Atomistry » Ruthenium » PDB 5iu5-6bo1 » 5jev
Atomistry »
  Ruthenium »
    PDB 5iu5-6bo1 »
      5jev »

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

Protein crystallography data

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

Other elements in 5jev:

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

Ruthenium Binding Sites:

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 5jev

Go back to Ruthenium Binding Sites List in 5jev
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 5jev

Go back to Ruthenium Binding Sites List in 5jev
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

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 02:08:33 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy