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Barium in PDB 3gom: Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4

Protein crystallography data

The structure of Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4, PDB code: 3gom was solved by A.Naseer, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.200, 23.800, 37.410, 90.00, 110.01, 90.00
R / Rfree (%) 26 / 34.9

Barium Binding Sites:

The binding sites of Barium atom in the Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 (pdb code 3gom). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 5 binding sites of Barium where determined in the Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4, PDB code: 3gom:
Jump to Barium binding site number: 1; 2; 3; 4; 5;

Barium binding site 1 out of 5 in 3gom

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Barium binding site 1 out of 5 in the Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba21

b:33.5
occ:0.40
O A:HOH28 1.7 18.9 1.0
O A:HOH53 1.7 17.5 1.0
O A:HOH29 2.1 27.4 1.0
O B:HOH48 2.6 22.5 1.0
O6 A:DG4 2.6 26.7 1.0
N7 A:DG3 3.5 25.2 1.0
C6 A:DG4 3.6 25.8 1.0
N4 B:DC17 3.9 31.9 1.0
N7 A:DG4 4.0 25.7 1.0
C5 A:DG4 4.2 25.2 1.0
C8 A:DG3 4.2 24.8 1.0
O6 B:DG16 4.3 25.6 1.0
C5 A:DG3 4.3 24.6 1.0
O6 A:DG3 4.4 26.7 1.0
C6 A:DG3 4.7 25.3 1.0
N7 B:DG16 4.8 23.9 1.0
N1 A:DG4 4.8 26.0 1.0
C6 B:DG16 4.9 22.6 1.0

Barium binding site 2 out of 5 in 3gom

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Barium binding site 2 out of 5 in the Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba23

b:43.2
occ:0.40
O B:HOH65 2.5 30.2 1.0
O B:HOH24 3.1 20.1 1.0

Barium binding site 3 out of 5 in 3gom

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Barium binding site 3 out of 5 in the Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba22

b:47.1
occ:0.40
C4' B:DC17 4.4 33.8 1.0
O4' B:DC17 4.7 34.0 1.0
C5' B:DC17 4.9 34.4 1.0
N2 A:DG6 5.0 24.9 1.0

Barium binding site 4 out of 5 in 3gom

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Barium binding site 4 out of 5 in the Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba25

b:46.0
occ:0.40
O B:HOH62 2.3 26.9 1.0
O B:HOH57 2.6 31.9 1.0
O B:HOH50 4.2 27.0 1.0
N2 B:DG13 4.6 28.7 1.0
O B:HOH45 4.8 12.8 1.0

Barium binding site 5 out of 5 in 3gom

Go back to Barium Binding Sites List in 3gom
Barium binding site 5 out of 5 in the Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Barium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba49

b:42.5
occ:0.30
O B:HOH50 2.5 27.0 1.0
N2 B:DG13 4.6 28.7 1.0
O4' B:DC15 4.8 33.6 1.0
N2 B:DG14 4.9 28.7 1.0
C4' B:DC15 5.0 33.4 1.0

Reference:

J.P.Hall, K.O'sullivan, A.Naseer, J.A.Smith, J.M.Kelly, C.J.Cardin. Structure Determination of An Intercalating Ruthenium Dipyridophenazine Complex Which Kinks Dna By Semiintercalation of A Tetraazaphenanthrene Ligand. Proc.Natl.Acad.Sci.Usa V. 108 17610 2011.
ISSN: ISSN 0027-8424
PubMed: 21969542
DOI: 10.1073/PNAS.1108685108
Page generated: Sat Dec 12 01:55:46 2020

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