Cobalt in PDB 8oe3: Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking

The structure of Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking, PDB code: 8oe3 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)	24.83 / 1.08
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	22.157, 59.156, 45.666, 90, 90, 90
R / Rfree (%)	16.4 / 18.5

The binding sites of Cobalt atom in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking (pdb code 8oe3). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking, PDB code: 8oe3:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:8.5 occ:1.00 CO A:NCO101 0.0 8.5 1.0 N6 A:NCO101 2.0 10.8 1.0 N1 A:NCO101 2.0 10.7 1.0 N5 A:NCO101 2.0 10.2 1.0 N4 A:NCO101 2.0 10.1 1.0 N2 A:NCO101 2.0 10.6 1.0 N3 A:NCO101 2.0 10.6 1.0 HN61 A:NCO101 2.5 12.9 1.0 HN63 A:NCO101 2.5 12.9 1.0 HN62 A:NCO101 2.5 12.9 1.0 HN11 A:NCO101 2.5 12.8 1.0 HN13 A:NCO101 2.5 12.8 1.0 HN12 A:NCO101 2.5 12.8 1.0 HN52 A:NCO101 2.5 12.3 1.0 HN53 A:NCO101 2.5 12.3 1.0 HN51 A:NCO101 2.5 12.3 1.0 HN42 A:NCO101 2.5 12.1 1.0 HN41 A:NCO101 2.5 12.1 1.0 HN43 A:NCO101 2.5 12.1 1.0 HN22 A:NCO101 2.6 12.7 1.0 HN21 A:NCO101 2.6 12.7 1.0 HN23 A:NCO101 2.6 12.7 1.0 HN33 A:NCO101 2.6 12.7 1.0 HN32 A:NCO101 2.6 12.7 1.0 HN31 A:NCO101 2.6 12.7 1.0 O A:HOH215 4.2 13.0 1.0 OP1 A:DA3 4.2 9.3 1.0 O A:HOH219 4.2 21.5 1.0 OP2 A:DA3 4.3 9.0 1.0 O A:HOH218 4.3 28.8 0.8 O A:HOH217 4.4 14.2 1.0 O A:HOH205 4.4 23.3 0.6 P A:DA3 4.8 8.1 1.0

Cobalt binding site 2 out of 6 in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:31.7 occ:1.00 CO A:NCO102 0.0 31.7 1.0 N6 A:NCO102 2.0 30.4 1.0 N4 A:NCO102 2.0 33.0 1.0 N1 A:NCO102 2.0 30.4 1.0 N5 A:NCO102 2.0 34.0 1.0 N2 A:NCO102 2.0 30.8 1.0 N3 A:NCO102 2.0 32.9 1.0 HN62 A:NCO102 2.5 36.5 1.0 HN63 A:NCO102 2.5 36.5 1.0 HN61 A:NCO102 2.5 36.5 1.0 HN42 A:NCO102 2.5 39.6 1.0 HN41 A:NCO102 2.5 39.6 1.0 HN43 A:NCO102 2.5 39.6 1.0 HN12 A:NCO102 2.5 36.4 1.0 HN13 A:NCO102 2.5 36.4 1.0 HN11 A:NCO102 2.5 36.4 1.0 HN51 A:NCO102 2.5 40.8 1.0 HN52 A:NCO102 2.5 40.8 1.0 HN53 A:NCO102 2.5 40.8 1.0 HN22 A:NCO102 2.5 37.0 1.0 HN23 A:NCO102 2.5 37.0 1.0 HN21 A:NCO102 2.5 37.0 1.0 HN32 A:NCO102 2.5 39.5 1.0 HN33 A:NCO102 2.5 39.5 1.0 HN31 A:NCO102 2.5 39.5 1.0 OP1 A:DC2 3.8 21.5 1.0 OP1 A:DC6 3.9 23.3 1.0 O3' A:DG5 4.8 17.7 1.0 O3' A:DG1 4.9 18.9 1.0 P A:DC2 4.9 18.7 1.0 P A:DC6 4.9 19.8 1.0

Cobalt binding site 3 out of 6 in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:91.0 occ:1.00 CO A:NCO103 0.0 91.0 1.0 N1 A:NCO103 2.0 91.0 1.0 N6 A:NCO103 2.0 91.2 1.0 N5 A:NCO103 2.0 90.7 1.0 N4 A:NCO103 2.0 91.4 1.0 N2 A:NCO103 2.0 91.2 1.0 N3 A:NCO103 2.0 91.3 1.0 HN12 A:NCO103 2.5 109.2 1.0 HN13 A:NCO103 2.5 109.2 1.0 HN11 A:NCO103 2.5 109.2 1.0 HN61 A:NCO103 2.5 109.5 1.0 HN63 A:NCO103 2.5 109.5 1.0 HN62 A:NCO103 2.5 109.5 1.0 HN53 A:NCO103 2.5 108.8 1.0 HN52 A:NCO103 2.5 108.8 1.0 HN51 A:NCO103 2.5 108.8 1.0 HN42 A:NCO103 2.5 109.7 1.0 HN41 A:NCO103 2.5 109.7 1.0 HN43 A:NCO103 2.5 109.7 1.0 HN22 A:NCO103 2.5 109.4 1.0 HN21 A:NCO103 2.5 109.4 1.0 HN23 A:NCO103 2.5 109.4 1.0 HN33 A:NCO103 2.5 109.6 1.0 HN31 A:NCO103 2.5 109.6 1.0 HN32 A:NCO103 2.5 109.6 1.0 O A:HOH201 3.8 21.1 0.2 O A:HOH204 4.2 23.1 0.2 O A:HOH202 4.4 30.5 1.0 OP2 A:DC6 4.4 19.9 1.0 O A:HOH209 4.8 31.8 0.7 OP1 A:DC6 5.0 23.3 1.0

Cobalt binding site 4 out of 6 in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:33.0 occ:0.49 CO A:NCO104 0.0 33.0 0.5 N5 A:NCO104 2.0 34.6 0.5 N2 A:NCO104 2.0 33.6 0.5 N1 A:NCO104 2.0 32.9 0.5 N3 A:NCO104 2.0 34.7 0.5 N4 A:NCO104 2.0 33.7 0.5 N6 A:NCO104 2.0 33.7 0.5 HN52 A:NCO104 2.5 41.5 0.5 HN53 A:NCO104 2.5 41.5 0.5 HN51 A:NCO104 2.5 41.5 0.5 HN23 A:NCO104 2.5 40.4 0.5 HN21 A:NCO104 2.5 40.4 0.5 HN22 A:NCO104 2.5 40.4 0.5 HN13 A:NCO104 2.5 39.5 0.5 HN12 A:NCO104 2.5 39.5 0.5 HN11 A:NCO104 2.5 39.5 0.5 HN31 A:NCO104 2.5 41.6 0.5 HN32 A:NCO104 2.5 41.6 0.5 HN33 A:NCO104 2.5 41.6 0.5 HN41 A:NCO104 2.5 40.4 0.5 HN42 A:NCO104 2.5 40.4 0.5 HN43 A:NCO104 2.5 40.4 0.5 HN61 A:NCO104 2.5 40.4 0.5 HN62 A:NCO104 2.5 40.4 0.5 HN63 A:NCO104 2.5 40.4 0.5 O A:HOH212 4.0 16.8 0.8 O B:HOH218 4.1 14.7 0.8 OP2 A:DT4 4.7 21.1 1.0 O A:HOH203 4.9 26.5 0.5

Cobalt binding site 5 out of 6 in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:56.1 occ:0.57 CO A:NCO105 0.0 56.1 0.6 N2 A:NCO105 2.0 56.2 0.6 N6 A:NCO105 2.0 55.6 0.6 N3 A:NCO105 2.0 55.7 0.6 N5 A:NCO105 2.0 56.4 0.6 N1 A:NCO105 2.0 55.7 0.6 N4 A:NCO105 2.0 56.4 0.6 HN23 A:NCO105 2.5 67.4 0.6 HN22 A:NCO105 2.5 67.4 0.6 HN21 A:NCO105 2.5 67.4 0.6 HN63 A:NCO105 2.5 66.7 0.6 HN62 A:NCO105 2.5 66.7 0.6 HN61 A:NCO105 2.5 66.7 0.6 HN33 A:NCO105 2.5 66.8 0.6 HN32 A:NCO105 2.5 66.8 0.6 HN31 A:NCO105 2.5 66.8 0.6 HN53 A:NCO105 2.5 67.7 0.6 HN51 A:NCO105 2.5 67.7 0.6 HN52 A:NCO105 2.5 67.7 0.6 HN12 A:NCO105 2.5 66.9 0.6 HN13 A:NCO105 2.5 66.9 0.6 HN11 A:NCO105 2.5 66.9 0.6 HN42 A:NCO105 2.5 67.7 0.6 HN43 A:NCO105 2.5 67.7 0.6 HN41 A:NCO105 2.5 67.7 0.6 O6 A:DG1 4.5 22.7 1.0 N7 A:DG1 4.6 19.7 1.0 H1' A:DT7 4.7 36.1 1.0 O A:HOH213 4.8 33.4 1.0 H41 A:DC2 4.8 12.4 1.0

Cobalt binding site 6 out of 6 in the Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the Non-Canonical Quadruplex D(Gcatgct) Before Soaking within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:19.5 occ:0.49 CO B:NCO101 0.0 19.5 0.5 N3 B:NCO101 2.0 19.3 0.5 N1 B:NCO101 2.0 19.0 0.5 N6 B:NCO101 2.0 20.0 0.5 N5 B:NCO101 2.0 19.5 0.5 N2 B:NCO101 2.0 21.0 0.5 N4 B:NCO101 2.0 20.8 0.5 HN31 B:NCO101 2.5 23.2 0.5 HN12 B:NCO101 2.5 22.8 0.5 HN11 B:NCO101 2.5 22.8 0.5 HN13 B:NCO101 2.5 22.8 0.5 HN33 B:NCO101 2.5 23.2 0.5 HN32 B:NCO101 2.5 23.2 0.5 HN62 B:NCO101 2.5 24.0 0.5 HN61 B:NCO101 2.5 24.0 0.5 HN63 B:NCO101 2.5 24.0 0.5 HN51 B:NCO101 2.5 23.4 0.5 HN52 B:NCO101 2.5 23.4 0.5 HN53 B:NCO101 2.5 23.4 0.5 HN22 B:NCO101 2.5 25.2 0.5 HN23 B:NCO101 2.5 25.2 0.5 HN21 B:NCO101 2.5 25.2 0.5 HN41 B:NCO101 2.5 24.9 0.5 HN42 B:NCO101 2.5 24.9 0.5 HN43 B:NCO101 2.5 24.9 0.5 O6 B:DG1 3.4 17.4 0.9 O6 B:DG1 3.6 16.9 0.1 N7 B:DG1 4.3 16.5 0.9 N7 B:DG1 4.3 15.8 0.1 C6 B:DG1 4.4 16.6 0.9 H1' B:DT7 4.5 33.7 0.6 C6 B:DG1 4.5 16.6 0.1 H1' B:DT7 4.5 31.0 0.4 C5 B:DG1 4.8 16.0 0.9 C5 B:DG1 4.8 15.9 0.1 H42 B:DC2 5.0 10.5 1.0

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