Ruthenium in PDB 5jev: Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine

The structure of Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine, PDB code: 5jev was solved by J.P.Hall, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.90 / 0.99
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.720, 48.720, 29.960, 90.00, 90.00, 90.00
R / Rfree (%)	12.3 / 14.1

The structure of Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Ruthenium atom in the Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine (pdb code 5jev). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine, PDB code: 5jev:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in the Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru101 b:12.4 occ:1.00 RU A:0TN101 0.0 12.4 1.0 N2 A:0TN101 2.1 11.8 1.0 N9 A:0TN101 2.1 11.8 1.0 N8 A:0TN101 2.1 13.7 1.0 N5 A:0TN101 2.1 14.1 1.0 N12 A:0TN101 2.1 11.5 1.0 N1 A:0TN101 2.1 12.6 1.0 C26 A:0TN101 2.9 15.0 1.0 C36 A:0TN101 2.9 11.3 1.0 C19 A:0TN101 2.9 15.2 1.0 C29 A:0TN101 2.9 11.4 1.0 C1 A:0TN101 2.9 11.9 1.0 C10 A:0TN101 2.9 12.3 1.0 C2 A:0TN101 3.1 12.7 1.0 C38 A:0TN101 3.1 12.0 1.0 C28 A:0TN101 3.1 14.5 1.0 C12 A:0TN101 3.1 13.9 1.0 C20 A:0TN101 3.1 15.0 1.0 C30 A:0TN101 3.1 12.1 1.0 H1 A:0TN101 3.2 15.3 1.0 H22 A:0TN101 3.2 14.4 1.0 H16 A:0TN101 3.2 17.4 1.0 H6 A:0TN101 3.2 16.7 1.0 H11 A:0TN101 3.2 18.0 1.0 H17 A:0TN101 3.2 14.6 1.0 C25 A:0TN101 4.2 16.2 1.0 C22 A:0TN101 4.2 16.4 1.0 C35 A:0TN101 4.3 11.8 1.0 C32 A:0TN101 4.3 12.2 1.0 C5 A:0TN101 4.3 12.8 1.0 C8 A:0TN101 4.3 13.0 1.0 C3 A:0TN101 4.4 13.4 1.0 C37 A:0TN101 4.4 12.9 1.0 C11 A:0TN101 4.4 14.8 1.0 C27 A:0TN101 4.4 16.3 1.0 C21 A:0TN101 4.4 17.3 1.0 C31 A:0TN101 4.4 13.2 1.0 C42 A:0TN101 4.8 16.9 1.0 C41 A:0TN101 4.8 17.6 1.0 C9 A:0TN101 4.8 14.0 1.0 C44 A:0TN101 4.8 12.2 1.0 C43 A:0TN101 4.9 13.4 1.0 C4 A:0TN101 4.9 13.7 1.0

Ruthenium binding site 2 out of 2 in the Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru102 b:15.1 occ:1.00 RU A:0TN102 0.0 15.1 1.0 N2 A:0TN102 2.1 15.0 1.0 N12 A:0TN102 2.1 14.7 1.0 N5 A:0TN102 2.1 14.2 1.0 N8 A:0TN102 2.1 14.6 1.0 N1 A:0TN102 2.1 15.0 1.0 N9 A:0TN102 2.1 16.1 1.0 C36 A:0TN102 2.9 16.3 1.0 C29 A:0TN102 2.9 16.8 1.0 C26 A:0TN102 2.9 13.7 1.0 C19 A:0TN102 2.9 13.7 1.0 C10 A:0TN102 2.9 14.7 1.0 C1 A:0TN102 2.9 13.8 1.0 C12 A:0TN102 3.0 16.4 1.0 C30 A:0TN102 3.1 17.7 1.0 C2 A:0TN102 3.1 15.6 1.0 C28 A:0TN102 3.1 15.9 1.0 C38 A:0TN102 3.1 14.2 1.0 C20 A:0TN102 3.1 14.7 1.0 H6 A:0TN102 3.2 19.6 1.0 H17 A:0TN102 3.2 21.2 1.0 H1 A:0TN102 3.2 18.8 1.0 H16 A:0TN102 3.2 19.1 1.0 H22 A:0TN102 3.2 17.0 1.0 H11 A:0TN102 3.2 17.7 1.0 C32 A:0TN102 4.2 18.9 1.0 C35 A:0TN102 4.2 16.6 1.0 C8 A:0TN102 4.2 14.7 1.0 C22 A:0TN102 4.2 13.4 1.0 C25 A:0TN102 4.2 14.1 1.0 C5 A:0TN102 4.3 13.9 1.0 C11 A:0TN102 4.3 17.2 1.0 C31 A:0TN102 4.3 19.7 1.0 C37 A:0TN102 4.4 14.9 1.0 C21 A:0TN102 4.4 14.7 1.0 C3 A:0TN102 4.4 15.6 1.0 C27 A:0TN102 4.4 16.6 1.0 O A:HOH241 4.6 29.1 1.0 O A:HOH244 4.8 24.1 1.0 C9 A:0TN102 4.8 15.8 1.0 C43 A:0TN102 4.8 19.9 1.0 C44 A:0TN102 4.8 16.4 1.0 C41 A:0TN102 4.8 14.2 1.0 C4 A:0TN102 4.8 14.8 1.0 C42 A:0TN102 4.9 15.8 1.0

J.P.Hall, P.M.Keane, H.Beer, K.Buchner, G.Winter, T.L.Sorensen, D.J.Cardin, J.A.Brazier, C.J.Cardin. Delta Chirality Ruthenium 'Light-Switch' Complexes Can Bind in the Minor Groove of Dna with Five Different Binding Modes. Nucleic Acids Res. V. 44 9472 2016.
ISSN: ESSN 1362-4962
PubMed: 27599841
DOI: 10.1093/NAR/GKW753