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Ruthenium in PDB 4r8j: D(Tcggcgccga) with Lambda-[Ru(Tap)2(Dppz)]2+ Soaked in D2O

Protein crystallography data

The structure of D(Tcggcgccga) with Lambda-[Ru(Tap)2(Dppz)]2+ Soaked in D2O, PDB code: 4r8j was solved by J.P.Hall, S.P.Gurung, G.W.Winter, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.66 / 1.21
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.370, 42.370, 39.420, 90.00, 90.00, 90.00
R / Rfree (%) 10.9 / 12.5

Other elements in 4r8j:

The structure of D(Tcggcgccga) with Lambda-[Ru(Tap)2(Dppz)]2+ Soaked in D2O also contains other interesting chemical elements:

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

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the D(Tcggcgccga) with Lambda-[Ru(Tap)2(Dppz)]2+ Soaked in D2O (pdb code 4r8j). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total only one binding site of Ruthenium was determined in the D(Tcggcgccga) with Lambda-[Ru(Tap)2(Dppz)]2+ Soaked in D2O, PDB code: 4r8j:

Ruthenium binding site 1 out of 1 in 4r8j

Go back to Ruthenium Binding Sites List in 4r8j
Ruthenium binding site 1 out of 1 in the D(Tcggcgccga) with Lambda-[Ru(Tap)2(Dppz)]2+ Soaked in D2O


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of D(Tcggcgccga) with Lambda-[Ru(Tap)2(Dppz)]2+ Soaked in D2O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:15.5
occ:1.00
RU A:RKL102 0.0 15.5 1.0
N5 A:RKL102 2.0 14.7 1.0
N9 A:RKL102 2.0 16.5 1.0
N12 A:RKL102 2.1 17.2 1.0
N2 A:RKL102 2.1 15.8 1.0
N1 A:RKL102 2.1 15.7 1.0
N8 A:RKL102 2.1 15.0 1.0
C36 A:RKL102 2.8 15.7 1.0
C29 A:RKL102 2.8 16.2 1.0
C1 A:RKL102 2.8 15.7 1.0
C19 A:RKL102 2.8 14.4 1.0
C10 A:RKL102 2.8 16.1 1.0
C26 A:RKL102 2.8 14.8 1.0
C20 A:RKL102 3.1 15.5 1.0
C38 A:RKL102 3.1 17.0 1.0
C2 A:RKL102 3.1 17.0 1.0
C12 A:RKL102 3.1 16.1 1.0
C30 A:RKL102 3.1 17.8 1.0
C28 A:RKL102 3.2 15.6 1.0
H20 A:RKL102 3.3 15.4 1.0
H12 A:RKL102 3.3 17.0 1.0
H2 A:RKL102 3.3 17.0 1.0
H38 A:RKL102 3.3 17.9 1.0
H30 A:RKL102 3.3 17.3 1.0
H28 A:RKL102 3.4 15.3 1.0
C35 A:RKL102 4.2 17.7 1.0
C22 A:RKL102 4.2 14.8 1.0
D21 A:DG9 4.2 17.3 1.0
C8 A:RKL102 4.2 16.7 1.0
C5 A:RKL102 4.2 16.9 1.0
C25 A:RKL102 4.2 14.0 1.0
C32 A:RKL102 4.2 17.9 1.0
C37 A:RKL102 4.4 17.7 1.0
C31 A:RKL102 4.4 18.6 1.0
C21 A:RKL102 4.4 15.4 1.0
C3 A:RKL102 4.4 16.7 1.0
C11 A:RKL102 4.4 18.0 1.0
C27 A:RKL102 4.4 15.3 1.0
O A:DOD209 4.5 17.4 1.0
D22 A:DG9 4.5 17.3 1.0
N2 A:DG9 4.6 16.9 1.0
CL A:CL103 4.6 23.7 0.8
N11 A:RKL102 4.8 18.8 1.0
N10 A:RKL102 4.8 19.1 1.0
C4 A:RKL102 4.8 17.0 1.0
N6 A:RKL102 4.8 15.1 1.0
N7 A:RKL102 4.8 14.9 1.0
C9 A:RKL102 4.8 17.2 1.0
O A:DOD234 4.9 37.9 1.0

Reference:

J.P.Hall, F.E.Poynton, P.M.Keane, S.P.Gurung, J.A.Brazier, D.J.Cardin, G.Winter, T.Gunnlaugsson, I.V.Sazanovich, M.Towrie, C.J.Cardin, J.M.Kelly, S.J.Quinn. Monitoring One-Electron Photo-Oxidation of Guanine in Dna Crystals Using Ultrafast Infrared Spectroscopy. Nat Chem V. 7 961 2015.
ISSN: ESSN 1755-4349
PubMed: 26587711
DOI: 10.1038/NCHEM.2369
Page generated: Wed Dec 16 02:08:21 2020

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