Cobalt in PDB 2d2l: Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39

The structure of Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39, PDB code: 2d2l 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)	30.67 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.200, 93.200, 122.190, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 24.9

The binding sites of Cobalt atom in the Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39 (pdb code 2d2l). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39, PDB code: 2d2l:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39


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, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:31.5 occ:1.00 CO B:NCO102 0.0 31.5 1.0 N5 B:NCO102 1.9 42.7 1.0 N4 B:NCO102 1.9 35.2 1.0 N3 B:NCO102 2.0 35.9 1.0 N6 B:NCO102 2.0 36.9 1.0 N2 B:NCO102 2.0 37.5 1.0 N1 B:NCO102 2.0 39.9 1.0 O6 B:G12 4.0 43.1 1.0 O1 A:SO4201 4.0 76.8 1.0 O6 B:G13 4.2 44.2 1.0 N7 B:G12 4.2 42.6 1.0 C6 B:G12 4.7 42.8 1.0 C5 B:G12 4.8 41.5 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39


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, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co101 b:27.4 occ:1.00 CO D:NCO101 0.0 27.4 1.0 N5 D:NCO101 1.9 39.5 1.0 N4 D:NCO101 1.9 42.6 1.0 N3 D:NCO101 2.0 40.2 1.0 N6 D:NCO101 2.0 41.4 1.0 N2 D:NCO101 2.0 40.1 1.0 N1 D:NCO101 2.0 37.0 1.0 OP1 D:A40 3.3 62.0 1.0 OP2 D:U41 3.8 47.7 1.0 OP2 C:A20 3.9 67.0 1.0 N7 C:G21 4.2 50.1 1.0 O6 C:G21 4.2 54.1 1.0 P D:A40 4.7 66.7 1.0 C5 C:G21 4.9 49.1 1.0 C6 C:G21 4.9 50.0 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of A Minimal, All-Rna Hairpin Ribozyme with A Propyl Linker (C3) at Position U39 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co103 b:95.1 occ:1.00 CO D:NCO103 0.0 95.1 1.0 N5 D:NCO103 2.0 94.8 1.0 N4 D:NCO103 2.0 96.5 1.0 N3 D:NCO103 2.0 96.5 1.0 N2 D:NCO103 2.0 95.2 1.0 N6 D:NCO103 2.0 95.7 1.0 N1 D:NCO103 2.0 96.7 1.0 O D:HOH7 3.4 53.9 1.0 N7 D:G36 3.9 52.9 1.0 O6 D:G36 4.0 49.0 1.0 C5 D:G36 4.6 49.9 1.0 N7 D:G35 4.6 47.4 1.0 C6 D:G36 4.6 49.6 1.0 C8 D:G36 4.9 54.5 1.0 O2' D:A38 4.9 77.3 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