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Barium in PDB 6rso: L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)

Protein crystallography data

The structure of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt), PDB code: 6rso was solved by K.T.Mcquaid, 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) 26.40 / 1.97
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 46.730, 46.730, 31.990, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.7

Other elements in 6rso:

The structure of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms

Barium Binding Sites:

The binding sites of Barium atom in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) (pdb code 6rso). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt), PDB code: 6rso:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in 6rso

Go back to Barium Binding Sites List in 6rso
Barium binding site 1 out of 2 in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:65.5
occ:1.00
O A:HOH207 2.6 50.2 1.0
O A:HOH201 2.6 67.4 1.0
O A:HOH204 2.7 58.0 1.0
O A:HOH202 2.8 77.2 1.0
N7 A:DG3 2.8 57.5 1.0
O6 A:DG4 2.9 59.8 1.0
O B:HOH205 2.9 53.9 1.0
O A:HOH212 3.0 65.2 1.0
N7 A:DG4 3.1 63.0 1.0
C8 A:DG3 3.5 59.6 1.0
C6 A:DG4 3.6 61.2 1.0
C5 A:DG4 3.7 64.2 1.0
C5 A:DG3 4.0 53.7 1.0
C8 A:DG4 4.3 64.9 1.0
O6 A:DG3 4.4 57.3 1.0
OP2 A:DG3 4.5 74.9 1.0
C6 A:DG3 4.6 50.8 1.0
O B:HOH210 4.7 70.8 1.0
O B:HOH212 4.7 47.7 1.0
O6 B:DG6 4.8 69.5 1.0
N9 A:DG3 4.8 55.9 1.0
N1 A:DG4 4.9 54.7 1.0
N4 B:DC7 5.0 59.8 1.0
C4 A:DG4 5.0 62.7 1.0

Barium binding site 2 out of 2 in 6rso

Go back to Barium Binding Sites List in 6rso
Barium binding site 2 out of 2 in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:65.1
occ:1.00
O B:HOH208 2.6 53.8 1.0
O B:HOH201 2.6 64.4 1.0
O B:HOH204 2.7 60.5 1.0
O B:HOH218 2.7 64.5 1.0
O B:HOH203 2.8 87.0 1.0
O A:HOH205 2.8 57.2 1.0
N7 B:DG3 2.9 55.8 1.0
O6 B:DG4 2.9 59.9 1.0
N7 B:DG4 3.1 63.8 1.0
C8 B:DG3 3.5 56.6 1.0
C6 B:DG4 3.6 64.4 1.0
C5 B:DG4 3.7 67.7 1.0
C5 B:DG3 4.1 55.2 1.0
C8 B:DG4 4.3 70.7 1.0
OP2 B:DG3 4.5 70.6 1.0
O6 B:DG3 4.5 58.1 1.0
C6 B:DG3 4.7 54.4 1.0
O A:HOH208 4.8 70.7 1.0
O6 A:DG6 4.8 70.0 1.0
O A:HOH210 4.8 44.6 1.0
N9 B:DG3 4.8 54.0 1.0
N1 B:DG4 5.0 56.9 1.0

Reference:

K.T.Mcquaid, J.P.Hall, C.J.Cardin. Structure of [Ru(Phen)2(10-NO2-Dppz)]2+ Bound to the Dna Sequence D(Tcggcgccga) To Be Published.
Page generated: Wed Jul 10 16:02:31 2024

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