Cobalt in PDB 5d8t: Rna Octamer Containing (S)-5' Methyl, 2'-F U.

The structure of Rna Octamer Containing (S)-5' Methyl, 2'-F U., PDB code: 5d8t 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)	29.24 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	31.172, 31.172, 84.325, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 15.7

The structure of Rna Octamer Containing (S)-5' Methyl, 2'-F U. also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Bromine	(Br)	2 atoms

The binding sites of Cobalt atom in the Rna Octamer Containing (S)-5' Methyl, 2'-F U. (pdb code 5d8t). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Rna Octamer Containing (S)-5' Methyl, 2'-F U., PDB code: 5d8t:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Rna Octamer Containing (S)-5' Methyl, 2'-F U.


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 (S)-5' Methyl, 2'-F U. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:11.1 occ:1.00 CO A:NCO101 0.0 11.1 1.0 N1 A:NCO101 2.0 13.7 1.0 N2 A:NCO101 2.0 14.6 1.0 N6 A:NCO101 2.0 11.6 1.0 N3 A:NCO101 2.0 12.5 1.0 N5 A:NCO101 2.0 10.6 1.0 N4 A:NCO101 2.0 14.8 1.0 HN13 A:NCO101 2.5 14.3 1.0 HN21 A:NCO101 2.5 14.3 1.0 HN11 A:NCO101 2.5 14.3 1.0 HN12 A:NCO101 2.5 14.5 1.0 HN23 A:NCO101 2.5 15.9 1.0 HN22 A:NCO101 2.5 14.9 1.0 HN62 A:NCO101 2.5 12.8 1.0 HN61 A:NCO101 2.5 13.2 1.0 HN63 A:NCO101 2.5 13.3 1.0 HN32 A:NCO101 2.5 13.8 1.0 HN52 A:NCO101 2.6 12.2 1.0 HN33 A:NCO101 2.6 13.3 1.0 HN31 A:NCO101 2.6 13.7 1.0 HN42 A:NCO101 2.6 14.4 1.0 HN43 A:NCO101 2.6 15.2 1.0 HN51 A:NCO101 2.6 12.8 1.0 HN53 A:NCO101 2.6 11.8 1.0 HN41 A:NCO101 2.6 15.3 1.0 O A:HOH225 4.0 23.9 1.0 O B:HOH222 4.0 13.9 1.0 O A:HOH236 4.0 24.9 1.0 O A:HOH223 4.0 12.5 1.0 O A:HOH237 4.2 14.7 1.0 OP2 A:A3 4.2 11.3 1.0 O A:HOH210 4.3 17.2 1.0 O4 A:U5M5 4.3 9.2 1.0 O A:HOH220 4.4 27.5 1.0 O A:HOH230 4.4 14.6 1.0 O A:HOH233 4.4 26.1 1.0 H5 A:U5M5 4.8 8.8 1.0 O A:HOH244 4.8 28.2 1.0

Cobalt binding site 2 out of 4 in the Rna Octamer Containing (S)-5' Methyl, 2'-F U.


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 (S)-5' Methyl, 2'-F U. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:17.4 occ:1.00 CO A:NCO102 0.0 17.4 1.0 N1 A:NCO102 1.9 17.7 1.0 N2 A:NCO102 2.0 21.1 1.0 N5 A:NCO102 2.0 23.7 1.0 N4 A:NCO102 2.0 23.7 1.0 N6 A:NCO102 2.0 18.0 1.0 N3 A:NCO102 2.0 17.0 1.0 HN13 A:NCO102 2.5 18.2 1.0 HN12 A:NCO102 2.5 18.1 1.0 HN11 A:NCO102 2.5 18.2 1.0 HN51 A:NCO102 2.5 22.1 1.0 HN42 A:NCO102 2.5 22.9 1.0 HN52 A:NCO102 2.5 22.4 1.0 HN22 A:NCO102 2.5 20.5 1.0 HN21 A:NCO102 2.5 21.0 1.0 HN43 A:NCO102 2.5 20.4 1.0 HN23 A:NCO102 2.5 18.2 1.0 HN41 A:NCO102 2.5 21.2 1.0 HN53 A:NCO102 2.5 21.4 1.0 HN61 A:NCO102 2.5 18.1 1.0 HN62 A:NCO102 2.5 18.2 1.0 HN63 A:NCO102 2.5 18.4 1.0 HN32 A:NCO102 2.6 16.8 1.0 HN33 A:NCO102 2.6 18.6 1.0 HN31 A:NCO102 2.6 16.2 1.0 OP1 A:A4 4.0 9.7 1.0 O A:HOH240 4.0 53.1 1.0 O A:HOH242 4.1 31.2 1.0 OP2 A:U5M5 4.4 11.6 1.0

Cobalt binding site 3 out of 4 in the Rna Octamer Containing (S)-5' Methyl, 2'-F U.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Rna Octamer Containing (S)-5' Methyl, 2'-F U. within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:11.5 occ:1.00 CO B:NCO101 0.0 11.5 1.0 N3 B:NCO101 1.9 14.8 1.0 N1 B:NCO101 2.0 13.3 1.0 N4 B:NCO101 2.0 12.4 1.0 N6 B:NCO101 2.0 12.2 1.0 N5 B:NCO101 2.0 12.1 1.0 N2 B:NCO101 2.0 9.8 1.0 HN33 B:NCO101 2.4 13.4 1.0 HN32 B:NCO101 2.4 13.4 1.0 HN31 B:NCO101 2.4 14.3 1.0 HN13 B:NCO101 2.5 13.0 1.0 HN12 B:NCO101 2.5 12.7 1.0 HN43 B:NCO101 2.5 12.3 1.0 HN41 B:NCO101 2.5 12.1 1.0 HN62 B:NCO101 2.5 12.1 1.0 HN63 B:NCO101 2.5 12.7 1.0 HN11 B:NCO101 2.5 12.9 1.0 HN42 B:NCO101 2.5 12.6 1.0 HN53 B:NCO101 2.5 11.6 1.0 HN51 B:NCO101 2.5 12.7 1.0 HN52 B:NCO101 2.5 12.4 1.0 HN61 B:NCO101 2.5 12.0 1.0 HN23 B:NCO101 2.6 9.8 1.0 HN21 B:NCO101 2.6 10.4 1.0 HN22 B:NCO101 2.6 10.3 1.0 OP2 B:A3 3.7 9.2 1.0 O A:HOH238 3.9 16.1 1.0 O A:HOH215 3.9 15.2 1.0 O B:HOH241 3.9 22.9 1.0 O B:HOH229 4.1 10.9 1.0 O B:HOH230 4.2 15.4 1.0 O B:HOH247 4.2 20.3 1.0 O5' A:CBV1 4.3 10.6 1.0 O B:HOH225 4.5 18.4 1.0 OP2 A:G2 4.5 10.6 1.0 OP2 B:G2 4.7 12.4 1.0

Cobalt binding site 4 out of 4 in the Rna Octamer Containing (S)-5' Methyl, 2'-F U.


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Rna Octamer Containing (S)-5' Methyl, 2'-F U. within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:14.5 occ:1.00 CO B:NCO102 0.0 14.5 1.0 N3 B:NCO102 2.0 18.1 1.0 N2 B:NCO102 2.0 20.1 1.0 N6 B:NCO102 2.0 27.7 1.0 N4 B:NCO102 2.0 20.0 1.0 N5 B:NCO102 2.0 21.5 1.0 N1 B:NCO102 2.0 14.9 1.0 HN31 B:NCO102 2.5 18.8 1.0 HN23 B:NCO102 2.5 19.0 1.0 HN32 B:NCO102 2.5 17.8 1.0 HN33 B:NCO102 2.5 16.1 1.0 HN21 B:NCO102 2.5 19.3 1.0 HN42 B:NCO102 2.5 19.0 1.0 HN22 B:NCO102 2.5 19.5 1.0 HN61 B:NCO102 2.5 24.6 1.0 HN43 B:NCO102 2.5 18.3 1.0 HN41 B:NCO102 2.5 19.2 1.0 HN63 B:NCO102 2.5 24.0 1.0 HN62 B:NCO102 2.5 25.3 1.0 HN52 B:NCO102 2.5 20.0 1.0 HN53 B:NCO102 2.5 19.5 1.0 HN51 B:NCO102 2.5 19.9 1.0 HN12 B:NCO102 2.5 15.9 1.0 HN13 B:NCO102 2.6 15.4 1.0 HN11 B:NCO102 2.6 15.6 1.0 O B:HOH215 4.1 31.9 1.0 O B:HOH224 4.1 17.9 1.0 O B:HOH225 4.4 18.4 1.0 O B:HOH247 4.7 20.3 1.0 O B:HOH206 4.8 18.0 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