Ruthenium in PDB 8rer: Major Groove Intercalation with Polypyridyl Ruthenium Complex

The structure of Major Groove Intercalation with Polypyridyl Ruthenium Complex, PDB code: 8rer was solved by A.Abdullrahman, C.J.Cardin, J.P.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.68 / 1.20
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	32.676, 32.676, 103.988, 90, 90, 90
R / Rfree (%)	17.2 / 20.3

The structure of Major Groove Intercalation with Polypyridyl Ruthenium Complex also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Ruthenium atom in the Major Groove Intercalation with Polypyridyl Ruthenium Complex (pdb code 8rer). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 5 binding sites of Ruthenium where determined in the Major Groove Intercalation with Polypyridyl Ruthenium Complex, PDB code: 8rer:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5;

Ruthenium binding site 1 out of 5 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru101 b:19.6 occ:0.52 RU A:KSB101 0.0 19.6 0.5 RU A:KSB101 0.3 20.1 0.5 N1 A:KSB101 1.8 19.0 0.5 N8 A:KSB101 1.8 19.6 0.5 N5 A:KSB101 2.0 18.6 0.5 N1 A:KSB101 2.0 18.8 0.5 N8 A:KSB101 2.0 19.0 0.5 N5 A:KSB101 2.0 19.1 0.5 N12 A:KSB101 2.0 17.3 0.5 N9 A:KSB101 2.0 17.2 0.5 N2 A:KSB101 2.0 18.4 0.5 N9 A:KSB101 2.1 18.3 0.5 N2 A:KSB101 2.2 19.5 0.5 N12 A:KSB101 2.3 19.2 0.5 C26 A:KSB101 2.7 18.5 0.5 C12 A:KSB101 2.7 19.3 0.5 C19 A:KSB101 2.7 18.9 0.5 C10 A:KSB101 2.8 18.8 0.5 C28 A:KSB101 2.8 20.2 0.5 C26 A:KSB101 2.8 19.2 0.5 C19 A:KSB101 2.8 18.2 0.5 C29 A:KSB101 2.9 17.7 0.5 H2 A:KSB101 2.9 23.1 0.5 C36 A:KSB101 2.9 16.7 0.5 C10 A:KSB101 2.9 19.1 0.5 C1 A:KSB101 2.9 18.2 0.5 C1 A:KSB101 2.9 19.6 0.5 C30 A:KSB101 3.0 17.9 0.5 C12 A:KSB101 3.0 17.9 0.5 C2 A:KSB101 3.0 17.6 0.5 C29 A:KSB101 3.0 18.4 0.5 C28 A:KSB101 3.0 20.1 0.5 C20 A:KSB101 3.0 19.5 0.5 C30 A:KSB101 3.0 17.8 0.5 C38 A:KSB101 3.0 18.1 0.5 H12 A:KSB101 3.1 24.3 0.5 C20 A:KSB101 3.1 18.6 0.5 H14 A:KSB101 3.1 21.5 0.5 C36 A:KSB101 3.1 19.0 0.5 H2 A:KSB101 3.2 21.5 0.5 H6 A:KSB101 3.2 21.2 0.5 H7 A:KSB101 3.2 23.4 0.5 H12 A:KSB101 3.2 24.1 0.5 H14 A:KSB101 3.2 21.3 0.5 H19 A:KSB101 3.2 21.7 0.5 C38 A:KSB101 3.3 19.3 0.5 C2 A:KSB101 3.3 19.5 0.5 H7 A:KSB101 3.3 22.3 0.5 H19 A:KSB101 3.4 23.2 0.5 H6 A:KSB101 3.5 23.4 0.5 C25 A:KSB101 4.0 18.2 0.5 C11 A:KSB101 4.0 19.2 0.5 C8 A:KSB101 4.1 19.4 0.5 C22 A:KSB101 4.1 20.1 0.5 C27 A:KSB101 4.1 19.8 0.5 C25 A:KSB101 4.2 19.7 0.5 C22 A:KSB101 4.2 19.1 0.5 C32 A:KSB101 4.2 19.3 0.5 C35 A:KSB101 4.2 16.4 0.5 C8 A:KSB101 4.2 19.0 0.5 C5 A:KSB101 4.2 18.0 0.5 C5 A:KSB101 4.3 20.1 0.5 C3 A:KSB101 4.3 17.5 0.5 C11 A:KSB101 4.3 18.9 0.5 C27 A:KSB101 4.3 20.3 0.5 C31 A:KSB101 4.3 18.6 0.5 C21 A:KSB101 4.3 20.3 0.5 C37 A:KSB101 4.3 16.8 0.5 C31 A:KSB101 4.3 20.2 0.5 C21 A:KSB101 4.3 19.4 0.5 C32 A:KSB101 4.3 19.5 0.5 C35 A:KSB101 4.4 19.7 0.5 C3 A:KSB101 4.5 19.5 0.5 N7 A:KSB101 4.5 19.8 0.5 C37 A:KSB101 4.6 19.7 0.5 C9 A:KSB101 4.6 19.0 0.5 O B:HOH213 4.6 21.3 1.0 N6 A:KSB101 4.7 20.1 0.5 N3 A:DA3 4.7 19.9 1.0 N7 A:KSB101 4.7 21.6 0.5 N10 A:KSB101 4.7 19.1 0.5 N6 A:KSB101 4.7 19.4 0.5 N11 A:KSB101 4.7 16.3 0.5 C9 A:KSB101 4.8 18.8 0.5 C4 A:KSB101 4.8 16.9 0.5 N10 A:KSB101 4.8 20.6 0.5 H2 A:DA3 4.9 22.3 1.0 H1 A:KSB101 4.9 23.0 0.5 C4 A:KSB101 4.9 20.1 0.5 H11 A:KSB101 5.0 23.7 0.5 C2 A:DA3 5.0 18.6 1.0

Ruthenium binding site 2 out of 5 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru101 b:20.1 occ:0.48 RU A:KSB101 0.0 20.1 0.5 RU A:KSB101 0.3 19.6 0.5 N8 A:KSB101 1.7 19.0 0.5 N1 A:KSB101 1.8 18.8 0.5 N5 A:KSB101 2.0 19.1 0.5 N2 A:KSB101 2.0 19.5 0.5 N9 A:KSB101 2.0 18.3 0.5 N12 A:KSB101 2.0 19.2 0.5 N1 A:KSB101 2.0 19.0 0.5 N8 A:KSB101 2.0 19.6 0.5 N5 A:KSB101 2.0 18.6 0.5 N9 A:KSB101 2.1 17.2 0.5 N12 A:KSB101 2.2 17.3 0.5 N2 A:KSB101 2.3 18.4 0.5 C26 A:KSB101 2.6 19.2 0.5 C19 A:KSB101 2.7 18.2 0.5 C12 A:KSB101 2.7 17.9 0.5 C28 A:KSB101 2.8 20.1 0.5 C10 A:KSB101 2.8 19.1 0.5 C36 A:KSB101 2.8 19.0 0.5 C26 A:KSB101 2.8 18.5 0.5 C29 A:KSB101 2.9 18.4 0.5 C19 A:KSB101 2.9 18.9 0.5 H2 A:KSB101 2.9 21.5 0.5 C10 A:KSB101 2.9 18.8 0.5 C1 A:KSB101 2.9 19.6 0.5 C1 A:KSB101 3.0 18.2 0.5 C29 A:KSB101 3.0 17.7 0.5 C2 A:KSB101 3.0 19.5 0.5 H12 A:KSB101 3.0 24.1 0.5 C12 A:KSB101 3.0 19.3 0.5 C30 A:KSB101 3.0 17.8 0.5 C30 A:KSB101 3.0 17.9 0.5 C28 A:KSB101 3.0 20.2 0.5 C20 A:KSB101 3.0 18.6 0.5 C38 A:KSB101 3.0 19.3 0.5 C36 A:KSB101 3.0 16.7 0.5 C20 A:KSB101 3.1 19.5 0.5 H14 A:KSB101 3.1 21.3 0.5 H6 A:KSB101 3.2 23.4 0.5 H2 A:KSB101 3.2 23.1 0.5 H14 A:KSB101 3.2 21.5 0.5 H12 A:KSB101 3.2 24.3 0.5 H7 A:KSB101 3.2 22.3 0.5 H19 A:KSB101 3.2 23.2 0.5 C38 A:KSB101 3.2 18.1 0.5 C2 A:KSB101 3.3 17.6 0.5 H7 A:KSB101 3.3 23.4 0.5 H19 A:KSB101 3.4 21.7 0.5 H6 A:KSB101 3.5 21.2 0.5 C25 A:KSB101 3.9 19.7 0.5 C27 A:KSB101 4.0 20.3 0.5 C22 A:KSB101 4.1 19.1 0.5 C11 A:KSB101 4.1 18.9 0.5 C8 A:KSB101 4.1 19.0 0.5 C35 A:KSB101 4.2 19.7 0.5 C25 A:KSB101 4.2 18.2 0.5 C32 A:KSB101 4.2 19.5 0.5 C22 A:KSB101 4.2 20.1 0.5 C5 A:KSB101 4.2 20.1 0.5 C8 A:KSB101 4.2 19.4 0.5 C3 A:KSB101 4.3 19.5 0.5 C11 A:KSB101 4.3 19.2 0.5 C27 A:KSB101 4.3 19.8 0.5 C37 A:KSB101 4.3 19.7 0.5 C21 A:KSB101 4.3 19.4 0.5 C31 A:KSB101 4.3 20.2 0.5 C32 A:KSB101 4.3 19.3 0.5 C21 A:KSB101 4.3 20.3 0.5 C31 A:KSB101 4.3 18.6 0.5 C5 A:KSB101 4.4 18.0 0.5 O B:HOH213 4.4 21.3 1.0 C35 A:KSB101 4.4 16.4 0.5 N7 A:KSB101 4.5 21.6 0.5 C37 A:KSB101 4.5 16.8 0.5 C3 A:KSB101 4.6 17.5 0.5 C9 A:KSB101 4.6 18.8 0.5 N6 A:KSB101 4.7 19.4 0.5 N7 A:KSB101 4.7 19.8 0.5 N11 A:KSB101 4.7 20.8 0.5 N6 A:KSB101 4.7 20.1 0.5 N10 A:KSB101 4.7 20.6 0.5 C4 A:KSB101 4.8 20.1 0.5 C9 A:KSB101 4.8 19.0 0.5 N10 A:KSB101 4.8 19.1 0.5 O A:HOH232 4.9 41.9 1.0 H1 A:KSB101 4.9 22.7 0.5 H11 A:KSB101 4.9 24.4 0.5 N11 A:KSB101 4.9 16.3 0.5 N3 A:DA3 5.0 19.9 1.0 H2 A:DA3 5.0 22.3 1.0 C24 A:KSB101 5.0 20.4 0.5 O A:HOH225 5.0 26.2 1.0 C4 A:KSB101 5.0 16.9 0.5

Ruthenium binding site 3 out of 5 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ru101 b:20.4 occ:1.00 RU B:KSB101 0.0 20.4 1.0 N12 B:KSB101 2.0 20.9 1.0 N1 B:KSB101 2.0 19.1 1.0 N5 B:KSB101 2.0 18.9 1.0 N8 B:KSB101 2.0 20.5 1.0 N9 B:KSB101 2.0 20.8 1.0 N2 B:KSB101 2.0 18.9 1.0 C26 B:KSB101 2.8 20.0 1.0 C19 B:KSB101 2.8 18.9 1.0 C36 B:KSB101 2.9 22.7 1.0 C29 B:KSB101 2.9 22.8 1.0 C10 B:KSB101 2.9 18.4 1.0 C1 B:KSB101 2.9 19.1 1.0 C12 B:KSB101 3.0 16.3 1.0 C38 B:KSB101 3.0 21.0 1.0 C2 B:KSB101 3.0 18.7 1.0 C20 B:KSB101 3.0 19.0 1.0 C28 B:KSB101 3.0 21.5 1.0 C30 B:KSB101 3.0 22.7 1.0 H2 B:KSB101 3.2 19.6 1.0 H6 B:KSB101 3.2 22.4 1.0 H19 B:KSB101 3.2 25.2 1.0 H7 B:KSB101 3.2 22.9 1.0 H12 B:KSB101 3.2 25.8 1.0 H14 B:KSB101 3.2 27.2 1.0 C25 B:KSB101 4.2 20.3 1.0 C22 B:KSB101 4.2 20.2 1.0 C35 B:KSB101 4.2 24.0 1.0 C32 B:KSB101 4.2 24.0 1.0 C8 B:KSB101 4.2 19.1 1.0 C5 B:KSB101 4.2 19.0 1.0 H71 B:DT3 4.2 24.6 1.0 H73 A:DT4 4.3 22.8 1.0 C11 B:KSB101 4.3 17.4 1.0 C37 B:KSB101 4.3 20.7 1.0 C21 B:KSB101 4.3 18.9 1.0 C27 B:KSB101 4.3 20.5 1.0 C3 B:KSB101 4.3 19.4 1.0 C31 B:KSB101 4.3 24.6 1.0 N11 B:KSB101 4.7 23.0 1.0 N7 B:KSB101 4.7 20.6 1.0 N6 B:KSB101 4.7 19.3 1.0 N10 B:KSB101 4.7 25.2 1.0 C9 B:KSB101 4.8 18.5 1.0 C4 B:KSB101 4.8 18.4 1.0 N11 C:KSB101 4.8 19.0 1.0 O4 B:DT3 4.8 19.0 1.0 O4 A:DT4 4.8 21.4 1.0 H18 C:KSB101 4.9 23.7 1.0

Ruthenium binding site 4 out of 5 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ru101 b:20.3 occ:1.00 RU C:KSB101 0.0 20.3 1.0 N1 C:KSB101 2.0 20.5 1.0 N8 C:KSB101 2.0 19.6 1.0 N2 C:KSB101 2.0 19.3 1.0 N9 C:KSB101 2.0 18.8 1.0 N12 C:KSB101 2.0 19.0 1.0 N5 C:KSB101 2.0 19.0 1.0 C26 C:KSB101 2.9 19.9 1.0 C36 C:KSB101 2.9 17.9 1.0 C29 C:KSB101 2.9 19.2 1.0 C10 C:KSB101 2.9 20.5 1.0 C1 C:KSB101 2.9 19.6 1.0 C19 C:KSB101 2.9 18.8 1.0 C12 C:KSB101 3.0 19.8 1.0 C2 C:KSB101 3.0 19.0 1.0 C28 C:KSB101 3.0 21.1 1.0 C38 C:KSB101 3.0 20.0 1.0 C30 C:KSB101 3.0 19.2 1.0 C20 C:KSB101 3.0 18.9 1.0 H2 C:KSB101 3.2 23.8 1.0 H6 C:KSB101 3.2 22.8 1.0 H12 C:KSB101 3.2 25.4 1.0 H19 C:KSB101 3.2 24.0 1.0 H14 C:KSB101 3.2 23.1 1.0 H7 C:KSB101 3.2 22.6 1.0 H18 B:KSB101 3.9 24.8 1.0 C25 C:KSB101 4.2 20.7 1.0 C35 C:KSB101 4.2 17.9 1.0 C32 C:KSB101 4.2 20.2 1.0 C8 C:KSB101 4.2 21.7 1.0 C22 C:KSB101 4.2 19.0 1.0 C5 C:KSB101 4.2 20.4 1.0 C11 C:KSB101 4.3 20.2 1.0 C3 C:KSB101 4.3 19.2 1.0 C27 C:KSB101 4.3 21.6 1.0 C31 C:KSB101 4.3 19.9 1.0 C37 C:KSB101 4.3 19.7 1.0 C21 C:KSB101 4.3 20.9 1.0 O D:HOH211 4.5 21.0 1.0 C37 B:KSB101 4.6 20.7 1.0 N7 C:KSB101 4.7 21.6 1.0 N11 C:KSB101 4.7 19.0 1.0 N10 C:KSB101 4.7 20.0 1.0 N6 C:KSB101 4.8 19.7 1.0 C9 C:KSB101 4.8 21.2 1.0 C4 C:KSB101 4.8 18.7 1.0 N3 C:DA3 4.9 19.9 1.0 N11 B:KSB101 4.9 23.0 1.0 H2 C:DA3 4.9 23.1 1.0

Ruthenium binding site 5 out of 5 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ru101 b:20.3 occ:1.00 RU D:KSB101 0.0 20.3 1.0 N12 D:KSB101 2.0 21.4 1.0 N1 D:KSB101 2.0 18.8 1.0 N8 D:KSB101 2.0 20.6 1.0 N5 D:KSB101 2.0 18.7 1.0 N9 D:KSB101 2.0 20.6 1.0 N2 D:KSB101 2.0 18.4 1.0 C26 D:KSB101 2.8 19.6 1.0 C19 D:KSB101 2.8 19.3 1.0 C36 D:KSB101 2.9 22.9 1.0 C29 D:KSB101 2.9 22.5 1.0 C10 D:KSB101 2.9 17.8 1.0 C1 D:KSB101 2.9 18.7 1.0 C12 D:KSB101 3.0 17.0 1.0 C38 D:KSB101 3.0 21.5 1.0 C2 D:KSB101 3.0 17.9 1.0 C28 D:KSB101 3.0 21.6 1.0 C20 D:KSB101 3.0 18.7 1.0 C30 D:KSB101 3.0 22.4 1.0 H2 D:KSB101 3.2 20.4 1.0 H6 D:KSB101 3.2 21.4 1.0 H19 D:KSB101 3.2 25.8 1.0 H12 D:KSB101 3.2 25.9 1.0 H7 D:KSB101 3.2 22.4 1.0 H14 D:KSB101 3.2 26.9 1.0 C25 D:KSB101 4.2 20.6 1.0 C22 D:KSB101 4.2 19.5 1.0 C35 D:KSB101 4.2 23.5 1.0 C32 D:KSB101 4.2 23.9 1.0 C8 D:KSB101 4.2 18.6 1.0 H73 D:DT3 4.2 24.4 1.0 C5 D:KSB101 4.2 18.7 1.0 H73 C:DT4 4.3 23.7 1.0 C11 D:KSB101 4.3 18.3 1.0 C37 D:KSB101 4.3 21.1 1.0 C27 D:KSB101 4.3 20.5 1.0 C21 D:KSB101 4.3 19.1 1.0 C3 D:KSB101 4.3 18.7 1.0 C31 D:KSB101 4.3 24.2 1.0 N7 D:KSB101 4.7 20.4 1.0 N11 D:KSB101 4.7 23.1 1.0 N6 D:KSB101 4.7 19.3 1.0 N10 D:KSB101 4.7 25.2 1.0 C9 D:KSB101 4.8 18.9 1.0 C4 D:KSB101 4.8 17.9 1.0 O4 D:DT3 4.8 20.4 1.0 O4 C:DT4 4.8 21.6 1.0

A.Abdullrahman, K.Mcquaid, C.J.Cardin, J.P.Hall. Ruthenium Polypyridyl Complex Intercalating in Major and Minor Groove Dna To Be Published.