Cobalt in PDB 8baf: Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine

The structure of Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine, PDB code: 8baf was solved by M.C.Lambert, J.P.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.79 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	22.035, 58.846, 45.488, 90, 90, 90
R / Rfree (%)	18.6 / 19.7

The binding sites of Cobalt atom in the Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine (pdb code 8baf). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine, PDB code: 8baf:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:6.0 occ:1.00 CO A:NCO101 0.0 6.0 1.0 N2 A:NCO101 1.9 7.1 1.0 N5 A:NCO101 2.0 7.9 1.0 N4 A:NCO101 2.0 8.0 1.0 N6 A:NCO101 2.0 7.8 1.0 N1 A:NCO101 2.0 7.0 1.0 N3 A:NCO101 2.0 7.5 1.0 HN22 A:NCO101 2.5 8.5 1.0 HN21 A:NCO101 2.5 8.5 1.0 HN23 A:NCO101 2.5 8.5 1.0 HN53 A:NCO101 2.5 9.5 1.0 HN52 A:NCO101 2.5 9.5 1.0 HN51 A:NCO101 2.5 9.5 1.0 HN41 A:NCO101 2.5 9.6 1.0 HN43 A:NCO101 2.5 9.6 1.0 HN42 A:NCO101 2.5 9.6 1.0 HN61 A:NCO101 2.5 9.4 1.0 HN63 A:NCO101 2.5 9.4 1.0 HN62 A:NCO101 2.5 9.4 1.0 HN12 A:NCO101 2.5 8.4 1.0 HN11 A:NCO101 2.5 8.4 1.0 HN13 A:NCO101 2.5 8.4 1.0 HN32 A:NCO101 2.5 9.0 1.0 HN33 A:NCO101 2.5 9.0 1.0 HN31 A:NCO101 2.5 9.0 1.0 OP1 A:DA3 4.1 7.1 1.0 O A:HOH214 4.1 10.0 1.0 O A:HOH213 4.2 19.2 1.0 OP2 A:DA3 4.3 7.3 1.0 O A:HOH211 4.3 8.5 1.0 P A:DA3 4.7 6.2 1.0

Cobalt binding site 2 out of 4 in the Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:14.4 occ:0.41 CO A:NCO102 0.0 14.4 0.4 N5 A:NCO102 2.0 18.5 0.4 N1 A:NCO102 2.0 17.0 0.4 N2 A:NCO102 2.0 17.0 0.4 N3 A:NCO102 2.0 20.4 0.4 N6 A:NCO102 2.0 16.5 0.4 N4 A:NCO102 2.0 16.5 0.4 HN53 A:NCO102 2.5 22.3 0.4 HN52 A:NCO102 2.5 22.3 0.4 HN51 A:NCO102 2.5 22.3 0.4 HN12 A:NCO102 2.5 20.5 0.4 HN11 A:NCO102 2.5 20.5 0.4 HN13 A:NCO102 2.5 20.5 0.4 HN23 A:NCO102 2.5 20.5 0.4 HN22 A:NCO102 2.5 20.5 0.4 HN21 A:NCO102 2.5 20.5 0.4 HN32 A:NCO102 2.5 24.6 0.4 HN33 A:NCO102 2.5 24.6 0.4 HN31 A:NCO102 2.5 24.6 0.4 HN62 A:NCO102 2.5 19.8 0.4 HN61 A:NCO102 2.5 19.8 0.4 HN63 A:NCO102 2.5 19.8 0.4 HN41 A:NCO102 2.5 19.8 0.4 HN42 A:NCO102 2.5 19.8 0.4 HN43 A:NCO102 2.5 19.8 0.4 O A:HOH207 3.9 13.4 1.0 O B:HOH116 4.0 10.7 1.0 OP2 A:DT4 4.8 19.0 1.0

Cobalt binding site 3 out of 4 in the Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:39.6 occ:1.00 CO A:NCO103 0.0 39.6 1.0 N3 A:NCO103 2.0 35.0 1.0 N4 A:NCO103 2.0 30.2 1.0 N2 A:NCO103 2.0 27.3 1.0 N1 A:NCO103 2.0 33.4 1.0 N6 A:NCO103 2.0 25.1 1.0 N5 A:NCO103 2.0 25.8 1.0 HN33 A:NCO103 2.5 42.1 1.0 HN31 A:NCO103 2.5 42.1 1.0 HN43 A:NCO103 2.5 36.3 1.0 HN41 A:NCO103 2.5 36.3 1.0 HN42 A:NCO103 2.5 36.3 1.0 HN32 A:NCO103 2.5 42.1 1.0 HN22 A:NCO103 2.5 32.8 1.0 HN21 A:NCO103 2.5 32.8 1.0 HN11 A:NCO103 2.5 40.1 1.0 HN12 A:NCO103 2.5 40.1 1.0 HN13 A:NCO103 2.5 40.1 1.0 HN23 A:NCO103 2.5 32.8 1.0 HN63 A:NCO103 2.5 30.2 1.0 HN62 A:NCO103 2.5 30.2 1.0 HN61 A:NCO103 2.5 30.2 1.0 HN53 A:NCO103 2.5 31.1 1.0 HN51 A:NCO103 2.5 31.1 1.0 HN52 A:NCO103 2.5 31.1 1.0 OP1 A:DC2 3.8 15.9 1.0 OP1 A:DC6 4.0 28.5 1.0 P A:DC2 4.8 14.3 1.0 O3' A:DG5 4.9 18.9 1.0 O3' A:8OG1 4.9 15.6 1.0

Cobalt binding site 4 out of 4 in the Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Non-Canonical Quadruplex Containing the Oxidation Product 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:51.9 occ:1.00 CO A:NCO104 0.0 51.9 1.0 N6 A:NCO104 2.0 40.1 1.0 N3 A:NCO104 2.0 33.7 1.0 N1 A:NCO104 2.0 41.9 1.0 N4 A:NCO104 2.0 33.8 1.0 N5 A:NCO104 2.0 39.0 1.0 N2 A:NCO104 2.0 35.8 1.0 HN63 A:NCO104 2.5 48.2 1.0 HN61 A:NCO104 2.5 48.2 1.0 HN62 A:NCO104 2.5 48.2 1.0 HN32 A:NCO104 2.5 40.5 1.0 HN31 A:NCO104 2.5 40.5 1.0 HN33 A:NCO104 2.5 40.5 1.0 HN13 A:NCO104 2.5 50.4 1.0 HN11 A:NCO104 2.5 50.4 1.0 HN12 A:NCO104 2.5 50.4 1.0 HN42 A:NCO104 2.5 40.6 1.0 HN43 A:NCO104 2.5 40.6 1.0 HN41 A:NCO104 2.5 40.6 1.0 HN53 A:NCO104 2.5 46.9 1.0 HN52 A:NCO104 2.5 46.9 1.0 HN51 A:NCO104 2.5 46.9 1.0 HN22 A:NCO104 2.5 43.0 1.0 HN23 A:NCO104 2.5 43.0 1.0 HN21 A:NCO104 2.5 43.0 1.0 OP2 A:DC6 4.4 26.6 1.0

M.C.Lambert, J.A.Brazier, C.J.Cardin, J.P.Hall. Oxidative Damage Induce Copper(II)-Dna Binding To Be Published.