Barium in PDB 4e1u: [Ru(Bpy)2 Dppz]2+ Bound to Dna

The structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna, PDB code: 4e1u was solved by H.Song, J.T.Kaiser, J.K.Barton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.33 / 0.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	24.039, 24.797, 37.521, 74.67, 84.42, 76.21
R / Rfree (%)	14 / 14.9

The structure of [Ru(Bpy)2 Dppz]2+ Bound to Dna also contains other interesting chemical elements:

Ruthenium

(Ru)

5 atoms

The binding sites of Barium atom in the [Ru(Bpy)2 Dppz]2+ Bound to Dna (pdb code 4e1u). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the [Ru(Bpy)2 Dppz]2+ Bound to Dna, PDB code: 4e1u:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba106 b:14.5 occ:0.31 O A:HOH244 2.7 30.9 1.0 O6 A:DG3 2.8 13.5 0.8 O B:HOH1102 2.8 27.4 1.0 N7 A:DG2 2.8 15.2 1.0 O6 A:DG2 2.9 14.8 1.0 O B:HOH1085 3.0 29.3 1.0 O A:HOH209 3.1 20.0 1.0 O6 A:DG3 3.2 14.7 0.2 C5 A:DG2 3.4 13.3 1.0 C6 A:DG2 3.4 13.0 1.0 C6 A:DG3 3.7 13.2 0.8 H42 B:DC10 3.8 17.9 1.0 C8 A:DG2 3.9 16.1 1.0 C6 A:DG3 4.0 15.1 0.2 H8 A:DG2 4.3 19.3 1.0 H42 B:DC11 4.3 16.9 1.0 C5 A:DG3 4.4 13.8 0.8 N4 B:DC10 4.4 14.9 1.0 N7 A:DG3 4.4 15.2 0.8 H41 B:DC10 4.6 17.9 1.0 C5 A:DG3 4.6 15.7 0.2 C4 A:DG2 4.6 12.5 1.0 N7 A:DG3 4.7 16.8 0.2 N1 A:DG3 4.7 12.7 0.8 H1 A:DG3 4.8 15.2 0.8 N1 A:DG2 4.8 11.8 1.0 H91 A:R1Z101 4.8 24.2 1.0 H101 A:R1Z101 4.9 23.6 1.0 N9 A:DG2 4.9 14.6 1.0 N1 A:DG3 5.0 13.8 0.2

Barium binding site 2 out of 2 in the [Ru(Bpy)2 Dppz]2+ Bound to Dna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of [Ru(Bpy)2 Dppz]2+ Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba101 b:19.6 occ:0.65 O B:HOH1054 2.5 21.8 1.0 O B:HOH1024 2.5 29.6 1.0 O B:HOH1004 2.9 18.6 1.0 O6 B:DG2 3.0 10.8 0.6 N7 B:DG2 3.0 13.4 0.6 O6 B:DG2 3.1 11.0 0.5 O B:HOH1033 3.1 27.9 1.0 N7 B:DG2 3.2 14.3 0.5 C6 B:DG2 3.6 10.6 0.6 C5 B:DG2 3.6 10.5 0.6 C6 B:DG2 3.8 10.8 0.5 C5 B:DG2 3.8 11.8 0.5 C8 B:DG2 4.2 13.3 0.6 H101 A:R1Z105 4.3 18.0 1.0 C8 B:DG2 4.3 13.8 0.5 O6 B:DG3 4.4 12.8 0.5 H42 A:DC11 4.5 14.6 1.0 H8 B:DG2 4.5 15.9 0.6 O B:HOH1003 4.6 20.1 1.0 H131 A:R1Z105 4.6 14.2 1.0 H8 B:DG2 4.6 16.6 0.5 OP2 B:DG2 4.8 27.9 0.6 O B:HOH1010 4.9 20.8 1.0 O6 B:DG3 4.9 9.1 0.5 OP2 B:DG2 4.9 27.6 0.5 C4 B:DG2 5.0 10.9 0.6 N1 B:DG2 5.0 9.6 0.6

H.Song, J.T.Kaiser, J.K.Barton. Crystal Structure of Delta-[Ru(Bpy)2DPPZ]2+ Bound to Mismatched Dna Reveals Side-By-Side Metalloinsertion and Intercalation. Nat Chem V. 4 615 2012.
ISSN: ISSN 1755-4349
PubMed: 22824892
DOI: 10.1038/NCHEM.1375