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Ruthenium in PDB 5ip8: Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg)

Protein crystallography data

The structure of Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg), PDB code: 5ip8 was solved by J.E.Souter, 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) 23.73 / 1.76
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 47.450, 47.450, 35.130, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22

Other elements in 5ip8:

The structure of Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg) also contains other interesting chemical elements:

Barium (Ba) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg) (pdb code 5ip8). 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)2DPPZ Bound to D(Ccggctccgg), PDB code: 5ip8:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 5ip8

Go back to Ruthenium Binding Sites List in 5ip8
Ruthenium binding site 1 out of 2 in the Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg)


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)2DPPZ Bound to D(Ccggctccgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru102

b:36.6
occ:1.00
RU B:RKL102 0.0 36.6 1.0
N5 B:RKL102 2.0 34.4 1.0
N1 B:RKL102 2.1 37.0 1.0
N2 B:RKL102 2.1 37.0 1.0
N9 B:RKL102 2.1 36.2 1.0
N8 B:RKL102 2.1 35.7 1.0
N12 B:RKL102 2.1 32.0 1.0
C1 B:RKL102 2.8 41.0 1.0
C10 B:RKL102 2.8 38.4 1.0
C19 B:RKL102 2.8 36.4 1.0
C26 B:RKL102 2.8 36.2 1.0
C36 B:RKL102 2.8 39.0 1.0
C29 B:RKL102 2.9 35.5 1.0
C20 B:RKL102 3.1 37.1 1.0
C12 B:RKL102 3.1 39.7 1.0
C2 B:RKL102 3.1 40.0 1.0
C38 B:RKL102 3.1 37.5 1.0
C28 B:RKL102 3.2 36.1 1.0
C30 B:RKL102 3.2 39.4 1.0
C22 B:RKL102 4.2 31.9 1.0
C5 B:RKL102 4.2 36.4 1.0
C35 B:RKL102 4.2 37.3 1.0
C8 B:RKL102 4.2 31.8 1.0
C25 B:RKL102 4.2 37.2 1.0
C32 B:RKL102 4.3 42.3 1.0
C21 B:RKL102 4.4 39.4 1.0
C11 B:RKL102 4.4 34.3 1.0
C37 B:RKL102 4.4 33.6 1.0
C3 B:RKL102 4.4 38.2 1.0
C27 B:RKL102 4.4 37.2 1.0
C31 B:RKL102 4.5 40.3 1.0
O A:HOH209 4.5 40.5 1.0
N11 B:RKL102 4.8 34.9 1.0
N6 B:RKL102 4.8 37.9 1.0
C4 B:RKL102 4.8 41.3 1.0
C9 B:RKL102 4.8 34.8 1.0
N10 B:RKL102 4.9 43.8 1.0
N7 B:RKL102 4.9 35.4 1.0
O B:HOH212 4.9 38.3 1.0

Ruthenium binding site 2 out of 2 in 5ip8

Go back to Ruthenium Binding Sites List in 5ip8
Ruthenium binding site 2 out of 2 in the Lambda-Ru(Tap)2DPPZ Bound to D(Ccggctccgg)


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)2DPPZ Bound to D(Ccggctccgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru103

b:36.4
occ:1.00
RU B:RKL103 0.0 36.4 1.0
N9 B:RKL103 2.0 35.5 1.0
N2 B:RKL103 2.1 36.2 1.0
N1 B:RKL103 2.1 39.6 1.0
N8 B:RKL103 2.1 34.1 1.0
N5 B:RKL103 2.1 36.4 1.0
N12 B:RKL103 2.1 35.5 1.0
C1 B:RKL103 2.8 36.1 1.0
C10 B:RKL103 2.8 40.7 1.0
C29 B:RKL103 2.8 37.3 1.0
C36 B:RKL103 2.8 35.1 1.0
C26 B:RKL103 2.8 40.2 1.0
C19 B:RKL103 2.9 37.5 1.0
C2 B:RKL103 3.1 40.4 1.0
C30 B:RKL103 3.1 35.0 1.0
C12 B:RKL103 3.2 37.6 1.0
C28 B:RKL103 3.2 40.0 1.0
C38 B:RKL103 3.2 35.0 1.0
C20 B:RKL103 3.2 41.2 1.0
C32 B:RKL103 4.2 31.5 1.0
C25 B:RKL103 4.2 39.8 1.0
C5 B:RKL103 4.2 32.8 1.0
C8 B:RKL103 4.2 39.3 1.0
C35 B:RKL103 4.2 36.5 1.0
C22 B:RKL103 4.3 40.6 1.0
C3 B:RKL103 4.4 37.6 1.0
C31 B:RKL103 4.4 37.6 1.0
C37 B:RKL103 4.4 36.2 1.0
C27 B:RKL103 4.4 36.2 1.0
C11 B:RKL103 4.4 37.8 1.0
C21 B:RKL103 4.5 40.9 1.0
O2 A:DC2 4.6 37.6 1.0
N7 B:RKL103 4.8 36.8 1.0
N10 B:RKL103 4.8 37.7 1.0
C4 B:RKL103 4.8 34.0 1.0
C9 B:RKL103 4.8 37.9 1.0
N6 B:RKL103 4.9 40.8 1.0
N2 B:DG9 4.9 39.8 1.0
N11 B:RKL103 4.9 35.0 1.0
O4' A:DC2 4.9 39.8 1.0

Reference:

J.P.Hall, J.E.Souter, S.P.Gurung, C.J.Cardin. Sequence Specific Binding of Light Activated Ru-Polypyridyls To Be Published.
Page generated: Wed Dec 16 02:08:28 2020

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