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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

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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

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