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Potassium in PDB 3qxr: Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna

Protein crystallography data

The structure of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna, PDB code: 3qxr was solved by D.Wei, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.90 / 1.62
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 37.570, 51.350, 58.340, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 21.3

Other elements in 3qxr:

The structure of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Magnesium (Mg) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna (pdb code 3qxr). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna, PDB code: 3qxr:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 3qxr

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Potassium binding site 1 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K23

b:9.9
occ:1.00
 O6 A:DG21 2.7 10.3 1.0
O6 A:DG6 2.7 7.9 1.0
O6 A:DG10 2.8 8.3 1.0
O6 A:DG3 2.8 9.2 1.0
O6 A:DG7 2.8 9.8 1.0
O6 A:DG14 2.8 12.3 1.0
O6 A:DG2 2.8 10.5 1.0
O6 A:DG13 2.8 9.6 1.0
K A:K24 3.4 9.3 1.0
K A:K25 3.5 11.4 1.0
C6 A:DG6 3.6 7.9 1.0
C6 A:DG13 3.6 10.1 1.0
C6 A:DG2 3.6 8.7 1.0
C6 A:DG10 3.7 9.1 1.0
C6 A:DG21 3.7 11.7 1.0
C6 A:DG3 3.7 9.3 1.0
C6 A:DG14 3.7 8.6 1.0
C6 A:DG7 3.8 8.3 1.0
N1 A:DG6 3.9 8.4 1.0
N1 A:DG13 3.9 10.9 1.0
N1 A:DG2 3.9 10.9 1.0
N1 A:DG10 3.9 8.2 1.0
N1 A:DG14 4.0 9.9 1.0
N1 A:DG21 4.0 8.8 1.0
N1 A:DG3 4.0 9.2 1.0
N1 A:DG7 4.0 7.3 1.0
C5 A:DG13 4.7 12.2 1.0
C5 A:DG6 4.8 10.1 1.0
C5 A:DG2 4.9 11.0 1.0
C5 A:DG21 4.9 10.7 1.0
C5 A:DG3 4.9 10.3 1.0
C5 A:DG10 4.9 9.8 1.0
C5 A:DG14 5.0 9.8 1.0

Potassium binding site 2 out of 9 in 3qxr

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Potassium binding site 2 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K24

b:9.3
occ:1.00
 O6 A:DG22 2.7 10.8 1.0
O6 A:DG4 2.7 10.2 1.0
O6 A:DG8 2.8 11.4 1.0
O6 A:DG14 2.8 12.3 1.0
O6 A:DG7 2.8 9.8 1.0
O6 A:DG15 2.9 11.9 1.0
O6 A:DG3 2.9 9.2 1.0
O6 A:DG21 2.9 10.3 1.0
K A:K23 3.4 9.9 1.0
C6 A:DG14 3.6 8.6 1.0
C6 A:DG4 3.6 9.5 1.0
C6 A:DG8 3.6 8.9 1.0
N2 A:DG20 3.7 9.8 1.0
C6 A:DG7 3.7 8.3 1.0
C6 A:DG21 3.7 11.7 1.0
C6 A:DG22 3.7 12.1 1.0
C6 A:DG15 3.8 8.9 1.0
C6 A:DG3 3.8 9.3 1.0
N1 A:DG4 3.9 10.8 1.0
N1 A:DG21 3.9 8.8 1.0
N1 A:DG14 3.9 9.9 1.0
N1 A:DG15 3.9 8.0 1.0
N1 A:DG8 3.9 9.4 1.0
N1 A:DG22 4.0 10.6 1.0
N1 A:DG3 4.0 9.2 1.0
N1 A:DG7 4.0 7.3 1.0
C2 A:DG20 4.6 11.2 1.0
C5 A:DG14 4.7 9.8 1.0
C5 A:DG7 4.8 11.1 1.0
C5 A:DG21 4.9 10.7 1.0
C5 A:DG4 4.9 10.1 1.0
C5 A:DG8 4.9 8.9 1.0
C5 A:DG3 4.9 10.3 1.0
C5 A:DG22 5.0 9.6 1.0

Potassium binding site 3 out of 9 in 3qxr

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Potassium binding site 3 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K25

b:11.4
occ:1.00
 O B:HOH48 2.7 10.3 1.0
O4 B:BRU12 2.7 12.3 1.0
O A:HOH47 2.8 13.3 1.0
O6 A:DG10 2.9 8.3 1.0
O6 A:DG13 3.0 9.6 1.0
O6 A:DG6 3.0 7.9 1.0
O6 A:DG2 3.0 10.5 1.0
K A:K23 3.5 9.9 1.0
BR B:BRU12 3.6 11.4 1.0
C6 A:DG10 3.6 9.1 1.0
C4 B:BRU12 3.7 10.1 1.0
C6 A:DG6 3.8 7.9 1.0
C6 A:DG2 3.9 8.7 1.0
N1 A:DG10 3.9 8.2 1.0
C6 A:DG13 4.0 10.1 1.0
C2 A:DA1 4.0 14.7 1.0
N1 A:DA1 4.0 14.7 1.0
N1 A:DG2 4.1 10.9 1.0
N1 A:DG6 4.1 8.4 1.0
C5 B:BRU12 4.2 10.6 1.0
N1 A:DG13 4.3 10.9 1.0
O4 A:BRU12 4.5 12.6 1.0
N3 A:BRU12 4.6 11.6 1.0
O2 B:DC11 4.8 10.6 1.0
O6 B:DG13 4.8 8.6 1.0
C5 A:DG10 4.8 9.8 1.0
N3 B:BRU12 4.8 11.2 1.0
O6 B:DG10 4.9 12.8 1.0
C5 A:DG6 5.0 10.1 1.0
N1 B:DG10 5.0 8.5 1.0

Potassium binding site 4 out of 9 in 3qxr

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Potassium binding site 4 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K26

b:27.3
occ:1.00
 OP1 A:DG7 2.7 19.1 1.0
O A:HOH75 2.8 32.8 1.0
O A:HOH74 2.8 25.6 1.0
O4' A:DA5 2.8 23.3 1.0
O A:HOH83 3.6 33.8 1.0
C4' A:DA5 3.7 19.8 1.0
C1' A:DA5 3.8 18.1 1.0
P A:DG7 4.0 22.0 1.0
C5' A:DA5 4.3 14.9 1.0
N9 A:DA5 4.3 16.1 1.0
C8 A:DA5 4.6 17.8 1.0
O3' A:DG6 4.7 19.1 1.0
OP2 A:DG7 4.8 20.9 1.0
C3' A:DA5 4.9 24.1 1.0
O3' A:DA5 4.9 31.0 1.0

Potassium binding site 5 out of 9 in 3qxr

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Potassium binding site 5 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K27

b:25.6
occ:1.00
 OP2 A:DC11 2.5 15.5 0.5
O A:HOH86 2.7 31.6 1.0
O A:HOH85 2.8 33.6 1.0
O3' A:DG10 2.8 16.4 1.0
O A:HOH40 2.8 16.2 1.0
O A:HOH53 2.9 16.4 1.0
OP2 A:DC11 2.9 14.3 0.5
O4' A:DG21 2.9 15.3 1.0
P A:DC11 3.3 17.4 0.5
C4' A:DG21 3.5 14.2 1.0
P A:DC11 3.5 14.4 0.5
C1' A:DG21 3.8 12.2 1.0
C3' A:DG10 3.9 10.6 1.0
OP2 A:BRU12 3.9 20.9 1.0
O A:HOH165 3.9 36.8 1.0
C2' A:DG10 3.9 12.4 1.0
C5' A:DG21 4.0 13.4 1.0
O A:HOH129 4.2 37.2 1.0
O A:HOH125 4.3 37.9 1.0
O5' A:DC11 4.3 15.3 0.5
OP1 A:DC11 4.4 19.0 0.5
C5' A:DC11 4.4 18.2 0.5
O A:HOH41 4.5 13.9 1.0
C1' A:DG10 4.6 10.2 1.0
OP1 A:DC11 4.6 12.4 0.5
N9 A:DG21 4.6 11.5 1.0
C8 A:DG21 4.7 10.7 1.0
O5' A:DC11 4.7 16.0 0.5
O A:HOH30 4.7 23.0 1.0
C4' A:DC11 4.7 18.7 0.5
C5' A:DC11 4.8 15.7 0.5
C3' A:DG21 4.8 13.5 1.0
C2' A:DG21 4.8 15.1 1.0
C4' A:DC11 4.9 17.3 0.5

Potassium binding site 6 out of 9 in 3qxr

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Potassium binding site 6 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K23

b:10.2
occ:1.00
 O6 B:DG10 2.6 12.8 1.0
O6 B:DG2 2.7 10.3 1.0
O6 B:DG6 2.7 11.0 1.0
O6 B:DG14 2.8 9.8 1.0
O6 B:DG13 2.8 8.6 1.0
O6 B:DG21 2.8 9.8 1.0
O6 B:DG3 2.8 11.8 1.0
O6 B:DG7 2.9 9.5 1.0
K B:K24 3.5 11.7 1.0
C6 B:DG10 3.5 11.6 1.0
C6 B:DG6 3.6 10.8 1.0
C6 B:DG2 3.6 12.3 1.0
C6 B:DG13 3.6 7.4 1.0
C6 B:DG14 3.7 11.3 1.0
C6 B:DG3 3.7 12.5 1.0
C6 B:DG21 3.7 9.3 1.0
N1 B:DG10 3.7 8.5 1.0
C6 B:DG7 3.8 12.7 1.0
N1 B:DG13 3.8 10.5 1.0
N1 B:DG6 3.9 10.7 1.0
N1 B:DG2 3.9 12.4 1.0
N1 B:DG14 4.0 11.2 1.0
O A:HOH47 4.0 13.3 1.0
N1 B:DG7 4.0 10.3 1.0
N1 B:DG3 4.1 8.6 1.0
N1 B:DG21 4.1 9.3 1.0
C5 B:DG10 4.8 8.9 1.0
C5 B:DG13 4.9 7.0 1.0
C5 B:DG6 4.9 13.8 1.0
C5 B:DG3 4.9 11.7 1.0
C5 B:DG2 4.9 11.1 1.0
C5 B:DG21 4.9 10.4 1.0
C5 B:DG14 5.0 10.4 1.0

Potassium binding site 7 out of 9 in 3qxr

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Potassium binding site 7 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K24

b:11.7
occ:1.00
 O6 B:DG4 2.7 12.6 1.0
O6 B:DG22 2.7 11.7 1.0
O6 B:DG8 2.8 10.8 1.0
O6 B:DG7 2.8 9.5 1.0
O6 B:DG15 2.8 13.0 1.0
O6 B:DG14 2.8 9.8 1.0
O6 B:DG3 2.9 11.8 1.0
O6 B:DG21 3.0 9.8 1.0
K B:K23 3.5 10.2 1.0
C6 B:DG4 3.6 15.3 1.0
C6 B:DG14 3.6 11.3 1.0
N2 B:DG20 3.7 10.8 1.0
C6 B:DG7 3.7 12.7 1.0
C6 B:DG8 3.7 12.4 1.0
C6 B:DG3 3.7 12.5 1.0
C6 B:DG15 3.7 9.6 1.0
C6 B:DG22 3.7 11.4 1.0
C6 B:DG21 3.7 9.3 1.0
N1 B:DG4 3.9 10.4 1.0
N1 B:DG15 3.9 12.8 1.0
N1 B:DG8 3.9 8.7 1.0
N1 B:DG14 3.9 11.2 1.0
N1 B:DG3 3.9 8.6 1.0
N1 B:DG21 4.0 9.3 1.0
N1 B:DG22 4.0 11.6 1.0
N1 B:DG7 4.1 10.3 1.0
C2 B:DG20 4.6 9.9 1.0
C5 B:DG14 4.7 10.4 1.0
C5 B:DG7 4.8 11.8 1.0
C5 B:DG4 4.8 15.0 1.0
C5 B:DG3 4.9 11.7 1.0
C5 B:DG21 4.9 10.4 1.0
C5 B:DG8 4.9 11.3 1.0
C5 B:DG15 5.0 13.0 1.0

Potassium binding site 8 out of 9 in 3qxr

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Potassium binding site 8 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K25

b:21.4
occ:1.00
 O B:HOH76 2.8 13.3 1.0
OP2 B:DC11 2.8 15.2 1.0
O B:HOH80 2.9 35.9 1.0
O3' B:DG10 3.0 12.0 1.0
O4' B:DG21 3.1 13.4 1.0
O B:HOH77 3.1 28.1 1.0
O B:HOH78 3.2 16.5 1.0
P B:DC11 3.5 15.0 1.0
C4' B:DG21 3.7 12.9 1.0
O B:HOH81 3.7 30.7 1.0
C1' B:DG21 3.7 7.7 1.0
C2' B:DG10 4.1 11.2 1.0
C3' B:DG10 4.1 11.5 1.0
C5' B:DG21 4.3 10.6 1.0
O5' B:DC11 4.4 14.3 1.0
O B:HOH123 4.5 31.6 1.0
N9 B:DG21 4.6 9.1 1.0
C1' B:DG10 4.6 14.2 1.0
C8 B:DG21 4.7 9.4 1.0
O B:HOH53 4.7 28.5 1.0
C3' B:DC11 4.7 11.5 1.0
OP2 B:BRU12 4.8 15.7 1.0
OP1 B:DC11 4.8 16.4 1.0
O B:HOH79 4.8 13.1 1.0
C2' B:DG21 4.8 9.2 1.0
C3' B:DG21 4.9 11.4 1.0

Potassium binding site 9 out of 9 in 3qxr

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Potassium binding site 9 out of 9 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


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 the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K26

b:33.6
occ:0.50
 O B:HOH147 2.5 30.1 1.0
O6 B:DG17 2.8 26.1 1.0
O B:HOH90 3.1 26.8 1.0
O B:HOH111 3.2 28.2 0.5
O B:HOH102 3.5 22.1 1.0
C6 B:DG17 3.8 24.8 1.0
O B:HOH101 4.1 19.9 1.0
N1 B:DG17 4.1 23.2 1.0
OP2 B:DG15 4.1 17.8 1.0
N7 B:DA16 4.2 21.0 1.0
N6 B:DA16 4.5 11.6 1.0
O B:HOH91 5.0 23.3 1.0

Reference:

D.Wei, G.N.Parkinson, A.P.Reszka, S.Neidle. Crystal Structure of A C-Kit Promoter Quadruplex Reveals the Structural Role of Metal Ions and Water Molecules in Maintaining Loop Conformation. Nucleic Acids Res. V. 40 4691 2012.
ISSN: ISSN 0305-1048
PubMed: 22287624
DOI: 10.1093/NAR/GKS023
Page generated: Mon Aug 12 09:15:00 2024

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