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Ruthenium in PDB 5jeu: Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+

Protein crystallography data

The structure of Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+, PDB code: 5jeu 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) 25.18 / 0.97
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.620, 48.620, 29.430, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 12.7

Other elements in 5jeu:

The structure of Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+ also contains other interesting chemical elements:

Barium (Ba) 1 atom
Chlorine (Cl) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+ (pdb code 5jeu). 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 BA2+, PDB code: 5jeu:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5jeu

Go back to Ruthenium Binding Sites List in 5jeu
Ruthenium binding site 1 out of 2 in the Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+


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 BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:9.9
occ:1.00
RU A:0TN102 0.0 9.9 1.0
N2 A:0TN102 2.1 9.9 1.0
N8 A:0TN102 2.1 10.9 1.0
N1 A:0TN102 2.1 10.4 1.0
N12 A:0TN102 2.1 9.7 1.0
N5 A:0TN102 2.1 11.1 1.0
N9 A:0TN102 2.1 9.8 1.0
C26 A:0TN102 2.9 11.4 1.0
C36 A:0TN102 2.9 9.7 1.0
C10 A:0TN102 2.9 10.0 1.0
C19 A:0TN102 2.9 11.9 1.0
C1 A:0TN102 2.9 10.0 1.0
C29 A:0TN102 2.9 9.9 1.0
C2 A:0TN102 3.1 10.6 1.0
C12 A:0TN102 3.1 11.4 1.0
C38 A:0TN102 3.1 10.1 1.0
C28 A:0TN102 3.1 12.1 1.0
C20 A:0TN102 3.1 12.3 1.0
C30 A:0TN102 3.1 10.4 1.0
H1 A:0TN102 3.2 12.7 1.0
H22 A:0TN102 3.2 12.2 1.0
H6 A:0TN102 3.2 13.7 1.0
H16 A:0TN102 3.2 14.5 1.0
H11 A:0TN102 3.2 14.7 1.0
H17 A:0TN102 3.2 12.5 1.0
C5 A:0TN102 4.2 10.9 1.0
C35 A:0TN102 4.2 10.4 1.0
C8 A:0TN102 4.2 10.6 1.0
C25 A:0TN102 4.2 13.3 1.0
C32 A:0TN102 4.3 10.5 1.0
C22 A:0TN102 4.3 13.3 1.0
C3 A:0TN102 4.4 11.3 1.0
C11 A:0TN102 4.4 12.3 1.0
C37 A:0TN102 4.4 10.3 1.0
C21 A:0TN102 4.4 13.6 1.0
C27 A:0TN102 4.4 13.7 1.0
C31 A:0TN102 4.4 11.3 1.0
C9 A:0TN102 4.8 11.4 1.0
C4 A:0TN102 4.8 11.2 1.0
C41 A:0TN102 4.8 14.2 1.0
C44 A:0TN102 4.8 10.6 1.0
C42 A:0TN102 4.8 14.0 1.0
C43 A:0TN102 4.9 11.4 1.0

Ruthenium binding site 2 out of 2 in 5jeu

Go back to Ruthenium Binding Sites List in 5jeu
Ruthenium binding site 2 out of 2 in the Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+


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 BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru103

b:14.1
occ:1.00
RU A:0TN103 0.0 14.1 1.0
N2 A:0TN103 2.1 15.3 1.0
N1 A:0TN103 2.1 14.4 1.0
N8 A:0TN103 2.1 13.3 1.0
N12 A:0TN103 2.1 14.6 1.0
N5 A:0TN103 2.1 15.2 1.0
N9 A:0TN103 2.1 14.0 1.0
C19 A:0TN103 2.9 15.9 1.0
C10 A:0TN103 2.9 14.8 1.0
C26 A:0TN103 2.9 14.6 1.0
C36 A:0TN103 2.9 14.6 1.0
C1 A:0TN103 2.9 15.3 1.0
C29 A:0TN103 2.9 14.5 1.0
C2 A:0TN103 3.0 17.3 1.0
C20 A:0TN103 3.1 17.8 1.0
C28 A:0TN103 3.1 13.4 1.0
C12 A:0TN103 3.1 14.8 1.0
C30 A:0TN103 3.1 14.8 1.0
C38 A:0TN103 3.1 16.0 1.0
H1 A:0TN103 3.2 20.7 1.0
H6 A:0TN103 3.2 17.8 1.0
H11 A:0TN103 3.2 21.3 1.0
H16 A:0TN103 3.2 16.1 1.0
H17 A:0TN103 3.2 17.8 1.0
H22 A:0TN103 3.2 19.2 1.0
C22 A:0TN103 4.2 18.5 1.0
C8 A:0TN103 4.2 14.7 1.0
C35 A:0TN103 4.2 15.2 1.0
C25 A:0TN103 4.2 15.9 1.0
C32 A:0TN103 4.2 14.7 1.0
C5 A:0TN103 4.2 16.2 1.0
C21 A:0TN103 4.3 19.6 1.0
C3 A:0TN103 4.3 17.5 1.0
C27 A:0TN103 4.3 13.8 1.0
C11 A:0TN103 4.4 14.7 1.0
C31 A:0TN103 4.4 15.6 1.0
C37 A:0TN103 4.4 17.1 1.0
O A:HOH249 4.7 24.5 1.0
C4 A:0TN103 4.8 17.1 1.0
C9 A:0TN103 4.8 15.0 1.0
C41 A:0TN103 4.8 19.6 1.0
C42 A:0TN103 4.8 14.6 1.0
C43 A:0TN103 4.8 15.3 1.0
C44 A:0TN103 4.8 16.6 1.0
O A:HOH246 4.9 18.5 1.0

Reference:

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
Page generated: Wed Dec 16 02:08:34 2020

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