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Barium in PDB 5jeu: Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+

Protein crystallography data

The structure of Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+, PDB code: 5jeu 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) 25.18 / 0.97
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.620, 48.620, 29.430, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 12.7

Other elements in 5jeu:

The structure of Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+ also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms
Chlorine (Cl) 1 atom

Barium Binding Sites:

The binding sites of Barium atom in the Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+ (pdb code 5jeu). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total only one binding site of Barium was determined in the Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+, PDB code: 5jeu:

Barium binding site 1 out of 1 in 5jeu

Go back to Barium Binding Sites List in 5jeu
Barium binding site 1 out of 1 in the Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Del-[Ru(Phen)2(Dppz)]2+ Bound to D(Tcggcgccga) with BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:16.0
occ:0.82
O A:HOH252 2.7 33.1 1.0
O A:HOH248 2.7 31.9 1.0
O A:HOH210 2.8 16.9 1.0
O A:HOH233 2.8 19.6 1.0
O A:HOH222 2.8 18.9 1.0
O A:HOH223 2.9 20.0 1.0
O6 A:DG4 2.9 16.0 1.0
N7 A:DG3 3.0 13.5 1.0
N7 A:DG4 3.1 16.3 1.0
C6 A:DG4 3.6 15.0 1.0
H8 A:DG3 3.6 16.8 1.0
C8 A:DG3 3.7 14.0 1.0
C5 A:DG4 3.7 15.2 1.0
C5 A:DG3 4.1 12.8 1.0
O A:HOH228 4.2 34.1 1.0
O A:HOH206 4.3 33.4 1.0
C8 A:DG4 4.3 16.2 1.0
O6 A:DG3 4.4 13.5 1.0
H41 A:DC5 4.6 16.3 1.0
H8 A:DG4 4.6 19.4 1.0
C6 A:DG3 4.7 12.8 1.0
O A:HOH202 4.8 29.4 0.6
OP2 A:DG3 4.8 18.5 1.0
H42 A:DC5 4.8 16.3 1.0
N9 A:DG3 4.9 13.4 1.0
N4 A:DC5 5.0 13.6 1.0

Reference:

J.P.Hall, P.M.Keane, H.Beer, K.Buchner, G.Winter, T.L.Sorensen, D.J.Cardin, J.A.Brazier, C.J.Cardin. Delta Chirality Ruthenium 'Light-Switch' Complexes Can Bind in the Minor Groove of Dna with Five Different Binding Modes. Nucleic Acids Res. V. 44 9472 2016.
ISSN: ESSN 1362-4962
PubMed: 27599841
DOI: 10.1093/NAR/GKW753
Page generated: Sat Dec 12 01:57:37 2020

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