Cobalt in PDB 4f2x: Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer

The structure of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer, PDB code: 4f2x was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.08 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.700, 33.862, 80.165, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 25.1

The structure of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Cobalt atom in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer (pdb code 4f2x). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer, PDB code: 4f2x:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:19.2 occ:1.00 CO A:NCO101 0.0 19.2 1.0 N3 A:NCO101 2.0 24.9 1.0 N4 A:NCO101 2.0 22.6 1.0 N6 A:NCO101 2.0 19.4 1.0 N5 A:NCO101 2.0 20.7 1.0 N2 A:NCO101 2.0 20.1 1.0 N1 A:NCO101 2.0 21.3 1.0 OP1 D:DC3 3.9 24.2 1.0 O6 A:DG1 4.1 18.4 1.0 O B:HOH205 4.1 25.0 1.0 N7 A:DG1 4.2 20.6 1.0 O B:HOH212 4.2 22.6 1.0 O A:HOH202 4.3 32.4 1.0 C6 A:DG1 4.8 18.5 1.0 C5 A:DG1 4.9 19.8 1.0

Cobalt binding site 2 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:20.4 occ:1.00 CO B:NCO101 0.0 20.4 1.0 N1 B:NCO101 1.9 20.9 1.0 N6 B:NCO101 2.0 24.0 1.0 N2 B:NCO101 2.0 20.9 1.0 N3 B:NCO101 2.0 25.5 1.0 N4 B:NCO101 2.0 20.4 1.0 N5 B:NCO101 2.0 19.6 1.0 O B:HOH201 3.9 23.9 1.0 OP1 B:DA4 3.9 26.5 1.0 O6 D:DG6 4.0 18.6 1.0 O6 C:DG1 4.2 22.1 1.0 O B:HOH232 4.4 33.8 1.0 N7 D:DG6 4.4 19.4 1.0 O B:HOH217 4.4 32.2 1.0 O B:HOH218 4.5 40.0 1.0 P B:DA4 4.6 24.0 1.0 OP2 B:DA4 4.6 23.6 1.0 C6 D:DG6 4.7 19.4 1.0 O3' B:DC3 4.8 23.1 1.0 O B:HOH220 4.8 61.4 1.0 C5 D:DG6 4.9 19.2 1.0

Cobalt binding site 3 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:31.5 occ:0.50 CO B:3CO103 1.7 38.8 0.5 OP2 B:DC5 4.0 22.5 1.0 OP1 B:DC5 4.3 25.1 1.0 OP1 D:DC5 4.3 21.7 1.0 P B:DC5 4.6 21.7 1.0 O B:HOH214 4.9 27.6 1.0

Cobalt binding site 4 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Co103 b:38.8 occ:0.50 CO B:3CO102 1.7 31.5 0.5 OP1 D:DC5 4.0 21.7 1.0 OP1 B:DC5 4.2 25.1 1.0 OP2 B:DC5 4.9 22.5 1.0

Cobalt binding site 5 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Co104 b:21.9 occ:0.50 CO B:3CO105 2.1 38.1 0.5 O5' B:DC1 3.7 25.9 1.0 O B:HOH230 4.1 41.4 1.0 C5' B:DC1 4.9 25.1 1.0

Cobalt binding site 6 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Co105 b:38.1 occ:0.50 CO B:3CO104 2.1 21.9 0.5 O5' B:DC1 4.6 25.9 1.0

Cobalt binding site 7 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co101 b:29.4 occ:0.50 CO C:3CO102 1.7 57.1 0.5 OP1 C:XTF4 4.1 40.6 1.0 OP2 C:XTF4 4.5 40.2 1.0 P C:XTF4 4.6 38.7 1.0 O5' C:XTF4 4.8 37.4 1.0

Cobalt binding site 8 out of 8 in the Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co102 b:57.1 occ:0.50 CO C:3CO101 1.7 29.4 0.5

P.P.Seth, J.Yu, A.Jazayeri, P.S.Pallan, C.R.Allerson, M.E.Ostergaard, F.Liu, P.Herdewijn, M.Egli, E.E.Swayze. Synthesis and Antisense Properties of Fluoro Cyclohexenyl Nucleic Acid (F-Cena), A Nuclease Stable Mimic of 2'-Fluoro Rna. J.Org.Chem. V. 77 5074 2012.
ISSN: ISSN 0022-3263
PubMed: 22591005
DOI: 10.1021/JO300594B