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Potassium in PDB 7klp: Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex

Protein crystallography data

The structure of Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex, PDB code: 7klp was solved by L.A.Yatsunyk, K.S.Li, E.V.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.31 / 1.35
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 56.686, 56.686, 42.31, 90, 90, 120
R / Rfree (%) 14.2 / 17.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex (pdb code 7klp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex, PDB code: 7klp:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 7klp

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Potassium binding site 1 out of 5 in the Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex


Mono view


Stereo pair view

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

b:16.7
occ:0.50
O6 A:DG2 2.7 18.5 0.5
O6 A:DG20 2.8 18.6 1.0
O6 A:DG8 2.8 18.8 1.0
O6 A:DG14 2.8 15.7 0.6
O6 A:DG2 2.8 18.2 0.5
O6 A:DG14 2.9 16.8 0.4
K A:K102 3.3 17.8 1.0
H1 A:DG14 3.4 20.7 0.4
H1 A:DG2 3.5 18.8 0.5
H1 A:DG20 3.5 21.7 1.0
C6 A:DG2 3.6 16.3 0.5
C6 A:DG20 3.6 18.3 1.0
H1 A:DG8 3.7 20.6 1.0
H1 A:DG2 3.7 19.9 0.5
C6 A:DG14 3.7 15.1 0.6
H1 A:DG14 3.7 18.0 0.6
C6 A:DG8 3.7 17.5 1.0
C6 A:DG2 3.7 16.8 0.5
C6 A:DG14 3.8 17.6 0.4
N1 A:DG2 3.9 15.6 0.5
N1 A:DG20 3.9 18.1 1.0
N1 A:DG14 4.0 17.3 0.4
N1 A:DG2 4.1 16.6 0.5
N1 A:DG8 4.1 17.2 1.0
N1 A:DG14 4.1 15.0 0.6
C5 A:DG2 4.7 17.1 0.5
C5 A:DG14 4.9 15.9 0.6
C5 A:DG20 4.9 19.8 1.0
C5 A:DG2 4.9 17.8 0.5
C5 A:DG8 5.0 18.4 1.0

Potassium binding site 2 out of 5 in 7klp

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Potassium binding site 2 out of 5 in the Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex


Mono view


Stereo pair view

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

b:17.8
occ:1.00
O6 A:DG3 2.5 19.7 0.5
O6 A:DG14 2.6 15.7 0.6
O6 A:DG2 2.7 18.5 0.5
O6 A:DG15 2.7 18.4 1.0
O6 A:DG21 2.7 19.3 1.0
O6 A:DG9 2.8 19.2 1.0
O6 A:DG3 2.8 16.5 0.5
O6 A:DG8 2.8 18.8 1.0
O6 A:DG20 2.8 18.6 1.0
O6 A:DG2 2.9 18.2 0.5
O6 A:DG14 3.1 16.8 0.4
K A:K101 3.3 16.7 0.5
K A:K103 3.4 18.6 1.0
H1 A:DG21 3.5 23.7 1.0
H1 A:DG2 3.5 19.9 0.5
H1 A:DG15 3.5 22.6 1.0
H1 A:DG8 3.5 20.6 1.0
H1 A:DG14 3.5 18.0 0.6
C6 A:DG14 3.5 15.1 0.6
H1 A:DG2 3.6 18.8 0.5
C6 A:DG3 3.6 19.8 0.5
H1 A:DG20 3.6 21.7 1.0
H1 A:DG9 3.6 21.9 1.0
H1 A:DG3 3.6 23.2 0.5
C6 A:DG21 3.6 18.9 1.0
C6 A:DG2 3.6 16.3 0.5
C6 A:DG8 3.6 17.5 1.0
C6 A:DG15 3.6 18.1 1.0
H1 A:DG3 3.7 20.3 0.5
H1 A:DG14 3.7 20.7 0.4
C6 A:DG20 3.7 18.3 1.0
C6 A:DG9 3.7 18.7 1.0
C6 A:DG2 3.7 16.8 0.5
C6 A:DG3 3.7 17.6 0.5
C6 A:DG14 3.8 17.6 0.4
N1 A:DG14 3.9 15.0 0.6
N1 A:DG8 3.9 17.2 1.0
N1 A:DG21 3.9 19.8 1.0
N1 A:DG15 3.9 18.8 1.0
N1 A:DG2 4.0 16.6 0.5
N1 A:DG2 4.0 15.6 0.5
N1 A:DG20 4.0 18.1 1.0
N1 A:DG3 4.0 19.4 0.5
N1 A:DG9 4.1 18.2 1.0
N1 A:DG3 4.1 16.9 0.5
N1 A:DG14 4.1 17.3 0.4
C5 A:DG14 4.7 15.9 0.6
C5 A:DG8 4.8 18.4 1.0
C5 A:DG3 4.8 19.8 0.5
C5 A:DG2 4.9 17.1 0.5
C5 A:DG21 4.9 20.2 1.0
C5 A:DG20 4.9 19.8 1.0
C5 A:DG15 4.9 18.8 1.0
C5 A:DG3 5.0 19.1 0.5
C5 A:DG2 5.0 17.8 0.5
C5 A:DG9 5.0 20.0 1.0

Potassium binding site 3 out of 5 in 7klp

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Potassium binding site 3 out of 5 in the Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex


Mono view


Stereo pair view

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

b:18.6
occ:1.00
O6 A:DG16 2.7 21.9 1.0
O6 A:DG4 2.7 20.5 1.0
O6 A:DG22 2.7 21.0 1.0
O6 A:DG10 2.7 20.7 1.0
O6 A:DG3 2.9 16.5 0.5
O6 A:DG21 2.9 19.3 1.0
O6 A:DG15 2.9 18.4 1.0
O6 A:DG9 3.0 19.2 1.0
O6 A:DG3 3.1 19.7 0.5
H1 A:DG16 3.4 25.1 1.0
K A:K102 3.4 17.8 1.0
H1 A:DG22 3.4 25.6 1.0
H1 A:DG4 3.5 23.9 1.0
H1 A:DG10 3.5 24.6 1.0
H1 A:DG3 3.6 20.3 0.5
C6 A:DG16 3.6 21.2 1.0
H1 A:DG15 3.6 22.6 1.0
C6 A:DG22 3.7 20.2 1.0
C6 A:DG3 3.7 17.6 0.5
C6 A:DG4 3.7 20.3 1.0
H1 A:DG21 3.7 23.7 1.0
H1 A:DG9 3.7 21.9 1.0
C6 A:DG9 3.7 18.7 1.0
C6 A:DG21 3.7 18.9 1.0
C6 A:DG10 3.7 20.2 1.0
C6 A:DG15 3.7 18.1 1.0
C6 A:DG3 3.9 19.8 0.5
H1 A:DG3 3.9 23.2 0.5
N1 A:DG16 3.9 20.9 1.0
N1 A:DG22 3.9 21.3 1.0
N1 A:DG3 3.9 16.9 0.5
N1 A:DG4 4.0 19.9 1.0
N1 A:DG10 4.0 20.5 1.0
N1 A:DG15 4.0 18.8 1.0
N1 A:DG9 4.0 18.2 1.0
N1 A:DG21 4.0 19.8 1.0
N1 A:DG3 4.2 19.4 0.5
C5 A:DG9 4.8 20.0 1.0
C5 A:DG15 4.8 18.8 1.0
C5 A:DG3 4.9 19.1 0.5
C5 A:DG21 4.9 20.2 1.0
C5 A:DG3 4.9 19.8 0.5
C5 A:DG16 5.0 22.0 1.0
C5 A:DG22 5.0 20.5 1.0
C5 A:DG4 5.0 21.5 1.0

Potassium binding site 4 out of 5 in 7klp

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Potassium binding site 4 out of 5 in the Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:63.8
occ:0.33
OP2 A:DG22 3.0 37.6 1.0
O A:HOH310 3.4 65.8 0.3
P A:DG22 3.8 38.1 1.0
O A:HOH278 3.8 49.3 1.0
OP1 A:DG22 4.0 40.6 1.0
O A:HOH210 4.3 42.7 1.0
O5' A:DG22 4.3 37.8 1.0

Potassium binding site 5 out of 5 in 7klp

Go back to Potassium Binding Sites List in 7klp
Potassium binding site 5 out of 5 in the Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of A Three-Tetrad, Parallel, K+ Stabilized Human Telomeric G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:48.4
occ:0.50
H19 A:P6G106 2.6 93.1 0.5
O10 A:P6G106 2.6 71.3 0.5
O4 A:P6G106 2.9 33.5 0.5
O7 A:P6G106 3.0 43.4 0.5
O13 A:P6G106 3.1 38.1 0.5
O19 A:P6G106 3.1 77.6 0.5
O2 A:DT6 3.1 34.4 1.0
O16 A:P6G106 3.2 40.8 0.5
O1 A:P6G106 3.3 61.6 0.5
H91 A:P6G106 3.4 52.2 0.5
C9 A:P6G106 3.4 43.5 0.5
H151 A:P6G106 3.5 38.9 0.5
H141 A:P6G106 3.5 46.2 0.5
C14 A:P6G106 3.6 38.5 0.5
C11 A:P6G106 3.6 55.3 0.5
C15 A:P6G106 3.6 32.4 0.5
C6 A:P6G106 3.7 30.1 0.5
H61 A:P6G106 3.7 36.1 0.5
C5 A:P6G106 3.7 28.2 0.5
C8 A:P6G106 3.7 42.7 0.5
H172 A:P6G106 3.8 47.5 0.5
C12 A:P6G106 3.8 36.4 0.5
C3 A:P6G106 3.8 40.1 0.5
C17 A:P6G106 3.8 39.6 0.5
H112 A:P6G106 3.8 66.3 0.5
C18 A:P6G106 3.9 37.9 0.5
H31 A:P6G106 3.9 48.2 0.5
H51 A:P6G106 3.9 33.8 0.5
H182 A:P6G106 3.9 45.4 0.5
H121 A:P6G106 4.0 43.7 0.5
C2 A:DT6 4.0 34.0 1.0
C2 A:P6G106 4.0 34.5 0.5
H82 A:P6G106 4.1 51.3 0.5
H1 A:P6G106 4.1 74.0 0.5
N3 A:DT6 4.2 33.6 1.0
H21 A:P6G106 4.2 41.3 0.5
H92 A:P6G106 4.4 52.2 0.5
H111 A:P6G106 4.6 66.3 0.5
H142 A:P6G106 4.7 46.2 0.5
H81 A:P6G106 4.7 51.3 0.5
H152 A:P6G106 4.7 38.9 0.5
H52 A:P6G106 4.7 33.8 0.5
H62 A:P6G106 4.7 36.1 0.5
H32 A:P6G106 4.8 48.2 0.5
H122 A:P6G106 4.8 43.7 0.5
H171 A:P6G106 4.9 47.5 0.5
H181 A:P6G106 4.9 45.4 0.5

Reference:

K.Li, L.Yatsunyk, S.Neidle. Water Spines and Networks in G-Quadruplex Structures. Nucleic Acids Res. V. 49 519 2021.
ISSN: ESSN 1362-4962
PubMed: 33290519
DOI: 10.1093/NAR/GKAA1177
Page generated: Sun Jan 24 17:56:59 2021

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