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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

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