Cobalt in PDB 5dek: Rna Octamer Containing Dt

The structure of Rna Octamer Containing Dt, PDB code: 5dek was solved by J.M.Harp, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.16 / 1.99
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.059, 44.059, 85.398, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 26.2

The binding sites of Cobalt atom in the Rna Octamer Containing Dt (pdb code 5dek). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Rna Octamer Containing Dt, PDB code: 5dek:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Rna Octamer Containing Dt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Rna Octamer Containing Dt within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:81.1 occ:1.00 CO B:NCO301 0.0 81.1 1.0 N5 B:NCO301 2.0 69.2 1.0 N6 B:NCO301 2.0 66.1 1.0 N3 B:NCO301 2.0 59.9 1.0 N2 B:NCO301 2.0 55.2 1.0 N4 B:NCO301 2.0 50.7 1.0 N1 B:NCO301 2.0 45.6 1.0 O B:HOH405 3.8 37.9 1.0 OP1 B:A212 4.2 46.7 1.0 OP2 B:A212 4.3 37.8 1.0 P B:A212 4.8 36.2 1.0

Cobalt binding site 2 out of 2 in the Rna Octamer Containing Dt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Rna Octamer Containing Dt within 5.0Å range: probe atom residue distance (Å) B Occ C:Co201 b:0.9 occ:1.00 CO C:NCO201 0.0 0.9 1.0 N1 C:NCO201 2.0 73.3 1.0 N2 C:NCO201 2.0 68.5 1.0 N3 C:NCO201 2.0 68.1 1.0 N4 C:NCO201 2.0 80.2 1.0 N6 C:NCO201 2.0 61.0 1.0 N5 C:NCO201 2.0 56.9 1.0 O C:HOH301 3.8 44.3 1.0 OP2 C:G108 4.7 45.8 1.0

A.V.Kel In, I.Zlatev, J.Harp, M.Jayaraman, A.Bisbe, J.O Shea, N.Taneja, R.M.Manoharan, S.Khan, K.Charisse, M.A.Maier, M.Egli, K.G.Rajeev, M.Manoharan. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. J.Org.Chem. V. 81 2261 2016.
ISSN: ISSN 0022-3263
PubMed: 26940174
DOI: 10.1021/ACS.JOC.5B02375