Potassium in PDB 7d5e: Left-Handed G-Quadruplex Containing Two Bulges

Protein crystallography data

The structure of Left-Handed G-Quadruplex Containing Two Bulges, PDB code: 7d5e was solved by P.Das, A.Maity, K.H.Ngo, F.R.Winnerdy, B.Bakalar, Y.Mechulam, E.Schmitt, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.09 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 29.1, 39.81, 54.97, 90, 91.28, 90
R / Rfree (%) 18.4 / 21.4

Other elements in 7d5e:

The structure of Left-Handed G-Quadruplex Containing Two Bulges also contains other interesting chemical elements:

Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Left-Handed G-Quadruplex Containing Two Bulges (pdb code 7d5e). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Left-Handed G-Quadruplex Containing Two Bulges, PDB code: 7d5e:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 7d5e

Go back to Potassium Binding Sites List in 7d5e
Potassium binding site 1 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:11.1
occ:1.00
O6 A:DG15 2.8 9.3 1.0
O6 A:DG10 2.8 10.2 1.0
O6 A:DG21 2.8 11.1 1.0
O6 A:DG2 2.8 11.7 1.0
O6 A:DG13 2.8 11.8 1.0
O6 A:DG6 2.8 11.5 1.0
O6 A:DG24 2.9 11.2 1.0
O6 A:DG18 2.9 10.3 1.0
K A:K103 3.5 11.2 1.0
K A:K102 3.6 10.0 1.0
C6 A:DG21 3.6 10.6 1.0
C6 A:DG10 3.6 10.2 1.0
C6 A:DG15 3.7 9.5 1.0
C6 A:DG24 3.7 11.3 1.0
C6 A:DG2 3.7 10.7 1.0
C6 A:DG13 3.7 9.5 1.0
C6 A:DG6 3.7 11.2 1.0
C6 A:DG18 3.7 11.1 1.0
N1 A:DG21 3.9 11.8 1.0
N1 A:DG10 4.0 9.6 1.0
N1 A:DG24 4.0 10.7 1.0
N1 A:DG15 4.0 10.1 1.0
N1 A:DG6 4.0 9.9 1.0
N1 A:DG13 4.0 10.2 1.0
N1 A:DG2 4.0 10.4 1.0
N1 A:DG18 4.1 11.3 1.0
C5 A:DG10 4.8 11.1 1.0
C5 A:DG21 4.8 11.5 1.0
C5 A:DG24 4.8 11.9 1.0
C5 A:DG15 4.9 10.6 1.0
C5 A:DG2 4.9 12.0 1.0
C5 A:DG13 4.9 9.3 1.0
C5 A:DG6 4.9 10.5 1.0
C5 A:DG18 5.0 11.7 1.0

Potassium binding site 2 out of 7 in 7d5e

Go back to Potassium Binding Sites List in 7d5e
Potassium binding site 2 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:10.0
occ:1.00
O6 A:DG26 2.7 11.9 1.0
O6 A:DG23 2.8 10.9 1.0
O6 A:DG15 2.8 9.3 1.0
O6 A:DG20 2.8 13.6 1.0
O6 A:DG18 2.9 10.3 1.0
O6 A:DG17 2.9 14.5 1.0
O6 A:DG24 3.0 11.2 1.0
O6 A:DG21 3.0 11.1 1.0
C6 A:DG23 3.6 10.4 1.0
C6 A:DG20 3.6 11.6 1.0
K A:K101 3.6 11.1 1.0
C6 A:DG26 3.6 10.8 1.0
C6 A:DG15 3.7 9.5 1.0
C6 A:DG17 3.7 12.4 1.0
C6 A:DG18 3.8 11.1 1.0
N1 A:DG23 3.8 10.3 1.0
N1 A:DG20 3.8 11.9 1.0
C6 A:DG21 3.9 10.6 1.0
C6 A:DG24 3.9 11.3 1.0
N1 A:DG17 3.9 13.1 1.0
N1 A:DG26 3.9 11.3 1.0
N1 A:DG15 4.0 10.1 1.0
N1 A:DG18 4.1 11.3 1.0
N1 A:DG24 4.2 10.7 1.0
N1 A:DG21 4.2 11.8 1.0
C5 A:DG23 4.8 11.6 1.0
C5 A:DG20 4.8 12.6 1.0
C5 A:DG15 4.8 10.6 1.0
C5 A:DG17 4.9 13.5 1.0
C5 A:DG26 4.9 11.6 1.0
C5 A:DG18 5.0 11.7 1.0

Potassium binding site 3 out of 7 in 7d5e

Go back to Potassium Binding Sites List in 7d5e
Potassium binding site 3 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:11.2
occ:1.00
O6 A:DG4 2.7 11.9 1.0
O6 A:DG8 2.7 11.4 1.0
O6 A:DG2 2.8 11.7 1.0
O6 A:DG13 2.8 11.8 1.0
O6 A:DG12 2.8 11.7 1.0
O6 A:DG10 2.9 10.2 1.0
O6 A:DG1 2.9 14.4 1.0
O6 A:DG6 3.0 11.5 1.0
K A:K101 3.5 11.1 1.0
C6 A:DG8 3.6 11.7 1.0
C6 A:DG4 3.6 11.7 1.0
C6 A:DG2 3.7 10.7 1.0
C6 A:DG12 3.7 10.7 1.0
C6 A:DG13 3.7 9.5 1.0
C6 A:DG1 3.7 12.6 1.0
C6 A:DG10 3.8 10.2 1.0
N1 A:DG8 3.9 10.6 1.0
C6 A:DG6 3.9 11.2 1.0
N1 A:DG4 3.9 11.7 1.0
N1 A:DG12 3.9 11.5 1.0
N1 A:DG1 3.9 11.0 1.0
N1 A:DG13 4.0 10.2 1.0
N1 A:DG2 4.0 10.4 1.0
N1 A:DG10 4.1 9.6 1.0
N1 A:DG6 4.2 9.9 1.0
C5 A:DG8 4.8 11.5 1.0
C5 A:DG2 4.8 12.0 1.0
C5 A:DG12 4.9 10.9 1.0
C5 A:DG1 4.9 12.2 1.0
C5 A:DG13 4.9 9.3 1.0
C5 A:DG4 4.9 11.1 1.0
C5 A:DG10 5.0 11.1 1.0

Potassium binding site 4 out of 7 in 7d5e

Go back to Potassium Binding Sites List in 7d5e
Potassium binding site 4 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K101

b:10.2
occ:1.00
O6 B:DG15 2.8 10.8 1.0
O6 B:DG10 2.8 9.7 1.0
O6 B:DG2 2.8 9.8 1.0
O6 B:DG21 2.8 9.1 1.0
O6 B:DG6 2.8 10.3 1.0
O6 B:DG24 2.9 10.0 1.0
O6 B:DG13 2.9 10.5 1.0
O6 B:DG18 2.9 11.1 1.0
K B:K103 3.5 10.0 1.0
K B:K102 3.6 10.4 1.0
C6 B:DG10 3.6 9.8 1.0
C6 B:DG15 3.6 9.9 1.0
C6 B:DG21 3.7 9.2 1.0
C6 B:DG24 3.7 9.5 1.0
C6 B:DG2 3.7 10.3 1.0
C6 B:DG6 3.7 9.3 1.0
C6 B:DG13 3.8 9.3 1.0
C6 B:DG18 3.8 10.0 1.0
N1 B:DG21 3.9 10.3 1.0
N1 B:DG10 4.0 9.8 1.0
N1 B:DG15 4.0 10.4 1.0
N1 B:DG6 4.0 8.8 1.0
N1 B:DG24 4.0 9.0 1.0
N1 B:DG2 4.1 10.2 1.0
N1 B:DG13 4.1 9.2 1.0
N1 B:DG18 4.1 9.9 1.0
C5 B:DG15 4.8 9.1 1.0
C5 B:DG10 4.8 10.6 1.0
C5 B:DG21 4.8 9.8 1.0
C5 B:DG24 4.9 9.6 1.0
C5 B:DG2 4.9 10.8 1.0
C5 B:DG6 4.9 9.1 1.0

Potassium binding site 5 out of 7 in 7d5e

Go back to Potassium Binding Sites List in 7d5e
Potassium binding site 5 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K102

b:10.4
occ:1.00
O6 B:DG23 2.7 10.3 1.0
O6 B:DG15 2.7 10.8 1.0
O6 B:DG26 2.8 11.1 1.0
O6 B:DG18 2.9 11.1 1.0
O6 B:DG20 2.9 13.2 1.0
O6 B:DG17 2.9 11.1 1.0
O6 B:DG24 2.9 10.0 1.0
O6 B:DG21 3.0 9.1 1.0
C6 B:DG23 3.5 10.0 1.0
K B:K101 3.6 10.2 1.0
C6 B:DG15 3.6 9.9 1.0
C6 B:DG20 3.6 12.1 1.0
C6 B:DG17 3.7 10.2 1.0
C6 B:DG26 3.7 10.7 1.0
C6 B:DG18 3.8 10.0 1.0
N1 B:DG23 3.8 10.4 1.0
N1 B:DG20 3.8 11.6 1.0
C6 B:DG21 3.9 9.2 1.0
C6 B:DG24 3.9 9.5 1.0
N1 B:DG17 3.9 11.1 1.0
N1 B:DG15 4.0 10.4 1.0
N1 B:DG26 4.0 10.5 1.0
N1 B:DG18 4.1 9.9 1.0
N1 B:DG24 4.2 9.0 1.0
N1 B:DG21 4.2 10.3 1.0
C3 B:SPM106 4.6 60.3 1.0
C5 B:DG23 4.7 9.7 1.0
C5 B:DG15 4.8 9.1 1.0
C5 B:DG20 4.8 12.2 1.0
C5 B:DG17 4.9 11.5 1.0
C5 B:DG18 5.0 11.2 1.0
N1 B:SPM106 5.0 28.8 1.0
C5 B:DG26 5.0 10.4 1.0

Potassium binding site 6 out of 7 in 7d5e

Go back to Potassium Binding Sites List in 7d5e
Potassium binding site 6 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K103

b:10.0
occ:1.00
O6 B:DG4 2.7 10.5 1.0
O6 B:DG8 2.7 11.0 1.0
O6 B:DG12 2.8 11.0 1.0
O6 B:DG1 2.8 11.6 1.0
O6 B:DG13 2.9 10.5 1.0
O6 B:DG2 2.9 9.8 1.0
O6 B:DG10 2.9 9.7 1.0
O6 B:DG6 3.0 10.3 1.0
K B:K101 3.5 10.2 1.0
C6 B:DG4 3.6 9.7 1.0
C6 B:DG8 3.6 11.0 1.0
C6 B:DG1 3.6 9.6 1.0
C6 B:DG12 3.6 9.9 1.0
C6 B:DG13 3.7 9.3 1.0
C6 B:DG10 3.7 9.8 1.0
C6 B:DG2 3.7 10.3 1.0
N1 B:DG1 3.9 8.7 1.0
N1 B:DG4 3.9 10.9 1.0
C6 B:DG6 3.9 9.3 1.0
N1 B:DG8 3.9 10.6 1.0
N1 B:DG12 3.9 9.9 1.0
N1 B:DG13 4.0 9.2 1.0
N1 B:DG10 4.0 9.8 1.0
N1 B:DG2 4.1 10.2 1.0
N1 B:DG6 4.2 8.8 1.0
C5 B:DG1 4.8 10.6 1.0
C5 B:DG12 4.8 9.2 1.0
C5 B:DG4 4.9 10.3 1.0
C5 B:DG8 4.9 10.3 1.0
C5 B:DG13 4.9 10.2 1.0
C5 B:DG2 4.9 10.8 1.0
C5 B:DG10 4.9 10.6 1.0

Potassium binding site 7 out of 7 in 7d5e

Go back to Potassium Binding Sites List in 7d5e
Potassium binding site 7 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K104

b:34.6
occ:1.00
N1 B:SPM106 3.0 28.8 1.0
N3 B:DT22 3.0 15.5 1.0
O B:HOH269 3.1 39.8 1.0
C2 B:SPM106 3.6 55.9 1.0
O2 B:DT22 3.7 16.5 1.0
O4 B:DT22 3.8 17.1 1.0
C2 B:DT22 3.8 15.2 1.0
C4 B:DT22 3.8 15.7 1.0
C6 B:DG20 4.0 12.1 1.0
C4 B:SPM106 4.0 29.4 1.0
C3 B:SPM106 4.0 60.3 1.0
N1 B:DG20 4.1 11.6 1.0
C5 B:DG20 4.1 12.2 1.0
C4 B:DG20 4.3 10.9 1.0
N5 B:SPM106 4.3 57.5 1.0
O6 B:DG20 4.3 13.2 1.0
C2 B:DG20 4.4 12.0 1.0
C6 B:SPM106 4.5 15.1 1.0
O2 B:DT19 4.5 21.3 1.0
N3 B:DG20 4.5 11.8 1.0
N7 B:DG20 4.7 12.8 1.0
O B:HOH256 4.9 26.2 1.0
N9 B:DG20 5.0 12.0 1.0

Reference:

P.Das, K.H.Ngo, F.R.Winnerdy, A.Maity, B.Bakalar, Y.Mechulam, E.Schmitt, A.T.Phan. Bulges in Left-Handed G-Quadruplexes. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33503265
DOI: 10.1093/NAR/GKAA1259
Page generated: Wed Mar 3 14:20:38 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy