Ruthenium in PDB 4jd8: Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution

The structure of Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution, PDB code: 4jd8 was solved by D.S.Cook, 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)	32.52 / 1.16
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	37.550, 37.550, 54.371, 90.00, 90.00, 120.00
R / Rfree (%)	13.8 / 16.2

The structure of Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Ruthenium atom in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution (pdb code 4jd8). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution, PDB code: 4jd8:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ru101 b:12.8 occ:1.00 RU B:0TN101 0.0 12.8 1.0 N12 B:0TN101 2.0 13.3 1.0 N8 B:0TN101 2.0 12.9 1.0 N1 B:0TN101 2.1 13.8 1.0 N5 B:0TN101 2.1 12.2 1.0 N2 B:0TN101 2.1 13.0 1.0 N9 B:0TN101 2.1 13.2 1.0 C36 B:0TN101 2.9 13.7 1.0 C29 B:0TN101 2.9 13.3 1.0 C10 B:0TN101 2.9 13.2 1.0 C1 B:0TN101 2.9 13.2 1.0 C19 B:0TN101 2.9 12.8 1.0 C26 B:0TN101 2.9 13.0 1.0 C2 B:0TN101 3.0 13.7 1.0 C28 B:0TN101 3.0 14.2 1.0 C38 B:0TN101 3.0 13.6 1.0 C20 B:0TN101 3.1 12.5 1.0 C12 B:0TN101 3.1 13.5 1.0 C30 B:0TN101 3.1 14.1 1.0 H1 B:0TN101 3.2 16.5 1.0 H16 B:0TN101 3.2 17.1 1.0 H22 B:0TN101 3.2 16.3 1.0 H11 B:0TN101 3.2 15.0 1.0 H6 B:0TN101 3.2 16.2 1.0 H17 B:0TN101 3.2 16.9 1.0 C35 B:0TN101 4.2 14.2 1.0 C8 B:0TN101 4.2 14.2 1.0 C5 B:0TN101 4.2 13.6 1.0 C25 B:0TN101 4.3 14.2 1.0 C32 B:0TN101 4.3 14.4 1.0 C22 B:0TN101 4.3 13.5 1.0 C27 B:0TN101 4.3 15.3 1.0 C3 B:0TN101 4.3 14.4 1.0 C37 B:0TN101 4.3 14.3 1.0 C11 B:0TN101 4.3 14.8 1.0 C21 B:0TN101 4.4 13.0 1.0 C31 B:0TN101 4.4 15.0 1.0 C44 B:0TN101 4.8 14.4 1.0 C9 B:0TN101 4.8 14.7 1.0 C42 B:0TN101 4.8 15.4 1.0 H21 A:DG3 4.8 16.1 1.0 C41 B:0TN101 4.8 13.6 1.0 C4 B:0TN101 4.8 14.7 1.0 C43 B:0TN101 4.9 14.8 1.0 O2 A:DT2 4.9 16.3 1.0 O4' A:DG3 5.0 16.6 1.0

Ruthenium binding site 2 out of 2 in the Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Racemic-[Ru(Phen)2(Dppz)]2+] Bound to Synthetic Dna at High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ru102 b:14.8 occ:1.00 RU B:RKP102 0.0 14.8 1.0 N9 B:RKP102 2.0 14.8 1.0 N12 B:RKP102 2.1 16.4 1.0 N5 B:RKP102 2.1 15.6 1.0 N8 B:RKP102 2.1 17.0 1.0 N2 B:RKP102 2.1 14.6 1.0 N1 B:RKP102 2.1 13.1 1.0 C36 B:RKP102 2.9 15.5 1.0 C29 B:RKP102 2.9 14.7 1.0 C1 B:RKP102 2.9 13.6 1.0 C19 B:RKP102 2.9 16.7 1.0 C26 B:RKP102 2.9 18.0 1.0 C10 B:RKP102 2.9 13.2 1.0 C30 B:RKP102 3.0 14.2 1.0 C2 B:RKP102 3.0 15.8 1.0 C28 B:RKP102 3.0 18.4 1.0 C38 B:RKP102 3.1 18.2 1.0 C20 B:RKP102 3.1 15.7 1.0 C12 B:RKP102 3.1 12.9 1.0 H30 B:RKP102 3.1 17.0 1.0 H2 B:RKP102 3.2 19.0 1.0 H28 B:RKP102 3.2 22.0 1.0 H38 B:RKP102 3.2 21.9 1.0 H12 B:RKP102 3.2 15.4 1.0 H20 B:RKP102 3.2 18.8 1.0 C32 B:RKP102 4.2 15.9 1.0 C35 B:RKP102 4.2 17.0 1.0 C5 B:RKP102 4.2 14.8 1.0 C22 B:RKP102 4.2 18.0 1.0 C25 B:RKP102 4.3 19.6 1.0 C8 B:RKP102 4.3 12.7 1.0 C31 B:RKP102 4.3 15.4 1.0 C3 B:RKP102 4.3 18.1 1.0 C27 B:RKP102 4.3 19.9 1.0 C37 B:RKP102 4.4 18.6 1.0 C21 B:RKP102 4.4 17.2 1.0 C11 B:RKP102 4.4 12.8 1.0 O B:HOH209 4.8 17.2 1.0 C42 B:RKP102 4.8 20.0 1.0 C43 B:RKP102 4.8 16.0 1.0 C41 B:RKP102 4.8 17.5 1.0 C4 B:RKP102 4.8 17.0 1.0 C44 B:RKP102 4.8 17.6 1.0 C9 B:RKP102 4.9 12.9 1.0 H2 A:DA5 5.0 15.9 1.0 H21 B:DG3 5.0 14.0 0.9

J.P.Hall, D.Cook, S.R.Morte, P.Mcintyre, K.Buchner, H.Beer, D.J.Cardin, J.A.Brazier, G.Winter, J.M.Kelly, C.J.Cardin. X-Ray Crystal Structure of Rac-[Ru(Phen)2DPPZ](2+) with D(Atgcat)2 Shows Enantiomer Orientations and Water Ordering. J.Am.Chem.Soc. V. 135 12652 2013.
ISSN: ISSN 0002-7863
PubMed: 23875832
DOI: 10.1021/JA403590E