Cobalt in PDB 8asm: Cobalt(II) Bound to A Non-Canonical Quadruplex

The structure of Cobalt(II) Bound to A Non-Canonical Quadruplex, PDB code: 8asm 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)	18.71 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	21.898, 58.659, 45.567, 90, 90, 90
R / Rfree (%)	17.8 / 19.2

The binding sites of Cobalt atom in the Cobalt(II) Bound to A Non-Canonical Quadruplex (pdb code 8asm). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Cobalt(II) Bound to A Non-Canonical Quadruplex, PDB code: 8asm:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Cobalt(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Cobalt(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:32.2 occ:0.89 O A:HOH210 1.9 30.9 1.0 O A:HOH216 2.2 22.4 0.5 N7 A:DG1 2.5 17.1 1.0 O A:HOH209 3.0 23.3 1.0 C8 A:DG1 3.4 9.1 1.0 H8 A:DG1 3.4 10.9 1.0 H41 A:DC2 3.6 7.9 1.0 C5 A:DG1 3.6 10.4 1.0 O6 A:DG1 3.9 17.5 1.0 C6 A:DG1 4.1 11.7 1.0 N4 A:DC2 4.1 6.6 1.0 HO3' A:DT7 4.3 35.5 1.0 H42 A:DC2 4.4 7.9 1.0 H1' A:DT7 4.5 26.5 1.0 O3' A:DT7 4.5 29.6 1.0 H4' A:DT7 4.5 29.0 1.0 O A:HOH219 4.6 21.8 0.5 H5 A:DC2 4.6 5.4 1.0 N9 A:DG1 4.7 14.2 1.0 C4 A:DG1 4.8 9.8 1.0 C4 A:DC2 4.9 7.8 1.0

Cobalt binding site 2 out of 6 in the Cobalt(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Cobalt(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:4.2 occ:1.00 CO A:NCO102 0.0 4.2 1.0 N4 A:NCO102 2.0 5.7 1.0 N2 A:NCO102 2.0 5.2 1.0 N3 A:NCO102 2.0 5.1 1.0 N5 A:NCO102 2.0 4.2 1.0 N1 A:NCO102 2.0 3.8 1.0 N6 A:NCO102 2.0 7.5 1.0 HN43 A:NCO102 2.5 6.8 1.0 HN41 A:NCO102 2.5 6.8 1.0 HN42 A:NCO102 2.5 6.8 1.0 HN23 A:NCO102 2.5 6.2 1.0 HN22 A:NCO102 2.5 6.2 1.0 HN31 A:NCO102 2.5 6.1 1.0 HN21 A:NCO102 2.5 6.2 1.0 HN33 A:NCO102 2.5 6.1 1.0 HN32 A:NCO102 2.5 6.1 1.0 HN51 A:NCO102 2.5 5.0 1.0 HN53 A:NCO102 2.5 5.0 1.0 HN52 A:NCO102 2.5 5.0 1.0 HN13 A:NCO102 2.5 4.5 1.0 HN11 A:NCO102 2.5 4.5 1.0 HN12 A:NCO102 2.5 4.5 1.0 HN63 A:NCO102 2.5 8.9 1.0 HN61 A:NCO102 2.5 8.9 1.0 HN62 A:NCO102 2.5 8.9 1.0 OP1 A:DA3 4.1 4.7 1.0 O A:HOH213 4.1 22.4 1.0 O A:HOH217 4.1 4.5 1.0 OP2 A:DA3 4.2 3.9 1.0 O A:HOH212 4.2 10.1 1.0 P A:DA3 4.7 3.8 1.0 O A:HOH204 4.9 10.9 0.5

Cobalt binding site 3 out of 6 in the Cobalt(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Cobalt(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:31.7 occ:1.00 CO A:NCO103 0.0 31.7 1.0 N2 A:NCO103 2.0 19.9 1.0 N3 A:NCO103 2.0 26.7 1.0 N4 A:NCO103 2.0 39.8 1.0 N6 A:NCO103 2.0 27.7 1.0 N5 A:NCO103 2.0 38.0 1.0 N1 A:NCO103 2.0 27.8 1.0 HN23 A:NCO103 2.5 23.9 1.0 HN21 A:NCO103 2.5 23.9 1.0 HN22 A:NCO103 2.5 23.9 1.0 HN33 A:NCO103 2.5 32.0 1.0 HN32 A:NCO103 2.5 32.0 1.0 HN41 A:NCO103 2.5 47.8 1.0 HN43 A:NCO103 2.5 47.8 1.0 HN42 A:NCO103 2.5 47.8 1.0 HN62 A:NCO103 2.5 33.2 1.0 HN31 A:NCO103 2.5 32.0 1.0 HN61 A:NCO103 2.5 33.2 1.0 HN63 A:NCO103 2.5 33.2 1.0 HN53 A:NCO103 2.5 45.6 1.0 HN51 A:NCO103 2.5 45.6 1.0 HN52 A:NCO103 2.5 45.6 1.0 HN12 A:NCO103 2.5 33.4 1.0 HN13 A:NCO103 2.5 33.4 1.0 HN11 A:NCO103 2.5 33.4 1.0 OP1 A:DC2 3.7 16.9 1.0 OP1 A:DC6 3.9 24.1 1.0 O A:HOH215 4.2 12.2 0.5 O3' A:DG1 4.7 14.2 1.0 O3' A:DG5 4.7 11.7 1.0 P A:DC2 4.8 14.1 1.0 P A:DC6 5.0 16.8 1.0

Cobalt binding site 4 out of 6 in the Cobalt(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Cobalt(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:39.4 occ:0.68 O B:HOH228 2.3 16.2 0.5 N7 B:DG1 2.3 10.8 1.0 C8 B:DG1 3.2 8.4 1.0 H8 B:DG1 3.3 10.1 1.0 C5 B:DG1 3.4 13.1 1.0 O B:HOH226 3.5 27.8 1.0 H41 B:DC2 3.5 5.9 1.0 O6 B:DG1 3.6 16.1 1.0 C6 B:DG1 3.9 9.2 1.0 N4 B:DC2 4.0 4.9 1.0 H42 B:DC2 4.1 5.9 1.0 H4' B:DT7 4.3 28.9 1.0 N9 B:DG1 4.4 9.5 1.0 C4 B:DG1 4.5 7.6 1.0 O B:HOH222 4.5 9.7 0.5 O B:HOH231 4.7 26.4 1.0 H1' B:DT7 4.7 33.4 1.0 H5 B:DC2 4.7 2.0 1.0 HO3' B:DT7 4.8 38.9 1.0 C4 B:DC2 4.8 2.5 1.0 O3' B:DT7 4.8 32.4 1.0 O4' B:DT7 5.0 23.1 1.0

Cobalt binding site 5 out of 6 in the Cobalt(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Cobalt(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:12.6 occ:0.44 CO B:NCO102 0.0 12.6 0.4 N1 B:NCO102 2.0 2.4 0.4 N4 B:NCO102 2.0 3.1 0.4 N5 B:NCO102 2.0 10.8 0.4 N3 B:NCO102 2.0 15.3 0.4 N2 B:NCO102 2.0 10.9 0.4 N6 B:NCO102 2.0 3.5 0.4 HN12 B:NCO102 2.5 2.9 0.4 HN11 B:NCO102 2.5 2.9 0.4 HN13 B:NCO102 2.5 2.9 0.4 HN43 B:NCO102 2.5 3.7 0.4 HN42 B:NCO102 2.5 3.7 0.4 HN41 B:NCO102 2.5 3.7 0.4 HN53 B:NCO102 2.5 13.0 0.4 HN32 B:NCO102 2.5 18.4 0.4 HN52 B:NCO102 2.5 13.0 0.4 HN51 B:NCO102 2.5 13.0 0.4 HN33 B:NCO102 2.5 18.4 0.4 HN31 B:NCO102 2.5 18.4 0.4 HN23 B:NCO102 2.5 13.1 0.4 HN22 B:NCO102 2.5 13.1 0.4 HN21 B:NCO102 2.5 13.1 0.4 HN61 B:NCO102 2.5 4.1 0.4 HN63 B:NCO102 2.5 4.1 0.4 HN62 B:NCO102 2.5 4.1 0.4 O B:HOH208 4.0 11.6 1.0 OP2 B:DT4 4.2 11.1 1.0 O B:HOH207 4.3 9.9 1.0 OP1 B:DT4 4.3 8.0 1.0 O B:HOH216 4.5 22.9 1.0 P B:DT4 4.7 8.9 1.0

Cobalt binding site 6 out of 6 in the Cobalt(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Cobalt(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co103 b:52.0 occ:1.00 CO B:NCO103 0.0 52.0 1.0 N4 B:NCO103 2.0 48.2 1.0 N6 B:NCO103 2.0 41.6 1.0 N3 B:NCO103 2.0 32.0 1.0 N1 B:NCO103 2.0 44.9 1.0 N5 B:NCO103 2.0 43.2 1.0 N2 B:NCO103 2.0 41.3 1.0 HN41 B:NCO103 2.5 57.9 1.0 HN42 B:NCO103 2.5 57.9 1.0 HN43 B:NCO103 2.5 57.9 1.0 HN62 B:NCO103 2.5 49.9 1.0 HN61 B:NCO103 2.5 49.9 1.0 HN32 B:NCO103 2.5 38.4 1.0 HN33 B:NCO103 2.5 38.4 1.0 HN63 B:NCO103 2.5 49.9 1.0 HN31 B:NCO103 2.5 38.4 1.0 HN13 B:NCO103 2.5 53.8 1.0 HN12 B:NCO103 2.5 53.8 1.0 HN11 B:NCO103 2.5 53.8 1.0 HN53 B:NCO103 2.5 51.9 1.0 HN51 B:NCO103 2.5 51.9 1.0 HN52 B:NCO103 2.5 51.9 1.0 HN23 B:NCO103 2.5 49.6 1.0 HN22 B:NCO103 2.5 49.6 1.0 HN21 B:NCO103 2.5 49.6 1.0 O4 B:DT4 3.9 16.9 1.0 O B:HOH201 4.2 31.7 1.0 C4 B:DT4 5.0 15.8 1.0

M.C.Lambert, J.P.Hall, J.A.Brazier, C.J.Cardin. Identifying Metal-Dna Binding Sites, What Is the Best Method to Get Transition Metals Into A Crystal System? To Be Published.