 1.0 N7 C:G21 4.6 47.6 1.0 OP2 C:G19 4.9 67.5 1.0

S.Alam, V.Grum-Tokars, J.Krucinska, M.L.Kundracik, J.E.Wedekind. Conformational Heterogeneity at Position U37 of An All-Rna Hairpin Ribozyme with Implications For Metal Binding and the Catalytic Structure of the S-Turn Biochemistry V. 44 14396 2005.
ISSN: ISSN 0006-2960
PubMed: 16262240
DOI: 10.1021/BI051550I