Potassium in PDB 6xcl: Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.

Protein crystallography data

The structure of Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex., PDB code: 6xcl was solved by C.E.Miron, L.M.Van Staalduinen, Z.Jia, A.Petitjean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.60 / 2.70
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 64.030, 64.030, 42.230, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 24.3

Other elements in 6xcl:

The structure of Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. also contains other interesting chemical elements:

Platinum (Pt) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. (pdb code 6xcl). 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 Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex., PDB code: 6xcl:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 6xcl

Go back to Potassium Binding Sites List in 6xcl
Potassium binding site 1 out of 5 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


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 Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K104

b:38.5
occ:1.00
O6 A:DG20 2.6 31.1 1.0
O6 A:DG2 2.6 31.4 1.0
O6 A:DG14 2.7 32.0 1.0
O6 A:DG21 2.8 31.3 1.0
O6 A:DG8 2.8 27.1 1.0
O6 A:DG3 3.0 31.5 1.0
O6 A:DG9 3.0 30.4 1.0
O6 A:DG15 3.1 34.2 1.0
C6 A:DG20 3.4 28.9 1.0
C6 A:DG2 3.5 30.8 1.0
N1 A:DG20 3.6 27.6 1.0
C6 A:DG8 3.6 27.2 1.0
C6 A:DG14 3.6 28.5 1.0
C6 A:DG21 3.7 33.6 1.0
N1 A:DG8 3.7 25.5 1.0
C6 A:DG3 3.8 27.4 1.0
K A:K105 3.8 35.6 1.0
N1 A:DG2 3.8 32.3 1.0
N1 A:DG14 3.8 29.1 1.0
C6 A:DG15 3.9 30.9 1.0
C6 A:DG9 4.0 29.4 1.0
N1 A:DG15 4.0 27.9 1.0
N1 A:DG21 4.1 34.4 1.0
N1 A:DG3 4.1 25.7 1.0
N1 A:DG9 4.2 27.6 1.0
PT A:V4A103 4.6 44.1 1.0
C5 A:DG20 4.7 34.4 1.0
C5 A:DG2 4.8 30.3 1.0
C5 A:DG21 4.8 34.2 1.0
C2 A:DG20 4.8 34.4 1.0
N3 A:V4A103 4.9 23.6 1.0
C5 A:DG14 4.9 31.2 1.0
C5 A:DG8 4.9 33.1 1.0
C5 A:DG3 4.9 28.4 1.0
NAJ A:V4A103 4.9 33.8 1.0
C2 A:DG8 4.9 29.0 1.0
NBD A:V4A103 5.0 20.8 1.0

Potassium binding site 2 out of 5 in 6xcl

Go back to Potassium Binding Sites List in 6xcl
Potassium binding site 2 out of 5 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


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 Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K105

b:35.6
occ:1.00
O6 A:DG10 2.6 28.0 1.0
O6 A:DG4 2.7 25.8 1.0
O6 A:DG21 2.8 31.3 1.0
O6 A:DG22 2.8 33.9 1.0
O6 A:DG3 2.8 31.5 1.0
O6 A:DG16 2.9 33.2 1.0
O6 A:DG15 3.0 34.2 1.0
O6 A:DG9 3.0 30.4 1.0
C6 A:DG10 3.5 32.7 1.0
C6 A:DG22 3.6 33.8 1.0
C6 A:DG4 3.6 28.2 1.0
C6 A:DG3 3.7 27.4 1.0
C6 A:DG21 3.7 33.6 1.0
N1 A:DG22 3.7 36.4 1.0
C6 A:DG9 3.7 29.4 1.0
C6 A:DG15 3.7 30.9 1.0
K A:K104 3.8 38.5 1.0
C6 A:DG16 3.8 32.8 1.0
N1 A:DG10 3.8 34.6 1.0
N1 A:DG4 3.8 26.6 1.0
N1 A:DG15 3.9 27.9 1.0
N1 A:DG3 3.9 25.7 1.0
N1 A:DG9 4.0 27.6 1.0
N1 A:DG16 4.0 28.3 1.0
N1 A:DG21 4.1 34.4 1.0
PT A:V4A101 4.5 57.7 1.0
N3 A:V4A101 4.8 24.1 1.0
C5 A:DG21 4.8 34.2 1.0
NAJ A:V4A101 4.8 25.3 1.0
C5 A:DG10 4.9 34.9 1.0
C5 A:DG9 4.9 31.4 1.0
C5 A:DG3 4.9 28.4 1.0
C5 A:DG22 4.9 37.5 1.0
C5 A:DG4 5.0 29.9 1.0
C5 A:DG15 5.0 29.8 1.0
C2 A:DG22 5.0 35.4 1.0

Potassium binding site 3 out of 5 in 6xcl

Go back to Potassium Binding Sites List in 6xcl
Potassium binding site 3 out of 5 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


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 Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K106

b:42.0
occ:1.00
O2 B:DT18 3.0 50.6 1.0
O2 A:EDO102 3.0 43.8 1.0
O2 A:DT18 3.0 44.9 1.0
O1 A:EDO102 3.3 42.6 1.0
C2 A:EDO102 3.5 40.0 1.0
C1 A:EDO102 3.7 41.8 1.0
C2 B:DT18 3.7 43.8 1.0
N3 B:DT18 3.8 38.7 1.0
C2 A:DT18 3.9 42.0 1.0
N3 A:DT18 4.1 38.5 1.0

Potassium binding site 4 out of 5 in 6xcl

Go back to Potassium Binding Sites List in 6xcl
Potassium binding site 4 out of 5 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


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 Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:37.4
occ:1.00
O6 B:DG10 2.6 25.3 1.0
O6 B:DG16 2.7 34.0 1.0
O6 B:DG4 2.7 27.8 1.0
O6 B:DG22 2.7 35.0 1.0
O6 B:DG21 2.9 36.5 1.0
O6 B:DG3 3.0 32.6 1.0
O6 B:DG15 3.0 36.5 1.0
O6 B:DG9 3.3 29.1 1.0
C6 B:DG10 3.5 29.7 1.0
C6 B:DG4 3.6 28.9 1.0
C6 B:DG22 3.6 35.3 1.0
C6 B:DG16 3.6 36.4 1.0
N1 B:DG22 3.8 37.1 1.0
N1 B:DG10 3.8 33.1 1.0
K B:K504 3.8 39.3 1.0
N1 B:DG4 3.8 26.0 1.0
C6 B:DG15 3.8 33.6 1.0
C6 B:DG21 3.8 36.1 1.0
C6 B:DG3 3.8 29.5 1.0
N1 B:DG16 3.9 35.5 1.0
C6 B:DG9 3.9 28.7 1.0
N1 B:DG15 4.0 31.1 1.0
N1 B:DG3 4.1 28.4 1.0
N1 B:DG9 4.2 27.8 1.0
N1 B:DG21 4.2 34.9 1.0
PT B:V4A503 4.3 58.7 1.0
NAJ B:V4A503 4.6 25.4 1.0
N3 B:V4A503 4.7 28.6 1.0
C5 B:DG10 4.9 31.6 1.0
N4 B:V4A503 4.9 27.1 1.0
C5 B:DG21 4.9 38.4 1.0
C5 B:DG4 4.9 32.5 1.0
C5 B:DG16 4.9 34.8 1.0
C5 B:DG22 5.0 40.5 1.0
C5 B:DG15 5.0 31.3 1.0

Potassium binding site 5 out of 5 in 6xcl

Go back to Potassium Binding Sites List in 6xcl
Potassium binding site 5 out of 5 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


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 Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:39.3
occ:1.00
O6 B:DG20 2.7 30.2 1.0
O6 B:DG2 2.8 35.5 1.0
O6 B:DG21 2.8 36.5 1.0
O6 B:DG9 2.9 29.1 1.0
O6 B:DG14 2.9 33.1 1.0
O6 B:DG15 2.9 36.5 1.0
O6 B:DG3 2.9 32.6 1.0
O6 B:DG8 2.9 27.5 1.0
C6 B:DG20 3.5 31.5 1.0
C6 B:DG2 3.6 33.4 1.0
C6 B:DG21 3.7 36.1 1.0
C6 B:DG8 3.7 26.5 1.0
C6 B:DG14 3.7 29.6 1.0
C6 B:DG3 3.7 29.5 1.0
N1 B:DG8 3.8 24.8 1.0
K B:K502 3.8 37.4 1.0
C6 B:DG15 3.8 33.6 1.0
N1 B:DG20 3.8 32.8 1.0
C6 B:DG9 3.9 28.7 1.0
N1 B:DG2 3.9 32.9 1.0
N1 B:DG14 3.9 29.3 1.0
N1 B:DG3 4.0 28.4 1.0
N1 B:DG21 4.0 34.9 1.0
N1 B:DG15 4.1 31.1 1.0
N1 B:DG9 4.1 27.8 1.0
PT A:V4A103 4.7 44.1 1.0
C5 B:DG20 4.8 38.5 1.0
C5 B:DG21 4.8 38.4 1.0
C5 B:DG2 4.9 33.0 1.0
N3 A:V4A103 4.9 23.6 1.0
C5 B:DG14 4.9 28.9 1.0
C5 B:DG3 4.9 30.8 1.0
C5 B:DG8 4.9 32.5 1.0
C2 B:DG8 5.0 28.3 1.0

Reference:

C.E.Miron, L.Van Staalduinen, A.M.M.Rangaswamy, M.Chen, Y.Liang, Z.Jia, J.L.Mergny, A.Petitjean. Going Platinum to the Tune of A Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 33090592
DOI: 10.1002/ANIE.202012520
Page generated: Mon Dec 14 02:25:08 2020

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