Cobalt in PDB 8bag: Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine

The structure of Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine, PDB code: 8bag 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)	29.43 / 1.13
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	21.99, 58.87, 45.46, 90, 90, 90
R / Rfree (%)	15.2 / 17.2

The structure of Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Cobalt atom in the Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine (pdb code 8bag). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine, PDB code: 8bag:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:11.0 occ:1.00 CO A:NCO101 0.0 11.0 1.0 N5 A:NCO101 2.0 11.6 1.0 N4 A:NCO101 2.0 13.3 1.0 N6 A:NCO101 2.0 14.0 1.0 N3 A:NCO101 2.0 12.7 1.0 N1 A:NCO101 2.0 12.7 1.0 N2 A:NCO101 2.0 12.4 1.0 HN53 A:NCO101 2.5 13.9 1.0 HN52 A:NCO101 2.5 13.9 1.0 HN51 A:NCO101 2.5 13.9 1.0 HN41 A:NCO101 2.5 16.0 1.0 HN43 A:NCO101 2.5 16.0 1.0 HN42 A:NCO101 2.5 16.0 1.0 HN61 A:NCO101 2.5 16.8 1.0 HN63 A:NCO101 2.5 16.8 1.0 HN62 A:NCO101 2.5 16.8 1.0 HN32 A:NCO101 2.5 15.2 1.0 HN31 A:NCO101 2.5 15.2 1.0 HN33 A:NCO101 2.5 15.2 1.0 HN12 A:NCO101 2.5 15.2 1.0 HN13 A:NCO101 2.5 15.2 1.0 HN11 A:NCO101 2.5 15.2 1.0 HN22 A:NCO101 2.5 14.9 1.0 HN21 A:NCO101 2.5 14.9 1.0 HN23 A:NCO101 2.5 14.9 1.0 O A:HOH207 4.1 14.2 0.9 OP2 A:DA3 4.2 12.1 1.0 O A:HOH214 4.2 16.8 1.0 O A:HOH213 4.2 37.8 0.9 OP1 A:DA3 4.2 14.7 1.0 O A:HOH209 4.3 14.6 0.9 O A:HOH212 4.7 29.1 0.7 P A:DA3 4.7 12.4 1.0

Cobalt binding site 2 out of 5 in the Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:11.4 occ:0.15 CO A:NCO102 0.0 11.4 0.1 N2 A:NCO102 0.4 42.1 0.6 HN23 A:NCO102 1.2 50.5 0.6 HN22 A:NCO102 1.2 50.5 0.6 HN21 A:NCO102 1.3 50.5 0.6 CO A:NCO102 1.6 40.5 0.6 N6 A:NCO102 2.0 12.5 0.1 N2 A:NCO102 2.0 15.7 0.1 N5 A:NCO102 2.0 13.3 0.1 N1 A:NCO102 2.0 17.2 0.1 N4 A:NCO102 2.0 14.2 0.1 N3 A:NCO102 2.0 12.6 0.1 HN41 A:NCO102 2.4 49.5 0.6 N4 A:NCO102 2.4 41.2 0.6 HN32 A:NCO102 2.5 50.7 0.6 HN53 A:NCO102 2.5 49.8 0.6 N3 A:NCO102 2.5 42.2 0.6 HN63 A:NCO102 2.5 15.1 0.1 N5 A:NCO102 2.5 41.5 0.6 HN12 A:NCO102 2.5 20.7 0.1 HN21 A:NCO102 2.5 18.9 0.1 HN52 A:NCO102 2.5 15.9 0.1 HN32 A:NCO102 2.5 15.1 0.1 HN41 A:NCO102 2.5 17.1 0.1 HN22 A:NCO102 2.5 18.9 0.1 HN51 A:NCO102 2.5 15.9 0.1 HN43 A:NCO102 2.5 17.1 0.1 HN13 A:NCO102 2.5 20.7 0.1 HN53 A:NCO102 2.5 15.9 0.1 HN42 A:NCO102 2.5 17.1 0.1 HN23 A:NCO102 2.5 18.9 0.1 HN33 A:NCO102 2.5 15.1 0.1 HN61 A:NCO102 2.5 15.1 0.1 HN62 A:NCO102 2.5 15.1 0.1 HN11 A:NCO102 2.5 20.7 0.1 HN31 A:NCO102 2.5 15.1 0.1 N6 A:NCO102 2.6 39.6 0.6 HN63 A:NCO102 2.7 47.6 0.6 HN43 A:NCO102 2.8 49.5 0.6 HN61 A:NCO102 2.9 47.6 0.6 HN31 A:NCO102 3.0 50.7 0.6 HN51 A:NCO102 3.0 49.8 0.6 HN42 A:NCO102 3.3 49.5 0.6 HN33 A:NCO102 3.4 50.7 0.6 HN52 A:NCO102 3.4 49.8 0.6 HN62 A:NCO102 3.5 47.6 0.6 N1 A:NCO102 3.5 38.3 0.6 O B:HOH211 3.9 18.0 1.0 O A:HOH206 3.9 19.3 0.9 HN12 A:NCO102 4.0 46.0 0.6 HN13 A:NCO102 4.0 46.0 0.6 HN11 A:NCO102 4.0 46.0 0.6 OP2 A:DT4 4.7 26.4 1.0

Cobalt binding site 3 out of 5 in the Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:40.5 occ:0.55 CO A:NCO102 0.0 40.5 0.6 N1 A:NCO102 1.1 17.2 0.1 HN12 A:NCO102 1.2 20.7 0.1 HN13 A:NCO102 1.5 20.7 0.1 CO A:NCO102 1.6 11.4 0.1 HN43 A:NCO102 1.6 17.1 0.1 N4 A:NCO102 1.8 14.2 0.1 N2 A:NCO102 2.0 42.1 0.6 N6 A:NCO102 2.0 39.6 0.6 N4 A:NCO102 2.0 41.2 0.6 N5 A:NCO102 2.0 41.5 0.6 N3 A:NCO102 2.0 42.2 0.6 N1 A:NCO102 2.0 38.3 0.6 HN11 A:NCO102 2.1 20.7 0.1 HN33 A:NCO102 2.2 15.1 0.1 N3 A:NCO102 2.3 12.6 0.1 HN42 A:NCO102 2.5 17.1 0.1 HN21 A:NCO102 2.5 50.5 0.6 HN23 A:NCO102 2.5 50.5 0.6 HN22 A:NCO102 2.5 50.5 0.6 HN63 A:NCO102 2.5 47.6 0.6 HN61 A:NCO102 2.5 47.6 0.6 HN62 A:NCO102 2.5 47.6 0.6 HN13 A:NCO102 2.5 46.0 0.6 HN41 A:NCO102 2.5 49.5 0.6 HN43 A:NCO102 2.5 49.5 0.6 HN51 A:NCO102 2.5 49.8 0.6 HN42 A:NCO102 2.5 49.5 0.6 HN11 A:NCO102 2.5 46.0 0.6 HN53 A:NCO102 2.5 49.8 0.6 HN52 A:NCO102 2.5 49.8 0.6 HN32 A:NCO102 2.5 50.7 0.6 HN33 A:NCO102 2.5 50.7 0.6 HN31 A:NCO102 2.5 50.7 0.6 HN12 A:NCO102 2.5 46.0 0.6 HN52 A:NCO102 2.6 15.9 0.1 HN41 A:NCO102 2.6 17.1 0.1 N5 A:NCO102 2.7 13.3 0.1 HN32 A:NCO102 3.1 15.1 0.1 HN31 A:NCO102 3.1 15.1 0.1 N6 A:NCO102 3.1 12.5 0.1 HN62 A:NCO102 3.2 15.1 0.1 HN53 A:NCO102 3.3 15.9 0.1 HN51 A:NCO102 3.4 15.9 0.1 N2 A:NCO102 3.4 15.7 0.1 HN61 A:NCO102 3.5 15.1 0.1 OP2 A:DT4 3.6 26.4 1.0 HN23 A:NCO102 3.7 18.9 0.1 HN22 A:NCO102 3.8 18.9 0.1 HN63 A:NCO102 3.8 15.1 0.1 OP1 A:DT4 4.0 26.7 1.0 HN21 A:NCO102 4.1 18.9 0.1 O A:HOH210 4.1 31.4 1.0 O A:HOH206 4.3 19.3 0.9 P A:DT4 4.3 24.2 1.0 O B:HOH211 4.4 18.0 1.0

Cobalt binding site 4 out of 5 in the Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:58.0 occ:1.00 CO A:NCO103 0.0 58.0 1.0 N1 A:NCO103 2.0 56.2 1.0 N6 A:NCO103 2.0 56.7 1.0 N3 A:NCO103 2.0 58.6 1.0 N2 A:NCO103 2.0 56.1 1.0 N4 A:NCO103 2.0 56.6 1.0 N5 A:NCO103 2.0 58.1 1.0 HN12 A:NCO103 2.5 67.5 1.0 HN13 A:NCO103 2.5 67.5 1.0 HN11 A:NCO103 2.5 67.5 1.0 HN62 A:NCO103 2.5 68.1 1.0 HN61 A:NCO103 2.5 68.1 1.0 HN63 A:NCO103 2.5 68.1 1.0 HN33 A:NCO103 2.5 70.4 1.0 HN32 A:NCO103 2.5 70.4 1.0 HN31 A:NCO103 2.5 70.4 1.0 HN23 A:NCO103 2.5 67.3 1.0 HN21 A:NCO103 2.5 67.3 1.0 HN22 A:NCO103 2.5 67.3 1.0 HN43 A:NCO103 2.5 67.9 1.0 HN41 A:NCO103 2.5 67.9 1.0 HN42 A:NCO103 2.5 67.9 1.0 HN53 A:NCO103 2.5 69.8 1.0 HN52 A:NCO103 2.5 69.8 1.0 HN51 A:NCO103 2.5 69.8 1.0 OP1 A:DC6 3.7 34.0 1.0 OP1 A:DC2 3.8 28.9 1.0 O A:HOH216 4.4 36.1 0.8 O A:HOH218 4.6 42.5 0.5 O3' A:DG5 4.8 25.6 1.0 P A:DC2 4.9 26.6 1.0 P A:DC6 4.9 29.9 1.0 O3' A:8OG1 4.9 26.6 1.0

Cobalt binding site 5 out of 5 in the Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Copper(II) Bound to A Non-Canonical Quadruplex Containing the Damaged Base 8-Oxoguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:31.8 occ:0.50 CO A:NCO104 0.0 31.8 0.5 N1 A:NCO104 2.0 30.5 0.5 N2 A:NCO104 2.0 30.8 0.5 N3 A:NCO104 2.0 31.0 0.5 N5 A:NCO104 2.0 32.3 0.5 N6 A:NCO104 2.0 31.1 0.5 N4 A:NCO104 2.0 32.6 0.5 HN12 A:NCO104 2.5 36.6 0.5 HN13 A:NCO104 2.5 36.6 0.5 HN11 A:NCO104 2.5 36.6 0.5 HN23 A:NCO104 2.5 37.0 0.5 HN22 A:NCO104 2.5 37.0 0.5 HN21 A:NCO104 2.5 37.0 0.5 HN32 A:NCO104 2.5 37.2 0.5 HN31 A:NCO104 2.5 37.2 0.5 HN33 A:NCO104 2.5 37.2 0.5 HN62 A:NCO104 2.5 37.3 0.5 HN52 A:NCO104 2.5 38.8 0.5 HN53 A:NCO104 2.5 38.8 0.5 HN51 A:NCO104 2.5 38.8 0.5 HN61 A:NCO104 2.5 37.3 0.5 HN63 A:NCO104 2.5 37.3 0.5 HN41 A:NCO104 2.5 39.1 0.5 HN43 A:NCO104 2.5 39.1 0.5 HN42 A:NCO104 2.5 39.1 0.5

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