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Ruthenium in PDB 5nbe: [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2

Protein crystallography data

The structure of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2, PDB code: 5nbe was solved by K.T.Mcquaid, 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) 24.89 / 1.51
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 47.880, 47.880, 29.140, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19

Other elements in 5nbe:

The structure of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 also contains other interesting chemical elements:

Barium (Ba) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 (pdb code 5nbe). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2, PDB code: 5nbe:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5nbe

Go back to Ruthenium Binding Sites List in 5nbe
Ruthenium binding site 1 out of 2 in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru101

b:16.2
occ:0.66
RU A:QHL101 0.0 16.2 0.7
RU A:QHL101 0.0 19.4 0.3
N5 A:QHL101 1.8 20.4 0.3
N8 A:QHL101 1.8 20.6 0.3
N12 A:QHL101 1.8 21.1 0.3
N9 A:QHL101 1.8 21.1 0.3
N2 A:QHL101 1.9 20.9 0.3
N1 A:QHL101 1.9 21.1 0.3
N1 A:QHL101 1.9 17.9 0.7
N9 A:QHL101 1.9 16.0 0.7
N5 A:QHL101 1.9 17.1 0.7
N2 A:QHL101 1.9 18.2 0.7
N12 A:QHL101 1.9 15.8 0.7
N8 A:QHL101 1.9 17.4 0.7
C26 A:QHL101 2.7 20.2 0.3
C19 A:QHL101 2.7 20.3 0.3
C36 A:QHL101 2.7 21.2 0.3
C29 A:QHL101 2.7 21.4 0.3
C1 A:QHL101 2.7 20.6 0.3
C10 A:QHL101 2.7 20.4 0.3
C10 A:QHL101 2.8 17.9 0.7
C36 A:QHL101 2.8 15.0 0.7
C1 A:QHL101 2.8 17.6 0.7
C29 A:QHL101 2.8 15.1 0.7
C26 A:QHL101 2.8 17.2 0.7
C19 A:QHL101 2.8 17.8 0.7
C38 A:QHL101 2.9 20.9 0.3
C30 A:QHL101 2.9 21.0 0.3
C20 A:QHL101 2.9 20.6 0.3
C28 A:QHL101 2.9 21.0 0.3
C2 A:QHL101 2.9 20.9 0.3
C12 A:QHL101 2.9 20.9 0.3
C12 A:QHL101 2.9 18.5 0.7
C20 A:QHL101 3.0 16.8 0.7
C2 A:QHL101 3.0 18.1 0.7
C28 A:QHL101 3.0 16.6 0.7
C38 A:QHL101 3.0 15.7 0.7
C30 A:QHL101 3.0 15.4 0.7
C25 A:QHL101 4.0 21.0 0.3
C22 A:QHL101 4.0 20.6 0.3
C35 A:QHL101 4.0 21.5 0.3
C32 A:QHL101 4.1 21.4 0.3
C5 A:QHL101 4.1 20.8 0.3
C8 A:QHL101 4.1 20.7 0.3
C8 A:QHL101 4.1 18.3 0.7
C27 A:QHL101 4.1 21.2 0.3
C21 A:QHL101 4.1 20.6 0.3
C37 A:QHL101 4.1 21.5 0.3
C31 A:QHL101 4.1 21.1 0.3
C5 A:QHL101 4.2 18.2 0.7
C35 A:QHL101 4.2 15.5 0.7
C32 A:QHL101 4.2 15.1 0.7
C3 A:QHL101 4.2 20.9 0.3
C11 A:QHL101 4.2 21.1 0.3
C25 A:QHL101 4.2 17.8 0.7
C22 A:QHL101 4.2 17.6 0.7
C11 A:QHL101 4.2 18.5 0.7
C21 A:QHL101 4.2 17.2 0.7
C3 A:QHL101 4.3 18.4 0.7
C37 A:QHL101 4.3 15.2 0.7
C27 A:QHL101 4.3 17.4 0.7
C31 A:QHL101 4.3 15.2 0.7
O2 A:DC2 4.6 18.6 1.0
N7 A:QHL101 4.6 21.1 0.3
N6 A:QHL101 4.6 20.8 0.3
N11 A:QHL101 4.6 21.6 0.3
N10 A:QHL101 4.6 21.8 0.3
C4 A:QHL101 4.7 21.3 0.3
C9 A:QHL101 4.7 21.0 0.3
C9 A:QHL101 4.7 19.5 0.7
C4 A:QHL101 4.7 18.4 0.7
N11 A:QHL101 4.8 16.0 0.7
N6 A:QHL101 4.8 17.9 0.7
N10 A:QHL101 4.8 15.0 0.7
N7 A:QHL101 4.8 17.5 0.7
O4' A:DC2 4.9 22.2 1.0
O A:HOH259 4.9 26.4 1.0
C24 A:QHL101 5.0 20.4 0.3

Ruthenium binding site 2 out of 2 in 5nbe

Go back to Ruthenium Binding Sites List in 5nbe
Ruthenium binding site 2 out of 2 in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru101

b:19.4
occ:0.34
RU A:QHL101 0.0 19.4 0.3
RU A:QHL101 0.0 16.2 0.7
N5 A:QHL101 1.8 20.4 0.3
N9 A:QHL101 1.8 21.1 0.3
N8 A:QHL101 1.8 20.6 0.3
N1 A:QHL101 1.8 21.1 0.3
N12 A:QHL101 1.8 21.1 0.3
N2 A:QHL101 1.8 20.9 0.3
N2 A:QHL101 1.9 18.2 0.7
N1 A:QHL101 1.9 17.9 0.7
N5 A:QHL101 1.9 17.1 0.7
N9 A:QHL101 1.9 16.0 0.7
N12 A:QHL101 1.9 15.8 0.7
N8 A:QHL101 1.9 17.4 0.7
C26 A:QHL101 2.7 20.2 0.3
C19 A:QHL101 2.7 20.3 0.3
C1 A:QHL101 2.7 20.6 0.3
C10 A:QHL101 2.7 20.4 0.3
C29 A:QHL101 2.7 21.4 0.3
C36 A:QHL101 2.7 21.2 0.3
C10 A:QHL101 2.7 17.9 0.7
C1 A:QHL101 2.7 17.6 0.7
C36 A:QHL101 2.8 15.0 0.7
C29 A:QHL101 2.8 15.1 0.7
C19 A:QHL101 2.8 17.8 0.7
C26 A:QHL101 2.8 17.2 0.7
C30 A:QHL101 2.9 21.0 0.3
C20 A:QHL101 2.9 20.6 0.3
C12 A:QHL101 2.9 20.9 0.3
C2 A:QHL101 2.9 20.9 0.3
C28 A:QHL101 2.9 21.0 0.3
C38 A:QHL101 2.9 20.9 0.3
C20 A:QHL101 2.9 16.8 0.7
C2 A:QHL101 2.9 18.1 0.7
C12 A:QHL101 2.9 18.5 0.7
C38 A:QHL101 3.0 15.7 0.7
C30 A:QHL101 3.0 15.4 0.7
C28 A:QHL101 3.0 16.6 0.7
C25 A:QHL101 4.0 21.0 0.3
C22 A:QHL101 4.0 20.6 0.3
C32 A:QHL101 4.1 21.4 0.3
C35 A:QHL101 4.1 21.5 0.3
C8 A:QHL101 4.1 20.7 0.3
C5 A:QHL101 4.1 20.8 0.3
C8 A:QHL101 4.1 18.3 0.7
C5 A:QHL101 4.1 18.2 0.7
C31 A:QHL101 4.1 21.1 0.3
C21 A:QHL101 4.1 20.6 0.3
C27 A:QHL101 4.1 21.2 0.3
C11 A:QHL101 4.2 21.1 0.3
C3 A:QHL101 4.2 20.9 0.3
C37 A:QHL101 4.2 21.5 0.3
C35 A:QHL101 4.2 15.5 0.7
C32 A:QHL101 4.2 15.1 0.7
C22 A:QHL101 4.2 17.6 0.7
C25 A:QHL101 4.2 17.8 0.7
C3 A:QHL101 4.2 18.4 0.7
C11 A:QHL101 4.2 18.5 0.7
C21 A:QHL101 4.2 17.2 0.7
C37 A:QHL101 4.3 15.2 0.7
C31 A:QHL101 4.3 15.2 0.7
C27 A:QHL101 4.3 17.4 0.7
O2 A:DC2 4.6 18.6 1.0
N7 A:QHL101 4.6 21.1 0.3
N6 A:QHL101 4.6 20.8 0.3
N10 A:QHL101 4.6 21.8 0.3
C9 A:QHL101 4.6 21.0 0.3
N11 A:QHL101 4.6 21.6 0.3
C4 A:QHL101 4.6 21.3 0.3
C4 A:QHL101 4.7 18.4 0.7
C9 A:QHL101 4.7 19.5 0.7
N11 A:QHL101 4.8 16.0 0.7
N6 A:QHL101 4.8 17.9 0.7
N10 A:QHL101 4.8 15.0 0.7
N7 A:QHL101 4.8 17.5 0.7
O A:HOH259 4.9 26.4 1.0
O4' A:DC2 4.9 22.2 1.0

Reference:

K.Mcquaid, J.P.Hall, J.A.Brazier, D.J.Cardin, C.J.Cardin. X-Ray Crystal Structures Show Dna Stacking Advantage of Terminal Nitrile Substitution in Ru-Dppz Complexes. Chemistry V. 24 15859 2018.
ISSN: ISSN 0947-6539
PubMed: 30063271
DOI: 10.1002/CHEM.201803021
Page generated: Wed Dec 16 02:08:38 2020

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