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

Ruthenium in PDB 3uyb: X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga)

Protein crystallography data

The structure of X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga), PDB code: 3uyb was solved by H.N.Niyazi, S.C.M.Texeira, E.P.Mitchell, J.C.Cardin, V.T.Forsyth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.45 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 54.376, 54.376, 28.995, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 16.7

Other elements in 3uyb:

The structure of X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga) also contains other interesting chemical elements:

Barium (Ba) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga) (pdb code 3uyb). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga), PDB code: 3uyb:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 3uyb

Go back to Ruthenium Binding Sites List in 3uyb
Ruthenium binding site 1 out of 2 in the X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru11

b:16.4
occ:0.50
RU A:RKL11 0.0 16.4 0.5
N8 A:RKL11 1.9 19.7 0.5
N5 A:RKL11 1.9 15.9 0.5
N12 A:RKL11 1.9 15.9 0.5
N9 A:RKL11 1.9 15.1 0.5
N1 A:RKL11 1.9 15.3 0.5
N2 A:RKL11 1.9 15.1 0.5
C26 A:RKL11 2.7 18.3 0.5
C19 A:RKL11 2.7 16.3 0.5
C36 A:RKL11 2.7 13.7 0.5
C10 A:RKL11 2.8 14.8 0.5
C29 A:RKL11 2.8 13.8 0.5
C1 A:RKL11 2.8 11.5 0.5
C38 A:RKL11 3.0 19.1 0.5
C28 A:RKL11 3.0 19.5 0.5
C20 A:RKL11 3.0 15.5 0.5
C2 A:RKL11 3.0 11.3 0.5
C12 A:RKL11 3.0 15.8 0.5
C30 A:RKL11 3.1 13.8 0.5
C25 A:RKL11 4.1 16.3 0.5
C22 A:RKL11 4.1 19.4 0.5
C35 A:RKL11 4.1 11.9 0.5
C8 A:RKL11 4.2 12.6 0.5
C32 A:RKL11 4.2 16.2 0.5
C5 A:RKL11 4.2 11.8 0.5
C27 A:RKL11 4.2 17.4 0.5
C37 A:RKL11 4.2 19.5 0.5
C21 A:RKL11 4.3 16.9 0.5
C11 A:RKL11 4.3 12.1 0.5
C3 A:RKL11 4.3 12.7 0.5
C31 A:RKL11 4.4 15.9 0.5
N3 A:DA6 4.6 15.4 1.0
N7 A:RKL11 4.6 20.7 0.5
N11 A:RKL11 4.7 18.3 0.5
N6 A:RKL11 4.8 18.4 0.5
O A:HOH15 4.8 25.5 1.0
O4' A:DA6 4.8 18.1 1.0
C9 A:RKL11 4.8 14.6 0.5
C4 A:RKL11 4.8 11.6 0.5
N10 A:RKL11 4.8 13.9 0.5
O A:HOH58 4.9 33.8 1.0
C2 A:DA6 5.0 16.5 1.0

Ruthenium binding site 2 out of 2 in 3uyb

Go back to Ruthenium Binding Sites List in 3uyb
Ruthenium binding site 2 out of 2 in the X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of X-Ray Crystal Structure of the Ruthenium Complex [Ru(Tap)2(Dppz)]2+ Bound to D(Tcggtaccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru12

b:14.0
occ:1.00
RU A:RKL12 0.0 14.0 1.0
N2 A:RKL12 1.9 15.6 1.0
N12 A:RKL12 1.9 15.4 1.0
N1 A:RKL12 2.0 15.7 1.0
N5 A:RKL12 2.0 13.9 1.0
N9 A:RKL12 2.0 14.1 1.0
N8 A:RKL12 2.0 13.2 1.0
C1 A:RKL12 2.8 12.4 1.0
C36 A:RKL12 2.8 15.1 1.0
C10 A:RKL12 2.8 11.5 1.0
C19 A:RKL12 2.8 11.5 1.0
C29 A:RKL12 2.8 13.9 1.0
C26 A:RKL12 2.9 12.1 1.0
C2 A:RKL12 3.0 13.3 1.0
C30 A:RKL12 3.0 14.4 1.0
C38 A:RKL12 3.1 16.3 1.0
C12 A:RKL12 3.1 14.6 1.0
C28 A:RKL12 3.1 14.0 1.0
C20 A:RKL12 3.1 12.9 1.0
C35 A:RKL12 4.2 13.0 1.0
C8 A:RKL12 4.2 14.0 1.0
C22 A:RKL12 4.2 12.2 1.0
C5 A:RKL12 4.2 13.0 1.0
C25 A:RKL12 4.2 12.9 1.0
C32 A:RKL12 4.3 14.2 1.0
C37 A:RKL12 4.3 18.2 1.0
C31 A:RKL12 4.3 15.8 1.0
C3 A:RKL12 4.3 13.2 1.0
C11 A:RKL12 4.4 14.1 1.0
C27 A:RKL12 4.4 14.9 1.0
C21 A:RKL12 4.4 14.1 1.0
O A:HOH72 4.7 18.0 1.0
N11 A:RKL12 4.8 15.8 1.0
N10 A:RKL12 4.8 14.4 1.0
C4 A:RKL12 4.8 14.3 1.0
O A:HOH24 4.8 25.4 1.0
N6 A:RKL12 4.8 13.0 1.0
C9 A:RKL12 4.9 15.2 1.0
N7 A:RKL12 4.9 12.4 1.0

Reference:

H.N.Niyazi, K.O'sullivan, S.C.M.Texeira, E.P.Mitchell, J.M.Kelly, J.C.Cardin, V.T.Forsyth. Crystal Structure of Lambda-[Ru(Tap)2(Dppz)]2+ with D(Tcggtaccga)2 Displaying Kinking of Dna Via Semiintercalation. To Be Published.
Page generated: Wed Dec 16 02:08:08 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy