Potassium in PDB 4l0a: X-Ray Structure of An All Lna Quadruplex
Protein crystallography data
The structure of X-Ray Structure of An All Lna Quadruplex, PDB code: 4l0a
was solved by
I.Russo Krauss,
G.Parkinson,
A.Merlino,
L.Mazzarella,
F.Sica,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.70
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
27.670,
27.670,
196.830,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16 /
18
|
Potassium Binding Sites:
The binding sites of Potassium atom in the X-Ray Structure of An All Lna Quadruplex
(pdb code 4l0a). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
X-Ray Structure of An All Lna Quadruplex, PDB code: 4l0a:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 4l0a
Go back to
Potassium Binding Sites List in 4l0a
Potassium binding site 1 out
of 6 in the X-Ray Structure of An All Lna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K101
b:19.5
occ:1.00
|
O6
|
D:LCG3
|
2.8
|
5.5
|
1.0
|
O6
|
C:LCG4
|
2.8
|
3.6
|
1.0
|
O6
|
B:LCG3
|
2.8
|
4.6
|
1.0
|
O6
|
D:LCG4
|
2.9
|
4.1
|
1.0
|
O6
|
C:LCG3
|
2.9
|
4.0
|
1.0
|
O6
|
A:LCG3
|
3.0
|
2.6
|
1.0
|
O6
|
B:LCG4
|
3.0
|
3.6
|
1.0
|
O6
|
A:LCG4
|
3.1
|
5.6
|
1.0
|
C6
|
C:LCG4
|
3.6
|
4.5
|
1.0
|
K
|
A:K103
|
3.6
|
20.5
|
1.0
|
C6
|
D:LCG4
|
3.7
|
4.3
|
1.0
|
K
|
A:K102
|
3.7
|
24.9
|
1.0
|
N1
|
C:LCG4
|
3.8
|
4.3
|
1.0
|
C6
|
B:LCG4
|
3.8
|
4.6
|
1.0
|
C6
|
D:LCG3
|
3.8
|
5.1
|
1.0
|
C6
|
A:LCG4
|
3.8
|
3.4
|
1.0
|
C6
|
C:LCG3
|
3.8
|
6.2
|
1.0
|
C6
|
B:LCG3
|
3.8
|
4.3
|
1.0
|
C6
|
A:LCG3
|
3.9
|
3.1
|
1.0
|
N1
|
D:LCG4
|
3.9
|
3.0
|
1.0
|
N1
|
A:LCG4
|
3.9
|
3.8
|
1.0
|
N1
|
C:LCG3
|
3.9
|
6.0
|
1.0
|
N1
|
D:LCG3
|
4.0
|
5.3
|
1.0
|
N1
|
B:LCG3
|
4.0
|
3.0
|
1.0
|
N1
|
B:LCG4
|
4.1
|
4.0
|
1.0
|
N1
|
A:LCG3
|
4.2
|
2.6
|
1.0
|
C5
|
C:LCG4
|
4.7
|
5.2
|
1.0
|
C5
|
D:LCG4
|
4.7
|
4.3
|
1.0
|
C5
|
B:LCG4
|
4.8
|
3.8
|
1.0
|
C5
|
A:LCG4
|
4.9
|
4.5
|
1.0
|
C5
|
D:LCG3
|
5.0
|
4.2
|
1.0
|
C2
|
C:LCG4
|
5.0
|
5.2
|
1.0
|
|
Potassium binding site 2 out
of 6 in 4l0a
Go back to
Potassium Binding Sites List in 4l0a
Potassium binding site 2 out
of 6 in the X-Ray Structure of An All Lna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K102
b:24.9
occ:1.00
|
O4
|
C:TLN5
|
2.9
|
7.5
|
1.0
|
O4
|
D:TLN5
|
2.9
|
6.2
|
1.0
|
O6
|
B:LCG4
|
3.0
|
3.6
|
1.0
|
O6
|
D:LCG4
|
3.0
|
4.1
|
1.0
|
O4
|
B:TLN5
|
3.0
|
5.7
|
1.0
|
O6
|
A:LCG4
|
3.1
|
5.6
|
1.0
|
O6
|
C:LCG4
|
3.1
|
3.6
|
1.0
|
O4
|
A:TLN5
|
3.1
|
3.5
|
1.0
|
K
|
A:K101
|
3.7
|
19.5
|
1.0
|
C4
|
C:TLN5
|
3.7
|
5.8
|
1.0
|
C4
|
D:TLN5
|
3.8
|
5.9
|
1.0
|
C4
|
B:TLN5
|
3.8
|
4.6
|
1.0
|
N3
|
C:TLN5
|
3.8
|
5.2
|
1.0
|
C6
|
D:LCG4
|
3.9
|
4.3
|
1.0
|
C6
|
B:LCG4
|
4.0
|
4.6
|
1.0
|
C6
|
A:LCG4
|
4.0
|
3.4
|
1.0
|
C6
|
C:LCG4
|
4.0
|
4.5
|
1.0
|
N3
|
D:TLN5
|
4.0
|
6.2
|
1.0
|
C4
|
A:TLN5
|
4.0
|
4.5
|
1.0
|
N3
|
B:TLN5
|
4.0
|
6.9
|
1.0
|
N1
|
A:LCG4
|
4.1
|
3.8
|
1.0
|
N3
|
A:TLN5
|
4.1
|
5.7
|
1.0
|
N1
|
C:LCG4
|
4.1
|
4.3
|
1.0
|
N1
|
D:LCG4
|
4.2
|
3.0
|
1.0
|
N1
|
B:LCG4
|
4.2
|
4.0
|
1.0
|
C5
|
C:TLN5
|
4.9
|
5.9
|
1.0
|
C5
|
D:TLN5
|
5.0
|
7.4
|
1.0
|
C5
|
B:TLN5
|
5.0
|
3.4
|
1.0
|
|
Potassium binding site 3 out
of 6 in 4l0a
Go back to
Potassium Binding Sites List in 4l0a
Potassium binding site 3 out
of 6 in the X-Ray Structure of An All Lna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K103
b:20.5
occ:1.00
|
O6
|
C:LCG2
|
2.8
|
6.3
|
1.0
|
O6
|
A:LCG2
|
2.8
|
6.1
|
1.0
|
O6
|
B:LCG2
|
2.9
|
4.2
|
1.0
|
O6
|
D:LCG2
|
2.9
|
6.6
|
1.0
|
O6
|
C:LCG3
|
3.0
|
4.0
|
1.0
|
O6
|
B:LCG3
|
3.1
|
4.6
|
1.0
|
O6
|
D:LCG3
|
3.1
|
5.5
|
1.0
|
O6
|
A:LCG3
|
3.2
|
2.6
|
1.0
|
K
|
A:K101
|
3.6
|
19.5
|
1.0
|
C6
|
C:LCG3
|
3.7
|
6.2
|
1.0
|
C6
|
A:LCG2
|
3.7
|
6.6
|
1.0
|
C6
|
C:LCG2
|
3.7
|
5.9
|
1.0
|
C6
|
B:LCG3
|
3.8
|
4.3
|
1.0
|
C6
|
D:LCG3
|
3.8
|
5.1
|
1.0
|
C6
|
B:LCG2
|
3.8
|
4.7
|
1.0
|
N1
|
A:LCG2
|
3.9
|
5.0
|
1.0
|
C6
|
D:LCG2
|
3.9
|
5.0
|
1.0
|
C6
|
A:LCG3
|
3.9
|
3.1
|
1.0
|
N1
|
C:LCG3
|
3.9
|
6.0
|
1.0
|
N1
|
C:LCG2
|
3.9
|
4.5
|
1.0
|
N1
|
B:LCG3
|
4.0
|
3.0
|
1.0
|
N1
|
B:LCG2
|
4.0
|
4.3
|
1.0
|
N1
|
D:LCG3
|
4.0
|
5.3
|
1.0
|
N1
|
A:LCG3
|
4.0
|
2.6
|
1.0
|
N1
|
D:LCG2
|
4.1
|
6.4
|
1.0
|
C5
|
C:LCG3
|
4.7
|
6.1
|
1.0
|
C5
|
B:LCG3
|
4.8
|
3.3
|
1.0
|
C5
|
D:LCG3
|
4.8
|
4.2
|
1.0
|
C5
|
A:LCG3
|
5.0
|
3.8
|
1.0
|
C5
|
A:LCG2
|
5.0
|
4.6
|
1.0
|
C5
|
C:LCG2
|
5.0
|
5.1
|
1.0
|
|
Potassium binding site 4 out
of 6 in 4l0a
Go back to
Potassium Binding Sites List in 4l0a
Potassium binding site 4 out
of 6 in the X-Ray Structure of An All Lna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K3003
b:22.8
occ:1.00
|
O6
|
G:LCG2
|
2.8
|
5.3
|
1.0
|
O6
|
E:LCG2
|
2.8
|
6.4
|
1.0
|
O6
|
F:LCG2
|
2.8
|
5.3
|
1.0
|
O6
|
H:LCG2
|
3.0
|
5.7
|
1.0
|
O6
|
E:LCG3
|
3.0
|
3.0
|
1.0
|
O6
|
F:LCG3
|
3.1
|
2.0
|
1.0
|
O6
|
G:LCG3
|
3.1
|
5.1
|
1.0
|
O6
|
H:LCG3
|
3.2
|
5.4
|
1.0
|
K
|
E:K3004
|
3.6
|
20.5
|
1.0
|
C6
|
E:LCG3
|
3.7
|
4.8
|
1.0
|
C6
|
E:LCG2
|
3.7
|
5.1
|
1.0
|
C6
|
G:LCG2
|
3.8
|
6.7
|
1.0
|
C6
|
F:LCG2
|
3.8
|
5.8
|
1.0
|
C6
|
F:LCG3
|
3.8
|
3.0
|
1.0
|
C6
|
G:LCG3
|
3.8
|
3.8
|
1.0
|
C6
|
H:LCG3
|
3.9
|
6.5
|
1.0
|
N1
|
E:LCG2
|
3.9
|
4.3
|
1.0
|
C6
|
H:LCG2
|
3.9
|
6.6
|
1.0
|
N1
|
E:LCG3
|
4.0
|
3.4
|
1.0
|
N1
|
F:LCG3
|
4.0
|
5.0
|
1.0
|
N1
|
F:LCG2
|
4.0
|
5.1
|
1.0
|
N1
|
G:LCG3
|
4.0
|
3.8
|
1.0
|
N1
|
H:LCG3
|
4.0
|
4.3
|
1.0
|
N1
|
G:LCG2
|
4.1
|
7.4
|
1.0
|
N1
|
H:LCG2
|
4.1
|
6.1
|
1.0
|
C5
|
E:LCG3
|
4.7
|
2.6
|
1.0
|
C5
|
G:LCG3
|
4.8
|
2.8
|
1.0
|
C5
|
F:LCG3
|
4.8
|
3.4
|
1.0
|
C5
|
H:LCG3
|
4.9
|
5.6
|
1.0
|
C5
|
E:LCG2
|
5.0
|
4.0
|
1.0
|
C5
|
G:LCG2
|
5.0
|
7.3
|
1.0
|
|
Potassium binding site 5 out
of 6 in 4l0a
Go back to
Potassium Binding Sites List in 4l0a
Potassium binding site 5 out
of 6 in the X-Ray Structure of An All Lna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K3004
b:20.5
occ:1.00
|
O6
|
H:LCG4
|
2.8
|
2.5
|
1.0
|
O6
|
F:LCG3
|
2.9
|
2.0
|
1.0
|
O6
|
H:LCG3
|
2.9
|
5.4
|
1.0
|
O6
|
E:LCG3
|
2.9
|
3.0
|
1.0
|
O6
|
F:LCG4
|
3.0
|
3.3
|
1.0
|
O6
|
G:LCG3
|
3.0
|
5.1
|
1.0
|
O6
|
E:LCG4
|
3.0
|
3.6
|
1.0
|
O6
|
G:LCG4
|
3.0
|
2.0
|
1.0
|
C6
|
H:LCG4
|
3.6
|
3.6
|
1.0
|
K
|
E:K3003
|
3.6
|
22.8
|
1.0
|
C6
|
F:LCG4
|
3.7
|
3.8
|
1.0
|
K
|
E:K3005
|
3.7
|
23.1
|
1.0
|
C6
|
G:LCG4
|
3.8
|
4.5
|
1.0
|
C6
|
H:LCG3
|
3.8
|
6.5
|
1.0
|
N1
|
H:LCG4
|
3.8
|
4.4
|
1.0
|
C6
|
E:LCG4
|
3.8
|
4.3
|
1.0
|
C6
|
F:LCG3
|
3.8
|
3.0
|
1.0
|
N1
|
F:LCG4
|
3.9
|
4.4
|
1.0
|
C6
|
G:LCG3
|
3.9
|
3.8
|
1.0
|
C6
|
E:LCG3
|
3.9
|
4.8
|
1.0
|
N1
|
G:LCG4
|
4.0
|
4.5
|
1.0
|
N1
|
H:LCG3
|
4.0
|
4.3
|
1.0
|
N1
|
E:LCG4
|
4.0
|
3.9
|
1.0
|
N1
|
F:LCG3
|
4.0
|
5.0
|
1.0
|
N1
|
G:LCG3
|
4.1
|
3.8
|
1.0
|
N1
|
E:LCG3
|
4.2
|
3.4
|
1.0
|
C5
|
H:LCG4
|
4.7
|
3.6
|
1.0
|
C5
|
F:LCG4
|
4.7
|
2.9
|
1.0
|
C5
|
G:LCG4
|
4.8
|
5.5
|
1.0
|
C5
|
E:LCG4
|
4.9
|
4.6
|
1.0
|
|
Potassium binding site 6 out
of 6 in 4l0a
Go back to
Potassium Binding Sites List in 4l0a
Potassium binding site 6 out
of 6 in the X-Ray Structure of An All Lna Quadruplex
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K3005
b:23.1
occ:1.00
|
O4
|
E:TLN5
|
2.8
|
5.5
|
1.0
|
O4
|
F:TLN5
|
2.9
|
6.0
|
1.0
|
O4
|
G:TLN5
|
2.9
|
6.9
|
1.0
|
O6
|
E:LCG4
|
3.0
|
3.6
|
1.0
|
O6
|
G:LCG4
|
3.1
|
2.0
|
1.0
|
O4
|
H:TLN5
|
3.1
|
6.2
|
1.0
|
O6
|
F:LCG4
|
3.1
|
3.3
|
1.0
|
O6
|
H:LCG4
|
3.2
|
2.5
|
1.0
|
C4
|
E:TLN5
|
3.6
|
4.9
|
1.0
|
K
|
E:K3004
|
3.7
|
20.5
|
1.0
|
C4
|
F:TLN5
|
3.8
|
5.7
|
1.0
|
N3
|
F:TLN5
|
3.8
|
6.7
|
1.0
|
C4
|
G:TLN5
|
3.8
|
7.8
|
1.0
|
N3
|
E:TLN5
|
3.9
|
5.5
|
1.0
|
C6
|
E:LCG4
|
3.9
|
4.3
|
1.0
|
C6
|
G:LCG4
|
4.0
|
4.5
|
1.0
|
C4
|
H:TLN5
|
4.0
|
6.4
|
1.0
|
C6
|
F:LCG4
|
4.0
|
3.8
|
1.0
|
N1
|
E:LCG4
|
4.1
|
3.9
|
1.0
|
C6
|
H:LCG4
|
4.1
|
3.6
|
1.0
|
N3
|
G:TLN5
|
4.1
|
7.1
|
1.0
|
N1
|
F:LCG4
|
4.1
|
4.4
|
1.0
|
N3
|
H:TLN5
|
4.2
|
9.1
|
1.0
|
N1
|
G:LCG4
|
4.2
|
4.5
|
1.0
|
N1
|
H:LCG4
|
4.3
|
4.4
|
1.0
|
C5
|
E:TLN5
|
4.9
|
3.5
|
1.0
|
|
Reference:
I.Russo Krauss,
G.N.Parkinson,
A.Merlino,
C.A.Mattia,
A.Randazzo,
E.Novellino,
L.Mazzarella,
F.Sica.
A Regular Thymine Tetrad and A Peculiar Supramolecular Assembly in the First Crystal Structure of An All-Lna G-Quadruplex. Acta Crystallogr.,Sect.D V. 70 362 2014.
ISSN: ISSN 0907-4449
PubMed: 24531470
DOI: 10.1107/S1399004713028095
Page generated: Mon Aug 12 11:14:53 2024
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