Potassium in PDB 2avj: G4(Br)UTTG4 Dimeric Quadruplex

The structure of G4(Br)UTTG4 Dimeric Quadruplex, PDB code: 2avj was solved by P.Hazel, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.40 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.681, 33.309, 79.234, 90.00, 91.49, 90.00
R / Rfree (%)	16.8 / 24.2

The structure of G4(Br)UTTG4 Dimeric Quadruplex also contains other interesting chemical elements:

Bromine	(Br)	6 atoms
Arsenic	(As)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Potassium atom in the G4(Br)UTTG4 Dimeric Quadruplex (pdb code 2avj). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 14 binding sites of Potassium where determined in the G4(Br)UTTG4 Dimeric Quadruplex, PDB code: 2avj:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K72 b:12.5 occ:1.00 O6 B:DG15 2.7 13.4 1.0 O6 A:DG1 2.7 11.7 1.0 O6 A:DG11 2.7 12.5 1.0 O6 B:DG19 2.7 15.7 1.0 O6 A:DG2 3.0 10.4 1.0 O6 B:DG14 3.0 13.3 1.0 O6 B:DG20 3.1 14.9 1.0 O6 A:DG10 3.1 11.1 1.0 C6 B:DG15 3.6 13.1 1.0 C6 B:DG19 3.6 15.2 1.0 C6 A:DG1 3.7 9.2 1.0 C6 A:DG11 3.7 12.2 1.0 N1 B:DG15 3.7 12.1 1.0 K A:K75 3.7 12.1 1.0 C6 B:DG14 3.8 10.2 1.0 N1 B:DG19 3.8 15.9 1.0 C6 B:DG20 3.9 14.4 1.0 C6 A:DG10 3.9 8.4 1.0 C6 A:DG2 3.9 9.4 1.0 N1 A:DG11 3.9 10.3 1.0 N1 A:DG1 4.0 10.4 1.0 N1 B:DG20 4.1 14.3 1.0 N1 B:DG14 4.1 8.9 1.0 N1 A:DG10 4.2 10.5 1.0 N1 A:DG2 4.2 7.4 1.0 C7 B:DT18 4.4 15.4 1.0 C5 A:DG1 4.9 9.1 1.0 C5 B:DG14 4.9 9.8 1.0 C5 B:DG19 4.9 15.0 1.0 C5 B:DG15 4.9 12.7 1.0 C5 A:DG10 5.0 9.6 1.0

Potassium binding site 2 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K73 b:14.8 occ:1.00 O6 B:DG22 2.7 23.1 1.0 O6 B:DG12 2.7 9.7 1.0 O6 A:DG8 2.8 19.7 1.0 O6 A:DG4 2.8 13.0 1.0 O6 A:DG9 2.9 12.2 1.0 O6 B:DG13 3.0 11.5 1.0 O6 B:DG21 3.0 20.0 1.0 O6 A:DG3 3.0 16.7 1.0 K A:K75 3.4 12.1 1.0 C6 B:DG12 3.7 9.1 1.0 C6 A:DG4 3.7 12.6 1.0 C6 B:DG22 3.7 23.4 1.0 C6 A:DG8 3.7 19.4 1.0 C6 B:DG21 3.7 18.9 1.0 C6 A:DG3 3.7 15.6 1.0 C6 A:DG9 3.8 12.8 1.0 C6 B:DG13 3.8 11.6 1.0 N1 A:DG4 3.8 14.3 1.0 N1 B:DG22 4.0 23.3 1.0 N1 A:DG3 4.0 13.8 1.0 N1 B:DG12 4.0 9.1 1.0 N1 A:DG8 4.0 18.8 1.0 N1 B:DG21 4.0 18.7 1.0 N1 B:DG13 4.1 10.3 1.0 N1 A:DG9 4.1 12.3 1.0 C7 A:DT7 4.3 24.9 1.0 C5 B:DG21 4.8 18.4 1.0 C5 A:DT7 4.9 26.0 1.0 C5 A:DG3 4.9 15.9 1.0 C5 B:DG12 4.9 11.1 1.0

Potassium binding site 3 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K75 b:12.1 occ:1.00 O6 A:DG3 2.7 16.7 1.0 O6 B:DG21 2.8 20.0 1.0 O6 A:DG10 2.8 11.1 1.0 O6 A:DG9 2.9 12.2 1.0 O6 B:DG13 2.9 11.5 1.0 O6 A:DG2 2.9 10.4 1.0 O6 B:DG20 2.9 14.9 1.0 O6 B:DG14 2.9 13.3 1.0 K A:K73 3.4 14.8 1.0 C6 A:DG2 3.7 9.4 1.0 C6 B:DG13 3.7 11.6 1.0 C6 A:DG3 3.7 15.6 1.0 C6 A:DG9 3.7 12.8 1.0 K A:K72 3.7 12.5 1.0 C6 B:DG20 3.8 14.4 1.0 C6 B:DG21 3.8 18.9 1.0 C6 A:DG10 3.8 8.4 1.0 N1 B:DG13 3.9 10.3 1.0 C6 B:DG14 3.9 10.2 1.0 N1 A:DG2 3.9 7.4 1.0 N1 A:DG9 3.9 12.3 1.0 N1 A:DG3 4.1 13.8 1.0 N1 A:DG10 4.1 10.5 1.0 N1 B:DG20 4.1 14.3 1.0 N1 B:DG21 4.1 18.7 1.0 N1 B:DG14 4.2 8.9 1.0 C5 A:DG2 4.8 9.0 1.0 C5 B:DG13 4.9 11.6 1.0 C5 A:DG3 4.9 15.9 1.0 C5 A:DG9 4.9 13.2 1.0 C5 B:DG20 5.0 15.1 1.0

Potassium binding site 4 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K79 b:35.5 occ:1.00 O A:HOH224 2.8 28.8 1.0 N2 A:DG8 3.5 19.4 1.0 N2 B:DG21 3.5 18.3 1.0 N3 A:DG8 3.8 20.9 1.0 O5' B:DG21 3.8 28.2 1.0 O A:HOH143 3.8 25.3 1.0 C2' B:DG20 4.0 20.3 1.0 C2' A:DG8 4.0 21.8 1.0 C2 A:DG8 4.1 20.5 1.0 N3 B:DG21 4.3 18.9 1.0 C5' B:DG21 4.3 25.6 1.0 C3' A:DG8 4.4 22.8 1.0 C2 B:DG21 4.4 18.5 1.0 C5' A:DG8 4.4 27.1 1.0 OP2 B:DG21 4.6 28.6 1.0 P B:DG21 4.8 27.9 1.0 OP2 A:DG8 4.9 34.7 1.0 C3' B:DG20 4.9 23.6 1.0 C4 A:DG8 4.9 20.6 1.0 C4' A:DG8 4.9 24.2 1.0

Potassium binding site 5 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ C:K67 b:18.5 occ:1.00 O6 F:DG56 2.7 23.7 1.0 O6 C:DG23 2.8 27.3 1.0 O6 E:DG45 2.9 23.1 1.0 O6 D:DG34 2.9 23.3 1.0 O6 D:DG44 3.0 23.8 1.0 O6 F:DG66 3.0 21.9 1.0 O6 C:DG33 3.1 26.4 1.0 O6 E:DG55 3.2 20.0 1.0 K C:K69 3.4 18.8 1.0 C6 F:DG56 3.5 22.4 1.0 K E:K68 3.6 18.2 1.0 C6 E:DG45 3.7 21.6 1.0 C6 D:DG34 3.7 21.6 1.0 C6 C:DG23 3.7 24.4 1.0 C6 D:DG44 3.8 21.9 1.0 N1 F:DG56 3.9 21.9 1.0 C6 C:DG33 3.9 24.6 1.0 N1 E:DG45 3.9 21.0 1.0 C6 F:DG66 3.9 21.8 1.0 N1 D:DG34 4.0 20.9 1.0 C6 E:DG55 4.0 19.1 1.0 N1 D:DG44 4.0 21.9 1.0 N1 C:DG33 4.1 23.8 1.0 N1 C:DG23 4.1 23.0 1.0 N1 F:DG66 4.3 20.2 1.0 N1 E:DG55 4.3 18.3 1.0 C5 F:DG56 4.7 22.3 1.0 C5 E:DG45 4.8 21.9 1.0 C5 D:DG34 4.9 20.9 1.0 C5 C:DG23 4.9 24.3 1.0 C5 D:DG44 5.0 21.4 1.0

Potassium binding site 6 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ C:K69 b:18.8 occ:1.00 O6 D:DG43 2.8 26.2 1.0 O6 D:DG34 2.8 23.3 1.0 O6 C:DG32 2.8 23.5 1.0 O6 C:DG23 2.9 27.3 1.0 O6 C:DG33 2.9 26.4 1.0 O6 D:DG44 2.9 23.8 1.0 O6 D:DG35 3.0 26.8 1.0 O6 C:DG24 3.0 25.6 1.0 K C:K67 3.4 18.5 1.0 K C:K74 3.4 18.7 1.0 C6 D:DG43 3.7 24.6 1.0 C6 D:DG34 3.7 21.6 1.0 C6 C:DG32 3.7 21.0 1.0 C6 C:DG23 3.8 24.4 1.0 C6 C:DG33 3.8 24.6 1.0 C6 D:DG44 3.8 21.9 1.0 C6 D:DG35 3.8 25.9 1.0 C6 C:DG24 3.8 25.8 1.0 N1 D:DG34 3.9 20.9 1.0 N1 D:DG43 4.0 24.5 1.0 N1 C:DG33 4.0 23.8 1.0 N1 C:DG32 4.0 20.5 1.0 N1 D:DG44 4.0 21.9 1.0 N1 D:DG35 4.0 25.9 1.0 N1 C:DG24 4.1 25.6 1.0 N1 C:DG23 4.1 23.0 1.0 C5 D:DG43 4.9 24.9 1.0 C5 C:DG32 4.9 22.5 1.0 C5 C:DG23 4.9 24.3 1.0 C5 D:DG34 5.0 20.9 1.0

Potassium binding site 7 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ C:K74 b:18.7 occ:1.00 O6 C:DG24 2.7 25.6 1.0 O6 D:DG35 2.8 26.8 1.0 O6 D:DG42 2.8 27.8 1.0 O6 D:DG36 2.8 26.6 1.0 O6 C:DG31 2.8 29.1 1.0 O6 D:DG43 2.9 26.2 1.0 O6 C:DG25 3.0 29.2 1.0 O6 C:DG32 3.0 23.5 1.0 K C:K69 3.4 18.8 1.0 K C:K76 3.5 22.3 1.0 C6 C:DG24 3.7 25.8 1.0 C6 D:DG42 3.7 26.8 1.0 C6 C:DG31 3.7 28.5 1.0 C6 D:DG36 3.7 27.5 1.0 C6 D:DG35 3.7 25.9 1.0 C6 C:DG25 3.8 28.8 1.0 C6 D:DG43 3.8 24.6 1.0 C6 C:DG32 3.8 21.0 1.0 N1 D:DG42 3.9 24.8 1.0 N1 C:DG31 3.9 28.0 1.0 N1 C:DG24 4.0 25.6 1.0 N1 D:DG35 4.0 25.9 1.0 N1 C:DG25 4.0 27.7 1.0 N1 D:DG36 4.1 27.0 1.0 N1 C:DG32 4.1 20.5 1.0 N1 D:DG43 4.2 24.5 1.0 C5 C:DG24 4.9 25.8 1.0 C5 D:DG36 4.9 28.3 1.0 C5 D:DG35 4.9 26.1 1.0 C5 D:DG42 4.9 27.5 1.0 C5 C:DG31 4.9 29.0 1.0 C5 D:DG43 5.0 24.9 1.0

Potassium binding site 8 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ C:K76 b:22.3 occ:1.00 O6 D:DG41 2.7 27.4 1.0 O6 C:DG30 2.7 26.8 1.0 O6 D:DG37 2.7 30.4 1.0 O6 C:DG26 2.8 28.7 1.0 O6 D:DG36 3.0 26.6 1.0 O6 C:DG25 3.0 29.2 1.0 O6 C:DG31 3.0 29.1 1.0 O6 D:DG42 3.1 27.8 1.0 K C:K74 3.5 18.7 1.0 C6 C:DG30 3.6 27.2 1.0 C6 D:DG41 3.6 25.4 1.0 C6 D:DG37 3.7 29.8 1.0 C6 C:DG25 3.8 28.8 1.0 C6 C:DG26 3.8 28.9 1.0 C6 D:DG36 3.8 27.5 1.0 N1 D:DG41 3.8 24.4 1.0 N1 C:DG30 3.9 26.7 1.0 C6 D:DG42 3.9 26.8 1.0 C6 C:DG31 3.9 28.5 1.0 N1 D:DG37 3.9 29.1 1.0 N1 C:DG25 4.0 27.7 1.0 N1 D:DG36 4.1 27.0 1.0 N1 D:DG42 4.1 24.8 1.0 N1 C:DG26 4.1 28.9 1.0 N1 C:DG31 4.2 28.0 1.0 C5 D:DT40 4.5 31.5 1.0 C7 D:DT40 4.6 31.3 1.0 C4 D:DT40 4.8 32.6 1.0 C6 D:DT40 4.8 31.9 1.0 C5 C:DG30 4.8 28.4 1.0 C5 D:DG41 4.9 25.3 1.0 C5 C:DG25 4.9 28.7 1.0 C5 D:DG37 5.0 30.3 1.0

Potassium binding site 9 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ C:K77 b:25.4 occ:1.00 O5' C:DG23 3.2 34.1 1.0 N2 C:DG23 3.4 24.4 1.0 N2 C:DG32 3.5 22.6 1.0 N3 C:DG23 3.9 24.9 1.0 O5' C:DG32 3.9 38.5 1.0 C2' C:DG31 3.9 34.9 1.0 N3 C:DG32 4.0 22.0 1.0 C2 C:DG23 4.1 23.6 1.0 OP2 C:DG32 4.2 41.9 1.0 C2 C:DG32 4.2 20.9 1.0 C2' F:DG66 4.2 28.6 1.0 C2' C:DG23 4.3 30.0 1.0 C5' C:DG32 4.5 33.2 1.0 C3' C:DG23 4.5 32.8 1.0 C5' C:DG23 4.6 33.2 1.0 O3' F:DG66 4.6 30.9 1.0 P C:DG32 4.6 41.6 1.0 C2' C:DG32 4.7 28.2 1.0 C3' C:DG31 4.7 37.2 1.0 C1' F:DG66 5.0 27.5 1.0 O3' C:DG31 5.0 40.0 1.0 C1' C:DG31 5.0 32.0 1.0

Potassium binding site 10 out of 14 in the G4(Br)UTTG4 Dimeric Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of G4(Br)UTTG4 Dimeric Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ E:K68 b:18.2 occ:1.00 O6 E:DG54 2.6 21.7 1.0 O6 F:DG65 2.8 18.5 1.0 O6 E:DG45 2.8 23.1 1.0 O6 E:DG55 2.9 20.0 1.0 O6 F:DG57 2.9 19.5 1.0 O6 E:DG46 2.9 21.8 1.0 O6 F:DG56 2.9 23.7 1.0 O6 F:DG66 3.0 21.9 1.0 K E:K70 3.2 15.5 1.0 C6 E:DG54 3.5 21.2 1.0 K C:K67 3.6 18.5 1.0 C6 F:DG65 3.6 19.2 1.0 C6 E:DG45 3.7 21.6 1.0 C6 E:DG55 3.7 19.1 1.0 C6 E:DG46 3.8 20.7 1.0 C6 F:DG57 3.8 20.3 1.0 C6 F:DG56 3.8 22.4 1.0 N1 E:DG54 3.8 21.5 1.0 C6 F:DG66 3.9 21.8 1.0 N1 E:DG55 3.9 18.3 1.0 N1 F:DG65 3.9 16.9 1.0 N1 E:DG45 4.0 21.0 1.0 N1 E:DG46 4.0 21.0 1.0 N1 F:DG66 4.1 20.2 1.0 N1 F:DG57 4.1 19.5 1.0 N1 F:DG56 4.1 21.9 1.0 C5 E:DG54 4.7 21.4 1.0 C5 F:DG65 4.8 20.4 1.0 C5 E:DG45 4.9 21.9 1.0 C5 F:DG56 5.0 22.3 1.0

P.Hazel, G.N.Parkinson, S.Neidle. Topology Variation and Loop Structural Homology in Crystal and Simulated Structures of A Bimolecular Dna Quadruplex. J.Am.Chem.Soc. V. 128 5480 2006.
ISSN: ISSN 0002-7863
PubMed: 16620121
DOI: 10.1021/JA058577+