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Ruthenium in PDB 5lfw: Lambda-[Ru(Phen)2(Dppz)]2+ Bound to A Short Substituted Dna Sequence

Protein crystallography data

The structure of Lambda-[Ru(Phen)2(Dppz)]2+ Bound to A Short Substituted Dna Sequence, PDB code: 5lfw was solved by 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) 24.52 / 1.28
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.340, 67.340, 35.790, 90.00, 90.00, 120.00
R / Rfree (%) 14.1 / 17.1

Other elements in 5lfw:

The structure of Lambda-[Ru(Phen)2(Dppz)]2+ Bound to A Short Substituted Dna Sequence also contains other interesting chemical elements:

Bromine (Br) 1 atom
Barium (Ba) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Lambda-[Ru(Phen)2(Dppz)]2+ Bound to A Short Substituted Dna Sequence (pdb code 5lfw). 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 Lambda-[Ru(Phen)2(Dppz)]2+ Bound to A Short Substituted Dna Sequence, PDB code: 5lfw:

Ruthenium binding site 1 out of 1 in 5lfw

Go back to Ruthenium Binding Sites List in 5lfw
Ruthenium binding site 1 out of 1 in the Lambda-[Ru(Phen)2(Dppz)]2+ Bound to A Short Substituted Dna Sequence


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Lambda-[Ru(Phen)2(Dppz)]2+ Bound to A Short Substituted Dna Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ru101

b:13.3
occ:1.00
RU C:RKP101 0.0 13.3 1.0
N1 C:RKP101 2.0 12.1 1.0
N5 C:RKP101 2.1 13.2 1.0
N9 C:RKP101 2.1 14.4 1.0
N12 C:RKP101 2.1 14.2 1.0
N8 C:RKP101 2.1 11.9 1.0
N2 C:RKP101 2.1 14.3 1.0
C26 C:RKP101 2.8 13.2 1.0
C19 C:RKP101 2.8 13.1 1.0
C29 C:RKP101 2.8 14.5 1.0
C10 C:RKP101 2.8 14.2 1.0
C1 C:RKP101 2.8 13.8 1.0
C36 C:RKP101 2.8 14.2 1.0
C12 C:RKP101 3.1 14.4 1.0
C30 C:RKP101 3.1 14.7 1.0
C20 C:RKP101 3.1 13.8 1.0
C38 C:RKP101 3.1 14.8 1.0
C2 C:RKP101 3.1 13.5 1.0
C28 C:RKP101 3.1 12.7 1.0
H12 C:RKP101 3.2 14.6 1.0
H30 C:RKP101 3.3 15.2 1.0
H20 C:RKP101 3.3 13.7 1.0
H38 C:RKP101 3.3 15.1 1.0
H2 C:RKP101 3.3 13.4 1.0
H28 C:RKP101 3.3 13.6 1.0
C22 C:RKP101 4.2 13.2 1.0
C25 C:RKP101 4.2 13.1 1.0
C8 C:RKP101 4.2 15.3 1.0
C32 C:RKP101 4.2 16.1 1.0
C5 C:RKP101 4.2 15.0 1.0
C35 C:RKP101 4.2 15.0 1.0
C11 C:RKP101 4.3 15.1 1.0
C31 C:RKP101 4.4 16.7 1.0
C37 C:RKP101 4.4 15.4 1.0
C21 C:RKP101 4.4 14.4 1.0
C3 C:RKP101 4.4 14.0 1.0
C27 C:RKP101 4.4 13.8 1.0
O C:HOH219 4.5 14.0 1.0
H22 A:DG4 4.6 16.6 1.0
C9 C:RKP101 4.8 16.0 1.0
C41 C:RKP101 4.8 13.9 1.0
C43 C:RKP101 4.8 17.0 1.0
C4 C:RKP101 4.8 13.3 1.0
C42 C:RKP101 4.8 13.3 1.0
C44 C:RKP101 4.8 15.6 1.0
H1' A:DC3 4.9 17.6 1.0
H22 C:DG2 5.0 13.3 1.0

Reference:

J.P.Hall, S.P.Gurung, J.Henle, P.Poidl, J.Andersson, P.Lincoln, G.Winter, T.Sorensen, D.J.Cardin, J.A.Brazier, C.J.Cardin. Guanine Can Direct Binding Specificity of Ru-Dipyridophenazine (Dppz) Complexes to Dna Through Steric Effects. Chemistry V. 23 4981 2017.
ISSN: ISSN 1521-3765
PubMed: 28105682
DOI: 10.1002/CHEM.201605508
Page generated: Wed Dec 16 02:08:36 2020

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