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

Ruthenium in PDB 4iii: Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution

Protein crystallography data

The structure of Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution, PDB code: 4iii 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) 28.93 / 1.02
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.340, 42.340, 39.630, 90.00, 90.00, 90.00
R / Rfree (%) 10.1 / 11.4

Other elements in 4iii:

The structure of Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution also contains other interesting chemical elements:

Barium (Ba) 1 atom
Chlorine (Cl) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution (pdb code 4iii). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution, PDB code: 4iii:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 4iii

Go back to Ruthenium Binding Sites List in 4iii
Ruthenium binding site 1 out of 2 in the Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:9.9
occ:0.66
RU A:RCZ102 0.0 9.9 0.7
RU A:RCZ102 0.0 14.2 0.3
N5 A:RCZ102 1.9 18.1 0.3
N12 A:RCZ102 2.0 18.8 0.3
N2 A:RCZ102 2.0 15.1 0.3
N9 A:RCZ102 2.0 13.5 0.3
N8 A:RCZ102 2.0 17.2 0.3
N1 A:RCZ102 2.0 13.0 0.3
N1 A:RCZ102 2.0 10.1 0.7
N5 A:RCZ102 2.0 9.4 0.7
N8 A:RCZ102 2.1 9.0 0.7
N9 A:RCZ102 2.1 11.6 0.7
N2 A:RCZ102 2.1 9.9 0.7
N12 A:RCZ102 2.1 10.7 0.7
C19 A:RCZ102 2.7 16.7 0.3
C36 A:RCZ102 2.8 15.5 0.3
C26 A:RCZ102 2.8 15.6 0.3
C1 A:RCZ102 2.8 15.5 0.3
C29 A:RCZ102 2.8 13.1 0.3
C10 A:RCZ102 2.8 13.6 0.3
C19 A:RCZ102 2.9 9.0 0.7
C29 A:RCZ102 2.9 12.6 0.7
C36 A:RCZ102 2.9 11.7 0.7
C10 A:RCZ102 2.9 10.5 0.7
C1 A:RCZ102 2.9 10.5 0.7
C26 A:RCZ102 2.9 8.8 0.7
C12 A:RCZ102 3.1 14.5 0.3
C20 A:RCZ102 3.1 17.8 0.3
C30 A:RCZ102 3.1 13.2 0.3
C20 A:RCZ102 3.1 9.7 0.7
C2 A:RCZ102 3.1 10.4 0.7
C38 A:RCZ102 3.1 10.8 0.7
C12 A:RCZ102 3.1 10.7 0.7
C28 A:RCZ102 3.1 9.7 0.7
C30 A:RCZ102 3.1 14.0 0.7
C2 A:RCZ102 3.1 15.9 0.3
C38 A:RCZ102 3.1 15.9 0.3
C28 A:RCZ102 3.1 19.6 0.3
H12 A:RCZ102 3.2 14.7 0.3
H12 A:RCZ102 3.2 11.0 0.7
H2 A:RCZ102 3.2 10.7 0.7
H20 A:RCZ102 3.3 9.7 0.7
H30 A:RCZ102 3.3 13.3 0.3
H38 A:RCZ102 3.3 11.3 0.7
H28 A:RCZ102 3.3 10.0 0.7
H30 A:RCZ102 3.3 13.9 0.7
H2 A:RCZ102 3.3 16.1 0.3
H20 A:RCZ102 3.3 18.1 0.3
H28 A:RCZ102 3.4 20.0 0.3
H38 A:RCZ102 3.4 16.1 0.3
C35 A:RCZ102 4.1 13.3 0.3
C22 A:RCZ102 4.2 17.8 0.3
C8 A:RCZ102 4.2 14.4 0.3
C32 A:RCZ102 4.2 12.7 0.3
C25 A:RCZ102 4.2 17.0 0.3
H21 A:DG9 4.2 13.2 0.5
C5 A:RCZ102 4.2 16.3 0.3
H21 A:DG9 4.2 13.2 0.5
C35 A:RCZ102 4.2 13.3 0.7
C5 A:RCZ102 4.2 11.4 0.7
C25 A:RCZ102 4.2 9.1 0.7
C22 A:RCZ102 4.3 9.7 0.7
C8 A:RCZ102 4.3 11.1 0.7
C32 A:RCZ102 4.3 13.9 0.7
C21 A:RCZ102 4.3 19.2 0.3
C3 A:RCZ102 4.3 11.3 0.7
C37 A:RCZ102 4.3 12.4 0.7
C11 A:RCZ102 4.3 15.0 0.3
C37 A:RCZ102 4.4 16.0 0.3
C31 A:RCZ102 4.4 14.3 0.3
C3 A:RCZ102 4.4 16.5 0.3
C11 A:RCZ102 4.4 12.8 0.7
C27 A:RCZ102 4.4 10.1 0.7
C21 A:RCZ102 4.4 10.7 0.7
C27 A:RCZ102 4.4 18.5 0.3
C31 A:RCZ102 4.4 15.2 0.7
H22 A:DG9 4.5 13.6 0.5
H22 A:DG9 4.5 13.6 0.5
O A:HOH275 4.6 13.6 1.0
N2 A:DG9 4.6 13.8 0.5
N2 A:DG9 4.6 13.8 0.5
N6 A:RCZ102 4.7 17.9 0.3
N11 A:RCZ102 4.8 14.4 0.3
C9 A:RCZ102 4.8 14.8 0.3
N7 A:RCZ102 4.8 20.1 0.3
N11 A:RCZ102 4.8 13.0 0.7
C9 A:RCZ102 4.8 11.5 0.7
C4 A:RCZ102 4.8 19.5 0.3
C4 A:RCZ102 4.8 11.7 0.7
N7 A:RCZ102 4.9 9.7 0.7
N6 A:RCZ102 4.9 9.8 0.7
N10 A:RCZ102 4.9 17.0 0.7
N10 A:RCZ102 4.9 14.0 0.3
O A:HOH266 4.9 34.0 1.0

Ruthenium binding site 2 out of 2 in 4iii

Go back to Ruthenium Binding Sites List in 4iii
Ruthenium binding site 2 out of 2 in the Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Lambda-[Ru(Tap)2(11-Cl-Dppz)] with A Dna Decamer at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:14.2
occ:0.33
RU A:RCZ102 0.0 14.2 0.3
RU A:RCZ102 0.0 9.9 0.7
N5 A:RCZ102 1.9 18.1 0.3
N12 A:RCZ102 2.0 18.8 0.3
N9 A:RCZ102 2.0 13.5 0.3
N2 A:RCZ102 2.0 15.1 0.3
N8 A:RCZ102 2.0 17.2 0.3
N1 A:RCZ102 2.0 13.0 0.3
N5 A:RCZ102 2.0 9.4 0.7
N1 A:RCZ102 2.0 10.1 0.7
N8 A:RCZ102 2.0 9.0 0.7
N2 A:RCZ102 2.1 9.9 0.7
N9 A:RCZ102 2.1 11.6 0.7
N12 A:RCZ102 2.1 10.7 0.7
C19 A:RCZ102 2.7 16.7 0.3
C36 A:RCZ102 2.7 15.5 0.3
C26 A:RCZ102 2.8 15.6 0.3
C29 A:RCZ102 2.8 13.1 0.3
C1 A:RCZ102 2.8 15.5 0.3
C10 A:RCZ102 2.8 13.6 0.3
C19 A:RCZ102 2.9 9.0 0.7
C29 A:RCZ102 2.9 12.6 0.7
C36 A:RCZ102 2.9 11.7 0.7
C10 A:RCZ102 2.9 10.5 0.7
C1 A:RCZ102 2.9 10.5 0.7
C26 A:RCZ102 2.9 8.8 0.7
C12 A:RCZ102 3.1 14.5 0.3
C30 A:RCZ102 3.1 13.2 0.3
C20 A:RCZ102 3.1 9.7 0.7
C20 A:RCZ102 3.1 17.8 0.3
C38 A:RCZ102 3.1 10.8 0.7
C12 A:RCZ102 3.1 10.7 0.7
C2 A:RCZ102 3.1 10.4 0.7
C28 A:RCZ102 3.1 9.7 0.7
C2 A:RCZ102 3.1 15.9 0.3
C30 A:RCZ102 3.1 14.0 0.7
C38 A:RCZ102 3.1 15.9 0.3
C28 A:RCZ102 3.1 19.6 0.3
H12 A:RCZ102 3.2 14.7 0.3
H12 A:RCZ102 3.2 11.0 0.7
H2 A:RCZ102 3.2 10.7 0.7
H20 A:RCZ102 3.3 9.7 0.7
H30 A:RCZ102 3.3 13.3 0.3
H38 A:RCZ102 3.3 11.3 0.7
H28 A:RCZ102 3.3 10.0 0.7
H30 A:RCZ102 3.3 13.9 0.7
H2 A:RCZ102 3.3 16.1 0.3
H20 A:RCZ102 3.3 18.1 0.3
H28 A:RCZ102 3.4 20.0 0.3
H38 A:RCZ102 3.4 16.1 0.3
C35 A:RCZ102 4.1 13.3 0.3
C22 A:RCZ102 4.2 17.8 0.3
C32 A:RCZ102 4.2 12.7 0.3
C8 A:RCZ102 4.2 14.4 0.3
C25 A:RCZ102 4.2 17.0 0.3
C5 A:RCZ102 4.2 16.3 0.3
H21 A:DG9 4.2 13.2 0.5
H21 A:DG9 4.2 13.2 0.5
C25 A:RCZ102 4.2 9.1 0.7
C35 A:RCZ102 4.2 13.3 0.7
C5 A:RCZ102 4.3 11.4 0.7
C22 A:RCZ102 4.3 9.7 0.7
C8 A:RCZ102 4.3 11.1 0.7
C32 A:RCZ102 4.3 13.9 0.7
C3 A:RCZ102 4.3 11.3 0.7
C21 A:RCZ102 4.3 19.2 0.3
C37 A:RCZ102 4.3 12.4 0.7
C11 A:RCZ102 4.3 15.0 0.3
C37 A:RCZ102 4.3 16.0 0.3
C31 A:RCZ102 4.4 14.3 0.3
C3 A:RCZ102 4.4 16.5 0.3
C11 A:RCZ102 4.4 12.8 0.7
C27 A:RCZ102 4.4 10.1 0.7
C21 A:RCZ102 4.4 10.7 0.7
C27 A:RCZ102 4.4 18.5 0.3
C31 A:RCZ102 4.4 15.2 0.7
H22 A:DG9 4.5 13.6 0.5
H22 A:DG9 4.5 13.6 0.5
O A:HOH275 4.6 13.6 1.0
N2 A:DG9 4.6 13.8 0.5
N2 A:DG9 4.6 13.8 0.5
N6 A:RCZ102 4.7 17.9 0.3
N11 A:RCZ102 4.8 14.4 0.3
C9 A:RCZ102 4.8 14.8 0.3
C9 A:RCZ102 4.8 11.5 0.7
N7 A:RCZ102 4.8 20.1 0.3
N11 A:RCZ102 4.8 13.0 0.7
C4 A:RCZ102 4.8 19.5 0.3
C4 A:RCZ102 4.8 11.7 0.7
N7 A:RCZ102 4.9 9.7 0.7
N6 A:RCZ102 4.9 9.8 0.7
N10 A:RCZ102 4.9 14.0 0.3
N10 A:RCZ102 4.9 17.0 0.7
O A:HOH266 4.9 34.0 1.0

Reference:

J.P.Hall, H.Beer, K.Buchner, D.J.Cardin, C.J.Cardin. Preferred Orientation in An Angled Intercalation Site of A Chloro-Substituted Lambda-[Ru(Tap)2(Dppz)]2+ Complex Bound to D(Tcggcgccga)2. Philos Trans A Math Phys Eng V. 371 20525 2013SCI.
ISSN: ISSN 1364-503X
PubMed: 23776304
DOI: 10.1098/RSTA.2012.0525
Page generated: Wed Dec 16 02:08:12 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