Nickel in PDB 8aso: Nickel(II) Bound to A Non-Canonical Quadruplex

The structure of Nickel(II) Bound to A Non-Canonical Quadruplex, PDB code: 8aso 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)	22.80 / 1.19
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	21.947, 58.973, 45.598, 90, 90, 90
R / Rfree (%)	14.1 / 17.6

The structure of Nickel(II) Bound to A Non-Canonical Quadruplex also contains other interesting chemical elements:

Cobalt

(Co)

5 atoms

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

Nickel binding site 1 out of 3 in the Nickel(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nickel(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni104 b:17.7 occ:0.41 NI A:NI104 0.0 17.7 0.4 NI A:NI104 1.8 59.7 0.6 O A:HOH232 2.0 44.5 0.9 O A:HOH227 2.0 51.0 0.9 O A:HOH223 2.1 28.7 1.0 O A:HOH226 2.3 59.1 1.0 N7 A:DG1 2.7 22.0 1.0 H8 A:DG1 3.4 23.1 1.0 C8 A:DG1 3.4 19.2 1.0 H41 A:DC2 3.5 11.6 1.0 C5 A:DG1 3.8 19.8 1.0 N4 A:DC2 4.2 9.6 1.0 O6 A:DG1 4.2 23.5 1.0 C6 A:DG1 4.4 20.5 1.0 H5 A:DC2 4.4 9.1 1.0 H42 A:DC2 4.5 11.6 1.0 N9 A:DG1 4.7 19.3 1.0 O A:HOH229 4.8 54.2 1.0 C4 A:DG1 4.9 18.7 1.0 H4' A:DT7 4.9 36.1 1.0 C4 A:DC2 4.9 8.7 1.0 C5 A:DC2 5.0 7.6 1.0

Nickel binding site 2 out of 3 in the Nickel(II) Bound to A Non-Canonical Quadruplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nickel(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni104 b:59.7 occ:0.59 NI A:NI104 0.0 59.7 0.6 O A:HOH227 1.6 51.0 0.9 NI A:NI104 1.8 17.7 0.4 N7 A:DG1 1.9 22.0 1.0 O A:HOH223 2.6 28.7 1.0 O A:HOH226 2.7 59.1 1.0 C5 A:DG1 2.8 19.8 1.0 C8 A:DG1 2.9 19.2 1.0 O6 A:DG1 3.1 23.5 1.0 H8 A:DG1 3.2 23.1 1.0 H4' A:DT7 3.3 36.1 1.0 C6 A:DG1 3.3 20.5 1.0 O A:HOH232 3.5 44.5 0.9 H1' A:DT7 3.6 39.3 1.0 O4' A:DT7 3.8 31.0 1.0 C4' A:DT7 4.0 30.1 1.0 C4 A:DG1 4.0 18.7 1.0 N9 A:DG1 4.1 19.3 1.0 HO3' A:DT7 4.1 39.0 1.0 C1' A:DT7 4.1 32.8 1.0 O A:HOH229 4.2 54.2 1.0 O A:HOH206 4.2 40.9 1.0 O3' A:DT7 4.2 32.5 1.0 H2'' A:DT7 4.2 39.1 1.0 H41 A:DC2 4.3 11.6 1.0 C3' A:DT7 4.5 30.7 1.0 C2' A:DT7 4.5 32.6 1.0 N4 A:DC2 4.6 9.6 1.0 N1 A:DG1 4.6 19.3 1.0 H42 A:DC2 4.8 11.6 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nickel(II) Bound to A Non-Canonical Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni102 b:71.7 occ:0.78 N7 B:DG1 1.8 14.3 0.9 O B:HOH219 1.9 26.8 0.8 N7 B:DG1 2.2 11.7 0.1 O B:HOH202 2.3 29.6 0.6 O B:HOH232 2.6 30.1 0.6 C8 B:DG1 2.8 12.8 0.9 C5 B:DG1 2.9 15.4 0.9 O B:HOH223 2.9 28.3 0.9 C8 B:DG1 2.9 11.7 0.1 H8 B:DG1 3.0 14.0 0.1 H8 B:DG1 3.0 15.4 0.9 O6 B:DG1 3.3 19.0 0.9 H4' B:DT7 3.3 20.3 0.4 C5 B:DG1 3.3 12.0 0.1 C6 B:DG1 3.4 16.6 0.9 H41 B:DC2 3.7 9.2 1.0 O B:HOH220 3.8 33.1 1.0 O6 B:DG1 3.9 12.3 0.1 O B:HOH235 3.9 30.3 0.5 C6 B:DG1 4.0 12.1 0.1 O B:HOH218 4.0 25.3 0.7 N9 B:DG1 4.0 11.6 0.9 H4' B:DT7 4.0 33.9 0.6 C4 B:DG1 4.1 12.9 0.9 N4 B:DC2 4.1 7.6 1.0 H1' B:DT7 4.1 36.3 0.6 C4' B:DT7 4.1 16.9 0.4 O4' B:DT7 4.1 18.4 0.4 N9 B:DG1 4.2 11.6 0.1 H42 B:DC2 4.2 9.2 1.0 HO5' B:DG1 4.3 14.2 0.1 O3' B:DT7 4.3 20.6 0.4 C4 B:DG1 4.4 11.8 0.1 HO5' B:DG1 4.5 18.5 0.9 HO3' B:DT7 4.6 24.7 0.4 O4' B:DT7 4.6 29.2 0.6 H1' B:DT7 4.6 24.9 0.4 HO3' B:DT7 4.7 31.9 0.6 C4' B:DT7 4.8 28.2 0.6 C1' B:DT7 4.8 30.3 0.6 N1 B:DG1 4.8 16.2 0.9 C4 B:DC2 4.8 6.9 1.0 O3' B:DT7 4.9 26.5 0.6 H5 B:DC2 4.9 7.6 1.0 C3' B:DT7 4.9 18.6 0.4 C1' B:DT7 5.0 20.7 0.4

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.