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Ruthenium in PDB 4ly2: X-Ray Crystal Structure of the Ruthenium Complex [Ru(Phen)2(Dppz)]2+ Bound to D(Tcggtaccga)

Protein crystallography data

The structure of X-Ray Crystal Structure of the Ruthenium Complex [Ru(Phen)2(Dppz)]2+ Bound to D(Tcggtaccga), PDB code: 4ly2 was solved by H Niyazi, S Teixeira, E Mitchell, T Forsyth, C Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.09 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 52.450, 52.450, 32.580, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.9

Other elements in 4ly2:

The structure of X-Ray Crystal Structure of the Ruthenium Complex [Ru(Phen)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(Phen)2(Dppz)]2+ Bound to D(Tcggtaccga) (pdb code 4ly2). 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(Phen)2(Dppz)]2+ Bound to D(Tcggtaccga), PDB code: 4ly2:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 4ly2

Go back to Ruthenium Binding Sites List in 4ly2
Ruthenium binding site 1 out of 2 in the X-Ray Crystal Structure of the Ruthenium Complex [Ru(Phen)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(Phen)2(Dppz)]2+ Bound to D(Tcggtaccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru101

b:31.8
occ:1.00
RU A:RKP101 0.0 31.8 1.0
N8 A:RKP101 1.9 35.2 1.0
N1 A:RKP101 2.0 29.5 1.0
N5 A:RKP101 2.0 30.9 1.0
N2 A:RKP101 2.0 31.9 1.0
N9 A:RKP101 2.0 31.4 1.0
N12 A:RKP101 2.0 31.7 1.0
C26 A:RKP101 2.7 35.1 1.0
C19 A:RKP101 2.8 36.3 1.0
C1 A:RKP101 2.8 31.2 1.0
C10 A:RKP101 2.8 28.1 1.0
C29 A:RKP101 2.9 31.7 1.0
C36 A:RKP101 2.9 29.5 1.0
C28 A:RKP101 3.0 31.1 1.0
C30 A:RKP101 3.0 32.0 1.0
C38 A:RKP101 3.1 32.8 1.0
C20 A:RKP101 3.1 30.6 1.0
C12 A:RKP101 3.1 28.5 1.0
C2 A:RKP101 3.1 34.8 1.0
C25 A:RKP101 4.1 33.8 1.0
C5 A:RKP101 4.1 29.1 1.0
C8 A:RKP101 4.1 27.8 1.0
C22 A:RKP101 4.2 32.4 1.0
C32 A:RKP101 4.2 30.1 1.0
C27 A:RKP101 4.2 30.2 1.0
C35 A:RKP101 4.2 31.7 1.0
C31 A:RKP101 4.3 28.9 1.0
C21 A:RKP101 4.3 30.3 1.0
C11 A:RKP101 4.3 25.9 1.0
C37 A:RKP101 4.4 32.9 1.0
C3 A:RKP101 4.4 30.8 1.0
C42 A:RKP101 4.7 29.8 1.0
C41 A:RKP101 4.7 33.6 1.0
C43 A:RKP101 4.7 28.9 1.0
C4 A:RKP101 4.7 29.6 1.0
C9 A:RKP101 4.8 24.9 1.0
C44 A:RKP101 4.9 32.7 1.0
O A:HOH203 4.9 29.1 1.0

Ruthenium binding site 2 out of 2 in 4ly2

Go back to Ruthenium Binding Sites List in 4ly2
Ruthenium binding site 2 out of 2 in the X-Ray Crystal Structure of the Ruthenium Complex [Ru(Phen)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(Phen)2(Dppz)]2+ Bound to D(Tcggtaccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:31.1
occ:0.50
RU A:RKP102 0.0 31.1 0.5
N8 A:RKP102 1.9 30.9 0.5
N12 A:RKP102 1.9 29.6 0.5
N1 A:RKP102 2.0 30.9 0.5
N2 A:RKP102 2.0 29.9 0.5
N5 A:RKP102 2.0 31.5 0.5
N9 A:RKP102 2.1 31.7 0.5
C26 A:RKP102 2.7 32.6 0.5
C10 A:RKP102 2.8 30.5 0.5
C1 A:RKP102 2.8 29.9 0.5
C19 A:RKP102 2.8 32.6 0.5
C36 A:RKP102 2.8 30.8 0.5
C38 A:RKP102 2.9 32.2 0.5
C29 A:RKP102 2.9 31.0 0.5
C28 A:RKP102 2.9 35.0 0.5
C12 A:RKP102 3.0 29.8 0.5
C20 A:RKP102 3.1 32.1 0.5
C2 A:RKP102 3.1 28.9 0.5
C30 A:RKP102 3.1 30.9 0.5
C25 A:RKP102 4.1 31.1 0.5
C8 A:RKP102 4.1 31.1 0.5
C5 A:RKP102 4.1 30.8 0.5
C35 A:RKP102 4.1 29.8 0.5
C22 A:RKP102 4.2 31.2 0.5
C37 A:RKP102 4.2 30.5 0.5
C27 A:RKP102 4.2 31.9 0.5
C32 A:RKP102 4.2 29.5 0.5
C11 A:RKP102 4.3 29.4 0.5
C21 A:RKP102 4.3 30.6 0.5
C3 A:RKP102 4.3 29.0 0.5
C31 A:RKP102 4.4 29.9 0.5
C42 A:RKP102 4.6 33.1 0.5
C44 A:RKP102 4.7 31.2 0.5
C9 A:RKP102 4.7 29.1 0.5
C4 A:RKP102 4.7 29.0 0.5
C41 A:RKP102 4.8 31.6 0.5
C43 A:RKP102 4.8 30.3 0.5

Reference:

H Niyazi, S Teixeira, E Mitchell, T Forsyth, C Cardin. X-Ray Crystal Structure of the Ruthenium Complex [Ru(Phen)2(Dppz)]2+ Bound to D(Tcggtaccga) To Be Published.
Page generated: Wed Dec 16 02:08:19 2020

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