Cobalt in PDB 3fl6: Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)

The structure of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc), PDB code: 3fl6 was solved by K.Robeyns, P.Herdewijn, L.Van Meervelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 1.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.720, 33.570, 81.200, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / n/a

The binding sites of Cobalt atom in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) (pdb code 3fl6). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc), PDB code: 3fl6:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co63 b:10.3 occ:0.78 CO A:NCO63 0.0 10.3 0.8 CO A:NCO63 1.2 13.6 0.2 N6 A:NCO63 1.5 13.1 0.2 N3 A:NCO63 1.6 13.0 0.2 N2 A:NCO63 1.7 13.1 0.2 N6 A:NCO63 1.9 11.9 0.8 N3 A:NCO63 1.9 11.6 0.8 N1 A:NCO63 1.9 12.3 0.8 N4 A:NCO63 1.9 12.3 0.8 N5 A:NCO63 2.0 11.7 0.8 N2 A:NCO63 2.0 12.0 0.8 N4 A:NCO63 2.7 13.3 0.2 N1 A:NCO63 2.8 13.4 0.2 N5 A:NCO63 2.9 13.3 0.2 O A:HOH165 4.1 17.3 1.0 O D:HOH213 4.6 15.6 0.5 OP1 A:XTR4 4.6 18.1 0.5 OP2 A:XTR4 4.9 17.5 0.5

Cobalt binding site 2 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co63 b:13.6 occ:0.22 CO A:NCO63 0.0 13.6 0.2 CO A:NCO63 1.2 10.3 0.8 N5 A:NCO63 1.2 11.7 0.8 N1 A:NCO63 1.8 12.3 0.8 N4 A:NCO63 1.8 12.3 0.8 N6 A:NCO63 1.9 13.1 0.2 N1 A:NCO63 1.9 13.4 0.2 N3 A:NCO63 1.9 13.0 0.2 N5 A:NCO63 1.9 13.3 0.2 N4 A:NCO63 1.9 13.3 0.2 N2 A:NCO63 2.0 13.1 0.2 N2 A:NCO63 2.7 12.0 0.8 N3 A:NCO63 2.7 11.6 0.8 N6 A:NCO63 3.0 11.9 0.8 O A:HOH165 4.5 17.3 1.0 OP1 A:XTR4 4.8 18.1 0.5 O A:HOH206 4.8 22.7 0.5

Cobalt binding site 3 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co61 b:6.5 occ:1.00 CO B:NCO61 0.0 6.5 1.0 N1 B:NCO61 1.9 7.0 1.0 N6 B:NCO61 1.9 7.1 1.0 N3 B:NCO61 1.9 7.2 1.0 N5 B:NCO61 1.9 7.3 1.0 N2 B:NCO61 2.0 8.0 1.0 N4 B:NCO61 2.0 6.2 1.0 O B:HOH106 3.8 8.6 1.0 OP1 B:DA4 4.0 9.6 1.0 O B:HOH133 4.4 20.0 1.0 O B:HOH122 4.4 20.9 1.0 P B:DA4 4.6 7.2 1.0 OP2 B:DA4 4.6 7.3 1.0 O B:HOH176 4.7 24.1 1.0 O3' B:DC3 4.8 7.5 1.0

Cobalt binding site 4 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co65 b:11.3 occ:0.59 CO B:NCO65 0.0 11.3 0.6 N1 B:NCO65 1.9 10.7 0.6 N3 B:NCO65 1.9 12.0 0.6 N6 B:NCO65 1.9 11.7 0.6 N4 B:NCO65 1.9 10.4 0.6 N5 B:NCO65 1.9 10.9 0.6 N2 B:NCO65 2.0 11.7 0.6 OP1 B:DC5 3.8 11.4 1.0 OP2 B:DC5 4.5 10.1 1.0 P B:DC5 4.7 9.0 1.0

Cobalt binding site 5 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co64 b:10.9 occ:0.64 CO C:NCO64 0.0 10.9 0.6 N6 C:NCO64 1.9 12.2 0.6 N3 C:NCO64 1.9 12.5 0.6 N1 C:NCO64 1.9 10.6 0.6 N4 C:NCO64 1.9 12.2 0.6 N5 C:NCO64 1.9 12.3 0.6 N2 C:NCO64 2.0 11.7 0.6 O A:HOH101 3.8 12.5 1.0 N7 C:DG7 4.1 9.9 1.0 O C:HOH139 4.1 17.3 1.0 O C:HOH188 4.4 30.7 1.0 O6 C:DG7 4.4 12.7 1.0 O C:HOH143 4.6 16.3 1.0 OP2 C:DG7 4.8 9.5 1.0 C5 C:DG7 5.0 9.3 1.0

Cobalt binding site 6 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co66 b:7.3 occ:0.25 CO C:NCO66 0.0 7.3 0.2 N6 C:NCO66 1.9 7.6 0.2 N1 C:NCO66 1.9 7.6 0.2 N3 C:NCO66 1.9 7.4 0.2 N5 C:NCO66 1.9 7.7 0.2 N4 C:NCO66 1.9 8.0 0.2 N2 C:NCO66 2.0 7.3 0.2 O C:HOH189 4.1 29.1 1.0

Cobalt binding site 7 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co67 b:16.1 occ:0.46 CO C:NCO67 0.0 16.1 0.5 N1 C:NCO67 1.9 13.9 0.5 N2 C:NCO67 1.9 13.7 0.5 OP1 C:DC2 3.7 24.6 1.0 P C:DC2 5.0 18.9 1.0

Cobalt binding site 8 out of 8 in the Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Influence of the Incorporation of A Cyclohexenyl Nucleic Acid (Cena) Residue Onto the Sequence D(Gcgtgcg)/D(Cgcacgc) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co62 b:7.2 occ:1.00 CO D:NCO62 0.0 7.2 1.0 N6 D:NCO62 1.9 9.2 1.0 N3 D:NCO62 1.9 8.9 1.0 N4 D:NCO62 1.9 8.3 1.0 N1 D:NCO62 1.9 8.1 1.0 N5 D:NCO62 2.0 8.2 1.0 N2 D:NCO62 2.0 8.3 1.0 N7 D:DG2 4.0 6.8 1.0 OP1 D:DG2 4.3 15.2 1.0 O6 D:DG2 4.5 7.0 1.0 C5 D:DG2 4.9 5.9 1.0 C8 D:DG2 4.9 7.2 1.0 O D:HOH134 4.9 20.7 1.0

K.Robeyns, P.Herdewijn, L.Van Meervelt. Direct Observation of Two Cyclohexenyl (Cena) Ring Conformations in Duplex Dna. Artif Dna Pna Xna V. 1 2 2010.
ISSN: ESSN 1949-0968
PubMed: 21687521
DOI: 10.4161/ADNA.1.1.10952