Atomistry » Ruthenium » PDB 3m0b-4kgc » 4e1u
Atomistry »
  Ruthenium »
    PDB 3m0b-4kgc »
      4e1u »

Ruthenium in PDB 4e1u: [Ru(Bpy)2 Dppz]2+ Bound to Dna

Protein crystallography data

The structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna, PDB code: 4e1u was solved by H.Song, J.T.Kaiser, J.K.Barton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.33 / 0.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 24.039, 24.797, 37.521, 74.67, 84.42, 76.21
R / Rfree (%) 14 / 14.9

Other elements in 4e1u:

The structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna also contains other interesting chemical elements:

Barium (Ba) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the [Ru(Bpy)2 Dppz]2+ Bound to Dna (pdb code 4e1u). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 5 binding sites of Ruthenium where determined in the [Ru(Bpy)2 Dppz]2+ Bound to Dna, PDB code: 4e1u:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5;

Ruthenium binding site 1 out of 5 in 4e1u

Go back to Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 1 out of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna


Mono view


Stereo pair view

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

b:16.0
occ:1.00
RU1 A:R1Z101 0.0 16.0 1.0
N1 A:R1Z101 1.9 14.6 1.0
N5 A:R1Z101 2.0 16.0 1.0
N6 A:R1Z101 2.0 16.9 1.0
N8 A:R1Z101 2.0 13.0 1.0
N2 A:R1Z101 2.1 14.6 1.0
N7 A:R1Z101 2.1 17.3 1.0
C2 A:R1Z101 2.7 15.6 1.0
C3 A:R1Z101 2.8 14.6 1.0
C24 A:R1Z101 2.8 17.4 1.0
C23 A:R1Z101 2.9 17.3 1.0
C33 A:R1Z101 2.9 16.7 1.0
C15 A:R1Z101 2.9 17.8 1.0
C34 A:R1Z101 2.9 15.1 1.0
C19 A:R1Z101 3.0 17.5 1.0
C38 A:R1Z101 3.0 12.8 1.0
C16 A:R1Z101 3.1 14.5 1.0
H151 A:R1Z101 3.1 21.3 1.0
C29 A:R1Z101 3.1 18.9 1.0
C28 A:R1Z101 3.1 17.3 1.0
H381 A:R1Z101 3.1 15.4 1.0
H191 A:R1Z101 3.2 21.0 1.0
H291 A:R1Z101 3.2 22.7 1.0
H161 A:R1Z101 3.2 17.4 1.0
H281 A:R1Z101 3.3 20.7 1.0
C1 A:R1Z101 4.1 17.0 1.0
C4 A:R1Z101 4.2 14.4 1.0
C22 A:R1Z101 4.2 19.5 1.0
C25 A:R1Z101 4.2 19.0 1.0
C14 A:R1Z101 4.2 19.4 1.0
C35 A:R1Z101 4.3 15.1 1.0
C32 A:R1Z101 4.3 19.9 1.0
C20 A:R1Z101 4.4 19.2 1.0
C17 A:R1Z101 4.4 14.0 1.0
C37 A:R1Z101 4.4 14.2 1.0
C30 A:R1Z101 4.4 19.9 1.0
C27 A:R1Z101 4.4 18.7 1.0
H21 A:DG2 4.7 14.3 1.0
C13 A:R1Z101 4.7 18.6 1.0
C21 A:R1Z101 4.8 18.9 1.0
C18 A:R1Z101 4.8 13.5 1.0
O A:HOH224 4.8 27.7 1.0
C26 A:R1Z101 4.8 19.6 1.0
C36 A:R1Z101 4.8 14.2 1.0
C31 A:R1Z101 4.9 20.2 1.0
H221 A:R1Z101 5.0 23.4 1.0
H251 A:R1Z101 5.0 22.8 1.0

Ruthenium binding site 2 out of 5 in 4e1u

Go back to Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 2 out of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:12.6
occ:1.00
RU1 A:R1Z102 0.0 12.6 1.0
N8 A:R1Z102 2.0 13.5 1.0
N5 A:R1Z102 2.0 12.9 1.0
N2 A:R1Z102 2.1 12.6 1.0
N6 A:R1Z102 2.1 13.3 1.0
N1 A:R1Z102 2.1 12.4 1.0
N7 A:R1Z102 2.1 14.7 1.0
C34 A:R1Z102 2.9 13.6 1.0
C2 A:R1Z102 2.9 12.3 1.0
C3 A:R1Z102 2.9 12.3 1.0
C23 A:R1Z102 2.9 14.4 1.0
C24 A:R1Z102 2.9 14.2 1.0
C33 A:R1Z102 2.9 14.0 1.0
C38 A:R1Z102 3.0 14.2 1.0
C19 A:R1Z102 3.0 13.9 1.0
C16 A:R1Z102 3.1 13.2 1.0
C15 A:R1Z102 3.1 12.4 1.0
C28 A:R1Z102 3.1 14.2 1.0
C29 A:R1Z102 3.1 15.4 1.0
H191 A:R1Z102 3.2 16.6 1.0
H161 A:R1Z102 3.2 15.9 1.0
H381 A:R1Z102 3.2 17.0 1.0
H151 A:R1Z102 3.2 14.9 1.0
H281 A:R1Z102 3.2 17.0 1.0
H291 A:R1Z102 3.3 18.5 1.0
C35 A:R1Z102 4.2 15.6 1.0
C22 A:R1Z102 4.2 15.4 1.0
C4 A:R1Z102 4.3 13.3 1.0
C1 A:R1Z102 4.3 12.9 1.0
C25 A:R1Z102 4.3 15.5 1.0
C32 A:R1Z102 4.3 14.9 1.0
C17 A:R1Z102 4.4 14.2 1.0
C14 A:R1Z102 4.4 13.4 1.0
C37 A:R1Z102 4.4 16.1 1.0
C27 A:R1Z102 4.4 15.9 1.0
C20 A:R1Z102 4.4 15.2 1.0
C30 A:R1Z102 4.4 15.8 1.0
C36 A:R1Z102 4.8 15.7 1.0
C21 A:R1Z102 4.8 16.0 1.0
C18 A:R1Z102 4.8 13.7 1.0
C26 A:R1Z102 4.9 15.8 1.0
C13 A:R1Z102 4.9 13.3 1.0
C31 A:R1Z102 4.9 15.2 1.0
H21 A:DG3 4.9 14.0 0.8
H21 A:DG3 4.9 16.9 0.2
H351 A:R1Z102 5.0 18.8 1.0

Ruthenium binding site 3 out of 5 in 4e1u

Go back to Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 3 out of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru103

b:10.3
occ:1.00
RU1 A:R1Z103 0.0 10.3 1.0
N5 A:R1Z103 2.0 10.0 1.0
N8 A:R1Z103 2.0 11.8 1.0
N1 A:R1Z103 2.0 10.2 1.0
N2 A:R1Z103 2.1 10.1 1.0
N7 A:R1Z103 2.1 10.9 1.0
N6 A:R1Z103 2.1 11.1 1.0
C2 A:R1Z103 2.9 10.0 1.0
C3 A:R1Z103 2.9 9.7 1.0
C33 A:R1Z103 2.9 11.4 1.0
C24 A:R1Z103 2.9 11.4 1.0
C34 A:R1Z103 2.9 12.1 1.0
C23 A:R1Z103 2.9 10.6 1.0
C19 A:R1Z103 3.0 10.3 1.0
C38 A:R1Z103 3.0 13.2 1.0
C15 A:R1Z103 3.0 10.5 1.0
C28 A:R1Z103 3.0 12.8 1.0
C16 A:R1Z103 3.1 11.2 1.0
C29 A:R1Z103 3.1 11.1 1.0
H191 A:R1Z103 3.1 12.3 1.0
H381 A:R1Z103 3.1 15.9 1.0
H151 A:R1Z103 3.1 12.7 1.0
H281 A:R1Z103 3.1 15.3 1.0
H161 A:R1Z103 3.2 13.4 1.0
H291 A:R1Z103 3.2 13.3 1.0
C4 A:R1Z103 4.2 11.2 1.0
C1 A:R1Z103 4.2 10.4 1.0
C35 A:R1Z103 4.2 15.8 1.0
C32 A:R1Z103 4.2 13.0 1.0
C22 A:R1Z103 4.3 11.9 1.0
C25 A:R1Z103 4.3 13.6 1.0
C14 A:R1Z103 4.3 11.3 1.0
C27 A:R1Z103 4.3 15.3 1.0
C30 A:R1Z103 4.3 11.6 1.0
C17 A:R1Z103 4.3 11.6 1.0
C20 A:R1Z103 4.4 10.9 1.0
C37 A:R1Z103 4.4 14.9 1.0
C18 A:R1Z103 4.8 12.0 1.0
C13 A:R1Z103 4.8 10.5 1.0
C26 A:R1Z103 4.8 16.0 1.0
C31 A:R1Z103 4.8 13.1 1.0
C36 A:R1Z103 4.8 15.8 1.0
C21 A:R1Z103 4.9 12.2 1.0
O B:HOH1026 4.9 28.6 1.0
O A:HOH245 4.9 29.2 1.0
H62 B:DA9 4.9 16.6 1.0
H62 A:DA9 5.0 15.0 1.0

Ruthenium binding site 4 out of 5 in 4e1u

Go back to Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 4 out of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru104

b:9.7
occ:1.00
RU1 A:R1Z104 0.0 9.7 1.0
N7 A:R1Z104 2.0 11.1 1.0
N5 A:R1Z104 2.0 9.6 1.0
N6 A:R1Z104 2.1 10.4 1.0
N1 A:R1Z104 2.1 9.8 1.0
N2 A:R1Z104 2.1 9.4 1.0
N8 A:R1Z104 2.1 11.2 1.0
C2 A:R1Z104 2.9 9.6 1.0
C3 A:R1Z104 2.9 9.4 1.0
C24 A:R1Z104 2.9 10.0 1.0
C33 A:R1Z104 2.9 13.0 1.0
C23 A:R1Z104 2.9 9.8 1.0
C34 A:R1Z104 3.0 12.9 1.0
C29 A:R1Z104 3.0 12.6 1.0
C19 A:R1Z104 3.0 9.7 1.0
C28 A:R1Z104 3.1 11.4 1.0
C15 A:R1Z104 3.1 10.7 1.0
C38 A:R1Z104 3.1 11.9 1.0
C16 A:R1Z104 3.1 10.2 1.0
H291 A:R1Z104 3.1 15.1 1.0
H191 A:R1Z104 3.1 11.6 1.0
H281 A:R1Z104 3.2 13.7 1.0
H151 A:R1Z104 3.2 12.9 1.0
H161 A:R1Z104 3.2 12.2 1.0
H381 A:R1Z104 3.2 14.2 1.0
C1 A:R1Z104 4.2 10.0 1.0
C22 A:R1Z104 4.2 11.5 1.0
C25 A:R1Z104 4.2 11.4 1.0
C32 A:R1Z104 4.2 14.9 1.0
C4 A:R1Z104 4.3 9.8 1.0
C35 A:R1Z104 4.3 15.3 1.0
C30 A:R1Z104 4.3 14.5 1.0
C27 A:R1Z104 4.4 12.5 1.0
C14 A:R1Z104 4.4 10.5 1.0
C20 A:R1Z104 4.4 10.4 1.0
C17 A:R1Z104 4.4 10.2 1.0
C37 A:R1Z104 4.4 14.9 1.0
H1' B:DA5 4.5 16.2 0.2
H2 B:DA4 4.6 12.7 1.0
H21 B:DG3 4.6 11.0 0.5
H21 B:DG3 4.7 11.2 0.5
H1' B:DA5 4.8 15.5 0.8
C31 A:R1Z104 4.8 16.0 1.0
C13 A:R1Z104 4.8 10.7 1.0
C26 A:R1Z104 4.8 12.0 1.0
C21 A:R1Z104 4.8 10.2 1.0
C18 A:R1Z104 4.9 10.3 1.0
O B:HOH1016 4.9 25.1 1.0
C36 A:R1Z104 4.9 16.0 1.0
C2 B:DA4 4.9 10.6 1.0
H22 B:DG3 5.0 11.0 0.5

Ruthenium binding site 5 out of 5 in 4e1u

Go back to Ruthenium Binding Sites List in 4e1u
Ruthenium binding site 5 out of 5 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru105

b:9.8
occ:1.00
RU1 A:R1Z105 0.0 9.8 1.0
N8 A:R1Z105 2.0 12.3 1.0
N5 A:R1Z105 2.0 10.7 1.0
N6 A:R1Z105 2.1 10.2 1.0
N7 A:R1Z105 2.1 11.0 1.0
N1 A:R1Z105 2.1 9.2 1.0
N2 A:R1Z105 2.1 10.0 1.0
C2 A:R1Z105 2.9 9.8 1.0
C24 A:R1Z105 2.9 10.8 1.0
C23 A:R1Z105 2.9 10.9 1.0
C33 A:R1Z105 2.9 11.8 1.0
C3 A:R1Z105 2.9 9.7 1.0
C34 A:R1Z105 2.9 13.2 1.0
C19 A:R1Z105 3.0 11.2 1.0
C38 A:R1Z105 3.0 14.2 1.0
C15 A:R1Z105 3.0 10.4 1.0
C29 A:R1Z105 3.0 10.7 1.0
C28 A:R1Z105 3.1 10.8 1.0
C16 A:R1Z105 3.1 11.0 1.0
H191 A:R1Z105 3.1 13.4 1.0
H291 A:R1Z105 3.1 12.8 1.0
H151 A:R1Z105 3.1 12.4 1.0
H381 A:R1Z105 3.2 17.1 1.0
H281 A:R1Z105 3.2 13.0 1.0
H161 A:R1Z105 3.2 13.2 1.0
C22 A:R1Z105 4.2 12.7 1.0
C25 A:R1Z105 4.3 12.3 1.0
C1 A:R1Z105 4.3 10.7 1.0
C35 A:R1Z105 4.3 16.1 1.0
C32 A:R1Z105 4.3 13.8 1.0
H21 B:DG2 4.3 12.2 0.5
C4 A:R1Z105 4.3 10.6 1.0
C14 A:R1Z105 4.3 11.8 1.0
C30 A:R1Z105 4.3 12.5 1.0
C27 A:R1Z105 4.3 11.5 1.0
C20 A:R1Z105 4.4 12.3 1.0
C17 A:R1Z105 4.4 11.3 1.0
C37 A:R1Z105 4.4 15.8 1.0
H21 B:DG2 4.6 12.1 0.6
C13 A:R1Z105 4.8 11.8 1.0
C26 A:R1Z105 4.8 12.6 1.0
C31 A:R1Z105 4.8 13.1 1.0
C21 A:R1Z105 4.8 12.7 1.0
C36 A:R1Z105 4.9 16.4 1.0
C18 A:R1Z105 4.9 11.4 1.0
N2 B:DG2 4.9 10.2 0.5
N3 B:DG2 4.9 11.6 0.5

Reference:

H.Song, J.T.Kaiser, J.K.Barton. Crystal Structure of Delta-[Ru(Bpy)2DPPZ]2+ Bound to Mismatched Dna Reveals Side-By-Side Metalloinsertion and Intercalation. Nat Chem V. 4 615 2012.
ISSN: ISSN 1755-4349
PubMed: 22824892
DOI: 10.1038/NCHEM.1375
Page generated: Wed Dec 16 02:08:11 2020

Last articles

Zn in 7O75
Zn in 7O73
Zn in 7O4I
Zn in 7O72
Zn in 7O4J
Zn in 7NVR
Zn in 7NVY
Zn in 7NVZ
Zn in 7NW0
Zn in 7O4K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy