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Potassium in PDB 7xdh: Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex

Protein crystallography data

The structure of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7xdh was solved by K.H.Ngo, C.W.Liew, S.Lattmann, F.R.Winnerdy, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.26 / 1.83
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 25.685, 30.34, 56.493, 79.02, 83.36, 78.2
R / Rfree (%) 22.7 / 25.3

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex (pdb code 7xdh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7xdh:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 7xdh

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Potassium binding site 1 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:34.4
occ:1.00
 O6 A:DG14 2.7 35.7 1.0
O6 A:DG4 2.7 34.7 1.0
O6 A:DG15 2.7 42.7 1.0
O6 A:DG11 2.8 42.8 1.0
O6 A:DG8 2.8 36.2 1.0
O6 A:DG3 2.9 35.8 1.0
O6 A:DG10 2.9 36.7 1.0
O6 A:DG7 2.9 35.6 1.0
O A:HOH201 3.3 44.7 1.0
K A:K102 3.4 32.0 1.0
C6 A:DG14 3.5 39.6 1.0
C6 A:DG15 3.6 42.9 1.0
C6 A:DG8 3.6 40.8 1.0
C6 A:DG4 3.7 41.0 1.0
C6 A:DG11 3.7 42.0 1.0
C6 A:DG10 3.7 44.1 1.0
C6 A:DG3 3.7 38.8 1.0
C6 A:DG7 3.8 38.6 1.0
N1 A:DG14 3.8 38.6 1.0
N1 A:DG15 3.9 42.7 1.0
N1 A:DG8 3.9 42.2 1.0
N1 A:DG11 3.9 41.1 1.0
N1 A:DG4 3.9 36.9 1.0
N1 A:DG10 3.9 38.9 1.0
N1 A:DG3 4.0 37.9 1.0
N1 A:DG7 4.1 36.6 1.0
C5 A:DG14 4.7 40.0 1.0
C5 A:DG8 4.9 42.5 1.0
C5 A:DG3 4.9 38.1 1.0
C5 A:DG15 4.9 44.4 1.0
C5 A:DG10 4.9 40.7 1.0
C5 A:DG4 4.9 37.4 1.0
C5 A:DG11 5.0 40.0 1.0

Potassium binding site 2 out of 10 in 7xdh

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Potassium binding site 2 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:32.0
occ:1.00
 O6 B:DG1 2.8 37.9 1.0
O6 A:DG3 2.8 35.8 1.0
O6 A:DG7 2.8 35.6 1.0
O6 A:DG10 2.8 36.7 1.0
O6 A:DG13 2.8 36.0 1.0
O6 A:DG14 2.8 35.7 1.0
O6 A:DG2 2.8 34.1 1.0
O6 A:DG6 2.9 33.3 1.0
K A:K103 3.3 31.1 1.0
K A:K101 3.4 34.4 1.0
C6 A:DG7 3.6 38.6 1.0
C6 A:DG13 3.6 38.0 1.0
C6 A:DG2 3.6 36.8 1.0
C6 B:DG1 3.7 38.0 1.0
C6 A:DG3 3.7 38.8 1.0
C6 A:DG10 3.7 44.1 1.0
C6 A:DG14 3.7 39.6 1.0
C6 A:DG6 3.7 37.4 1.0
N1 A:DG7 3.8 36.6 1.0
N1 A:DG13 3.9 39.5 1.0
N1 B:DG1 3.9 38.9 1.0
N1 A:DG2 4.0 36.5 1.0
N1 A:DG3 4.0 37.9 1.0
N1 A:DG6 4.0 37.0 1.0
N1 A:DG14 4.0 38.6 1.0
N1 A:DG10 4.0 38.9 1.0
C5 A:DG2 4.8 36.1 1.0
C5 A:DG13 4.8 37.0 1.0
C5 A:DG7 4.8 41.9 1.0
C5 A:DG6 4.9 37.3 1.0
C5 A:DG10 4.9 40.7 1.0
C5 A:DG3 4.9 38.1 1.0
C5 B:DG1 4.9 38.9 1.0
C5 A:DG14 4.9 40.0 1.0

Potassium binding site 3 out of 10 in 7xdh

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Potassium binding site 3 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:31.1
occ:1.00
 O6 A:DG13 2.7 36.0 1.0
O6 A:DG2 2.7 34.1 1.0
O6 B:DG1 2.8 37.9 1.0
O6 A:DG6 2.8 33.3 1.0
O6 B:DG13 2.8 33.2 1.0
O6 B:DG2 2.8 35.1 1.0
O6 B:DG6 2.8 32.2 1.0
O6 A:DG1 2.9 36.0 1.0
K A:K102 3.3 32.0 1.0
K B:K101 3.4 32.3 1.0
C6 B:DG1 3.6 38.0 1.0
C6 A:DG13 3.6 38.0 1.0
C6 A:DG6 3.6 37.4 1.0
C6 A:DG2 3.6 36.8 1.0
C6 B:DG2 3.6 37.1 1.0
C6 B:DG13 3.6 40.0 1.0
C6 B:DG6 3.7 36.4 1.0
C6 A:DG1 3.7 37.1 1.0
N1 A:DG6 3.9 37.0 1.0
N1 B:DG2 3.9 36.7 1.0
N1 A:DG13 3.9 39.5 1.0
N1 A:DG2 3.9 36.5 1.0
N1 B:DG6 3.9 32.4 1.0
N1 B:DG1 3.9 38.9 1.0
N1 B:DG13 3.9 37.8 1.0
N1 A:DG1 4.0 40.3 1.0
C5 B:DG1 4.8 38.9 1.0
C5 A:DG13 4.8 37.0 1.0
C5 B:DG13 4.9 36.6 1.0
C5 A:DG1 4.9 39.5 1.0
C5 B:DG2 4.9 39.5 1.0
C5 A:DG2 4.9 36.1 1.0
C5 A:DG6 4.9 37.3 1.0
C5 B:DG6 5.0 36.3 1.0

Potassium binding site 4 out of 10 in 7xdh

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Potassium binding site 4 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:32.3
occ:1.00
 O6 B:DG10 2.7 34.4 1.0
O6 B:DG7 2.7 35.5 1.0
O6 B:DG2 2.7 35.1 1.0
O6 B:DG3 2.7 35.8 1.0
O6 B:DG14 2.8 38.2 1.0
O6 A:DG1 2.9 36.0 1.0
O6 B:DG13 2.9 33.2 1.0
O6 B:DG6 2.9 32.2 1.0
K B:K102 3.3 36.1 1.0
K A:K103 3.4 31.1 1.0
C6 B:DG2 3.5 37.1 1.0
C6 B:DG7 3.6 38.7 1.0
C6 B:DG3 3.6 38.4 1.0
C6 B:DG10 3.6 42.0 1.0
C6 B:DG13 3.7 40.0 1.0
C6 B:DG14 3.7 39.9 1.0
C6 B:DG6 3.7 36.4 1.0
C6 A:DG1 3.8 37.1 1.0
N1 B:DG7 3.8 33.2 1.0
N1 B:DG2 3.8 36.7 1.0
N1 B:DG3 3.9 35.5 1.0
N1 B:DG13 3.9 37.8 1.0
N1 B:DG10 4.0 35.9 1.0
N1 B:DG6 4.0 32.4 1.0
N1 B:DG14 4.0 38.1 1.0
N1 A:DG1 4.1 40.3 1.0
C5 B:DG2 4.7 39.5 1.0
C5 B:DG7 4.8 37.5 1.0
C5 B:DG3 4.8 40.7 1.0
C5 B:DG13 4.9 36.6 1.0
C5 B:DG10 4.9 40.4 1.0
C5 B:DG6 4.9 36.3 1.0
C5 B:DG14 4.9 39.4 1.0

Potassium binding site 5 out of 10 in 7xdh

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Potassium binding site 5 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:36.1
occ:1.00
 O6 B:DG14 2.7 38.2 1.0
O6 B:DG15 2.7 36.5 1.0
O6 B:DG11 2.7 42.3 1.0
O6 B:DG4 2.8 38.2 1.0
O6 B:DG7 2.8 35.5 1.0
O6 B:DG3 2.8 35.8 1.0
O6 B:DG8 2.8 36.1 1.0
O6 B:DG10 2.9 34.4 1.0
K B:K101 3.3 32.3 1.0
C6 B:DG14 3.6 39.9 1.0
C6 B:DG8 3.6 40.0 1.0
C6 B:DG15 3.6 46.1 1.0
C6 B:DG7 3.6 38.7 1.0
C6 B:DG11 3.7 40.5 1.0
C6 B:DG3 3.7 38.4 1.0
C6 B:DG10 3.7 42.0 1.0
C6 B:DG4 3.7 41.0 1.0
N1 B:DG8 3.8 40.4 1.0
N1 B:DG15 3.9 46.1 1.0
N1 B:DG7 3.9 33.2 1.0
N1 B:DG10 3.9 35.9 1.0
N1 B:DG14 3.9 38.1 1.0
N1 B:DG11 3.9 39.5 1.0
N1 B:DG3 4.0 35.5 1.0
N1 B:DG4 4.0 39.3 1.0
C5 B:DG14 4.8 39.4 1.0
C5 B:DG8 4.8 41.4 1.0
C5 B:DG7 4.9 37.5 1.0
C5 B:DG3 4.9 40.7 1.0
C5 B:DG10 4.9 40.4 1.0
C5 B:DG15 4.9 47.1 1.0
C5 B:DG11 5.0 40.5 1.0
C5 B:DG4 5.0 38.2 1.0

Potassium binding site 6 out of 10 in 7xdh

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Potassium binding site 6 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K101

b:34.5
occ:1.00
 O6 C:DG11 2.7 40.6 1.0
O6 C:DG15 2.7 39.9 1.0
O6 C:DG4 2.7 36.6 1.0
O6 C:DG14 2.8 36.2 1.0
O6 C:DG8 2.8 38.4 1.0
O6 C:DG10 2.9 35.6 1.0
O6 C:DG7 2.9 36.6 1.0
O6 C:DG3 3.0 34.9 1.0
K C:K102 3.4 32.6 1.0
C6 C:DG14 3.6 37.7 1.0
C6 C:DG11 3.6 41.0 1.0
C6 C:DG15 3.6 40.0 1.0
C6 C:DG8 3.7 39.0 1.0
C6 C:DG4 3.7 38.7 1.0
C6 C:DG10 3.7 41.3 1.0
C6 C:DG3 3.8 40.0 1.0
C6 C:DG7 3.8 38.3 1.0
N1 C:DG11 3.9 40.3 1.0
N1 C:DG8 3.9 40.7 1.0
N1 C:DG10 3.9 36.3 1.0
N1 C:DG15 3.9 37.1 1.0
N1 C:DG4 3.9 36.4 1.0
N1 C:DG14 3.9 37.4 1.0
N1 C:DG7 4.1 36.5 1.0
N1 C:DG3 4.1 35.4 1.0
C5 C:DG14 4.8 40.2 1.0
C5 C:DG15 4.9 37.5 1.0
C5 C:DG8 4.9 41.6 1.0
C5 C:DG10 4.9 42.4 1.0
C5 C:DG11 4.9 42.5 1.0
C5 C:DG3 4.9 39.0 1.0
C5 C:DG4 5.0 37.0 1.0

Potassium binding site 7 out of 10 in 7xdh

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Potassium binding site 7 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K102

b:32.6
occ:1.00
 O6 C:DG3 2.7 34.9 1.0
O6 C:DG7 2.7 36.6 1.0
O6 C:DG10 2.7 35.6 1.0
O6 D:DG1 2.8 36.0 1.0
O6 C:DG13 2.8 33.1 1.0
O6 C:DG14 2.9 36.2 1.0
O6 C:DG6 2.9 33.0 1.0
O6 C:DG2 2.9 33.9 1.0
K C:K103 3.3 31.5 1.0
K C:K101 3.4 34.5 1.0
C6 C:DG7 3.5 38.3 1.0
C6 C:DG3 3.6 40.0 1.0
C6 C:DG13 3.7 38.2 1.0
C6 C:DG2 3.7 37.4 1.0
C6 C:DG10 3.7 41.3 1.0
C6 C:DG6 3.7 39.0 1.0
C6 D:DG1 3.7 39.0 1.0
C6 C:DG14 3.8 37.7 1.0
N1 C:DG7 3.8 36.5 1.0
N1 C:DG3 3.9 35.4 1.0
N1 C:DG2 3.9 36.7 1.0
N1 C:DG13 4.0 38.1 1.0
N1 D:DG1 4.0 40.6 1.0
N1 C:DG6 4.0 37.6 1.0
N1 C:DG14 4.0 37.4 1.0
N1 C:DG10 4.1 36.3 1.0
C5 C:DG7 4.8 37.7 1.0
C5 C:DG2 4.8 38.4 1.0
C5 C:DG3 4.9 39.0 1.0
C5 C:DG6 4.9 35.7 1.0
C5 C:DG13 4.9 36.1 1.0
C5 C:DG10 4.9 42.4 1.0
C5 D:DG1 4.9 40.2 1.0

Potassium binding site 8 out of 10 in 7xdh

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Potassium binding site 8 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K103

b:31.5
occ:1.00
 O6 D:DG2 2.7 33.8 1.0
O6 C:DG13 2.7 33.1 1.0
O6 D:DG1 2.7 36.0 1.0
O6 C:DG2 2.8 33.9 1.0
O6 C:DG6 2.8 33.0 1.0
O6 C:DG1 2.8 36.3 1.0
O6 D:DG13 2.9 32.6 1.0
O6 D:DG6 2.9 31.7 1.0
K C:K102 3.3 32.6 1.0
K D:K101 3.4 29.2 1.0
C6 C:DG13 3.6 38.2 1.0
C6 D:DG1 3.6 39.0 1.0
C6 D:DG2 3.6 35.2 1.0
C6 D:DG13 3.7 39.4 1.0
C6 C:DG1 3.7 36.4 1.0
C6 C:DG6 3.7 39.0 1.0
C6 C:DG2 3.7 37.4 1.0
C6 D:DG6 3.8 37.8 1.0
N1 C:DG13 3.9 38.1 1.0
N1 D:DG13 3.9 38.1 1.0
N1 D:DG1 3.9 40.6 1.0
N1 D:DG2 3.9 35.9 1.0
N1 C:DG6 3.9 37.6 1.0
N1 C:DG2 4.0 36.7 1.0
N1 D:DG6 4.0 34.5 1.0
N1 C:DG1 4.0 39.5 1.0
C5 D:DG1 4.8 40.2 1.0
C5 C:DG13 4.8 36.1 1.0
C5 C:DG1 4.8 39.6 1.0
C5 D:DG2 4.9 38.1 1.0
C5 D:DG13 4.9 35.4 1.0
C5 C:DG6 5.0 35.7 1.0
C5 C:DG2 5.0 38.4 1.0

Potassium binding site 9 out of 10 in 7xdh

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Potassium binding site 9 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K101

b:29.2
occ:1.00
 O6 D:DG2 2.7 33.8 1.0
O6 D:DG7 2.7 35.7 1.0
O6 D:DG3 2.7 36.8 1.0
O6 C:DG1 2.8 36.3 1.0
O6 D:DG13 2.8 32.6 1.0
O6 D:DG10 2.8 34.1 1.0
O6 D:DG14 2.8 34.9 1.0
O6 D:DG6 2.9 31.7 1.0
K D:K102 3.4 34.2 1.0
K C:K103 3.4 31.5 1.0
C6 D:DG2 3.5 35.2 1.0
C6 D:DG7 3.6 37.8 1.0
C6 D:DG13 3.6 39.4 1.0
C6 D:DG3 3.7 36.7 1.0
C6 C:DG1 3.7 36.4 1.0
C6 D:DG10 3.7 41.5 1.0
C6 D:DG14 3.7 40.0 1.0
C6 D:DG6 3.8 37.8 1.0
N1 D:DG7 3.8 36.4 1.0
N1 D:DG2 3.9 35.9 1.0
N1 D:DG13 3.9 38.1 1.0
N1 D:DG14 4.0 38.3 1.0
N1 C:DG1 4.0 39.5 1.0
N1 D:DG10 4.0 38.4 1.0
N1 D:DG3 4.0 35.9 1.0
N1 D:DG6 4.1 34.5 1.0
C5 D:DG2 4.6 38.1 1.0
C5 D:DG7 4.8 37.8 1.0
C5 D:DG13 4.9 35.4 1.0
C5 D:DG3 4.9 37.5 1.0
C5 D:DG10 4.9 41.5 1.0
C5 C:DG1 5.0 39.6 1.0
C5 D:DG14 5.0 42.4 1.0
C5 D:DG6 5.0 36.1 1.0

Potassium binding site 10 out of 10 in 7xdh

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Potassium binding site 10 out of 10 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K102

b:34.2
occ:1.00
 O6 D:DG4 2.7 36.6 1.0
O6 D:DG15 2.7 40.8 1.0
O6 D:DG8 2.7 37.0 1.0
O6 D:DG11 2.8 44.0 1.0
O6 D:DG7 2.8 35.7 1.0
O6 D:DG14 2.9 34.9 1.0
O6 D:DG10 2.9 34.1 1.0
O6 D:DG3 3.0 36.8 1.0
K D:K101 3.4 29.2 1.0
C6 D:DG4 3.6 40.1 1.0
C6 D:DG8 3.6 38.0 1.0
C6 D:DG15 3.6 46.9 1.0
C6 D:DG14 3.6 40.0 1.0
C6 D:DG7 3.7 37.8 1.0
C6 D:DG11 3.7 41.9 1.0
C6 D:DG10 3.7 41.5 1.0
C6 D:DG3 3.8 36.7 1.0
N1 D:DG4 3.8 39.0 1.0
N1 D:DG14 3.9 38.3 1.0
N1 D:DG15 3.9 40.9 1.0
N1 D:DG8 3.9 38.1 1.0
N1 D:DG11 3.9 42.2 1.0
N1 D:DG10 4.0 38.4 1.0
N1 D:DG7 4.0 36.4 1.0
N1 D:DG3 4.1 35.9 1.0
C5 D:DG14 4.8 42.4 1.0
C5 D:DG8 4.8 41.1 1.0
C5 D:DG4 4.9 36.5 1.0
C5 D:DG15 4.9 49.4 1.0
C5 D:DG7 4.9 37.8 1.0
C5 D:DG3 4.9 37.5 1.0
C5 D:DG10 4.9 41.5 1.0

Reference:

K.H.Ngo, C.W.Liew, S.Lattmann, F.R.Winnerdy, A.T.Phan. Crystal Structures of An Hiv-1 Integrase Aptamer: Formation of A Water-Mediated A.G.G.G.G Pentad in An Interlocked G-Quadruplex Biochem.Biophys.Res.Commun. 2022.
ISSN: ESSN 1090-2104
Page generated: Mon Aug 12 21:33:22 2024

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