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Barium in PDB 8d78: Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX

Protein crystallography data

The structure of Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX, PDB code: 8d78 was solved by E.V.Chen, D.Beseiso, L.A.Yatsunyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.40 / 2.12
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 35.081, 35.081, 103.191, 90, 90, 120
R / Rfree (%) 25.5 / 26.4

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX (pdb code 8d78). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX, PDB code: 8d78:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in 8d78

Go back to Barium Binding Sites List in 8d78
Barium binding site 1 out of 2 in the Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:71.4
occ:1.00
O6 A:DG21 2.7 70.7 1.0
O6 A:DG16 2.7 71.5 1.0
O6 A:DG3 2.7 80.6 1.0
O6 A:DG9 2.8 75.9 1.0
O6 A:DG15 2.8 79.1 1.0
O6 A:DG4 2.8 76.1 1.0
O6 A:DG10 2.9 83.4 1.0
O6 A:DG22 3.1 72.8 1.0
C6 A:DG21 3.5 75.1 1.0
C6 A:DG3 3.5 75.6 1.0
C6 A:DG9 3.6 76.6 1.0
C6 A:DG15 3.6 73.8 1.0
C6 A:DG16 3.6 76.6 1.0
N1 A:DG21 3.7 74.8 1.0
C6 A:DG4 3.7 80.0 1.0
N1 A:DG3 3.8 73.5 1.0
N1 A:DG9 3.8 77.5 1.0
C6 A:DG22 3.9 76.8 1.0
N1 A:DG15 3.9 72.9 1.0
N1 A:DG16 3.9 78.2 1.0
N1 A:DG22 4.0 78.8 1.0
C6 A:DG10 4.0 81.2 1.0
N1 A:DG4 4.0 84.1 1.0
C1 A:MMP101 4.1 87.8 1.0
N1 A:DG10 4.4 80.1 1.0
C5 A:DG21 4.8 79.3 1.0
C5 A:DG15 4.8 76.7 1.0
C5 A:DG9 4.8 80.1 1.0
C5 A:DG3 4.8 77.2 1.0
C5 A:DG16 4.9 82.8 1.0
C2 A:DG21 5.0 79.4 1.0

Barium binding site 2 out of 2 in 8d78

Go back to Barium Binding Sites List in 8d78
Barium binding site 2 out of 2 in the Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of A Ba Stabilized Four-Tetrad, Parallel Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:72.5
occ:1.00
O6 A:DG1 2.7 74.5 1.0
O6 A:DG14 2.7 75.8 1.0
O6 A:DG20 2.7 69.7 1.0
O6 A:DG19 2.8 73.8 1.0
O6 A:DG8 2.8 70.5 1.0
O6 A:DG2 2.8 78.6 1.0
O6 A:DG7 2.8 70.2 1.0
O6 A:DG13 2.9 70.8 1.0
N1 A:DG13 3.5 76.5 1.0
C6 A:DG14 3.5 74.3 1.0
C6 A:DG13 3.5 76.5 1.0
C6 A:DG20 3.6 78.0 1.0
N1 A:DG14 3.6 69.3 1.0
C6 A:DG19 3.7 76.9 1.0
C6 A:DG8 3.7 76.8 1.0
C6 A:DG1 3.7 76.9 1.0
C6 A:DG7 3.8 75.5 1.0
C6 A:DG2 3.8 78.5 1.0
N1 A:DG20 3.9 79.8 1.0
N1 A:DG19 4.0 83.1 1.0
N1 A:DG8 4.0 78.6 1.0
N1 A:DG7 4.0 79.5 1.0
N1 A:DG1 4.1 77.8 1.0
N1 A:DG2 4.2 76.9 1.0
C2 A:DG13 4.7 79.1 1.0
C5 A:DG20 4.8 82.6 1.0
C5 A:DG13 4.8 83.6 1.0
C5 A:DG14 4.8 77.7 1.0
C5 A:DG19 4.9 79.2 1.0
C2 A:DG14 4.9 78.0 1.0
C5 A:DG8 4.9 80.9 1.0
C5 A:DG1 5.0 78.0 1.0

Reference:

D.Beseiso, E.V.Chen, L.A.Yatsunyk. Biophysical and Structural Characterization of Telomeric G-Quadruplexes From Tetrahymena Thermophila in Complex with N-Methyl Mesoporphyrin IX To Be Published.
Page generated: Wed Jul 10 16:12:17 2024

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