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

Protein crystallography data

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

Other elements in 4e1u:

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

Ruthenium (Ru) 5 atoms

Barium Binding Sites:

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 4e1u

Go back to Barium Binding Sites List in 4e1u
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 4e1u

Go back to Barium Binding Sites List in 4e1u
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

Reference:

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
Page generated: Tue Oct 27 17:01:00 2020

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