Potassium in PDB 6l9z: 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Protein crystallography data
The structure of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X, PDB code: 6l9z
was solved by
Z.Adhireksan,
D.Sharma,
P.L.Lee,
C.A.Davey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
213.83 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.5,
101.41,
215.67,
90,
97.48,
90
|
R / Rfree (%)
|
20.4 /
25.6
|
Other elements in 6l9z:
The structure of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
(pdb code 6l9z). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the
338 Bp Di-Nucleosome Assembled with Linker Histone H1.X, PDB code: 6l9z:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 1 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K205
b:93.7
occ:1.00
|
O
|
G:ASN38
|
2.7
|
60.0
|
1.0
|
O
|
C:ASN38
|
2.8
|
77.1
|
1.0
|
C
|
G:ASN38
|
3.9
|
58.0
|
1.0
|
C
|
C:ASN38
|
4.0
|
66.7
|
1.0
|
OG
|
H:SER78
|
4.2
|
54.1
|
1.0
|
CB
|
C:ASN38
|
4.5
|
73.1
|
1.0
|
CB
|
G:ASN38
|
4.6
|
70.7
|
1.0
|
CA
|
G:TYR39
|
4.6
|
53.7
|
1.0
|
CD1
|
G:TYR39
|
4.7
|
46.3
|
1.0
|
CA
|
C:TYR39
|
4.7
|
59.4
|
1.0
|
N
|
G:TYR39
|
4.7
|
53.0
|
1.0
|
N
|
C:TYR39
|
4.8
|
62.6
|
1.0
|
OG
|
D:SER78
|
4.8
|
54.4
|
1.0
|
CA
|
G:ASN38
|
4.9
|
63.8
|
1.0
|
O
|
C:GLY37
|
4.9
|
62.0
|
1.0
|
CA
|
C:ASN38
|
4.9
|
70.5
|
1.0
|
CD1
|
C:TYR39
|
5.0
|
50.0
|
1.0
|
O
|
G:GLY37
|
5.0
|
58.8
|
1.0
|
|
Potassium binding site 2 out
of 10 in 6l9z
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Potassium Binding Sites List in 6l9z
Potassium binding site 2 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K429
b:80.5
occ:1.00
|
O
|
J:HOH529
|
2.4
|
64.2
|
1.0
|
O2
|
I:DT228
|
2.4
|
74.1
|
1.0
|
O
|
I:HOH525
|
2.7
|
48.1
|
1.0
|
O
|
J:HOH538
|
2.8
|
31.7
|
1.0
|
O4'
|
I:DA229
|
3.1
|
69.1
|
1.0
|
C2
|
I:DT228
|
3.6
|
70.7
|
1.0
|
C4'
|
I:DA229
|
3.6
|
65.2
|
1.0
|
O4'
|
J:DA113
|
3.9
|
70.0
|
1.0
|
C5'
|
I:DA229
|
4.0
|
64.2
|
1.0
|
O
|
I:HOH514
|
4.1
|
47.3
|
1.0
|
C1'
|
I:DA229
|
4.2
|
69.9
|
1.0
|
C1'
|
I:DT228
|
4.3
|
66.0
|
1.0
|
N1
|
I:DT228
|
4.4
|
71.3
|
1.0
|
N2
|
J:DG112
|
4.4
|
87.0
|
1.0
|
C4'
|
J:DA113
|
4.5
|
63.1
|
1.0
|
N3
|
I:DT228
|
4.5
|
75.8
|
1.0
|
O
|
P:HOH208
|
4.6
|
40.1
|
1.0
|
C2
|
J:DA111
|
4.6
|
63.3
|
1.0
|
N3
|
I:DA229
|
4.7
|
70.6
|
1.0
|
N9
|
I:DA229
|
4.8
|
71.6
|
1.0
|
N3
|
J:DG112
|
4.9
|
85.7
|
1.0
|
C3'
|
I:DA229
|
4.9
|
63.3
|
1.0
|
C5'
|
J:DA113
|
5.0
|
59.2
|
1.0
|
|
Potassium binding site 3 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 3 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K430
b:80.7
occ:1.00
|
O
|
I:HOH534
|
2.7
|
55.5
|
1.0
|
O2
|
I:DT59
|
2.7
|
61.5
|
1.0
|
O4'
|
J:DA282
|
3.5
|
66.5
|
1.0
|
O4'
|
I:DA60
|
3.7
|
67.8
|
1.0
|
C2
|
I:DT59
|
4.0
|
67.9
|
1.0
|
C4'
|
I:DA60
|
4.0
|
62.2
|
1.0
|
C4'
|
J:DA282
|
4.0
|
61.6
|
1.0
|
N2
|
J:DG281
|
4.4
|
79.0
|
1.0
|
C1'
|
J:DA282
|
4.5
|
70.9
|
1.0
|
C5'
|
I:DA60
|
4.5
|
58.0
|
1.0
|
C1'
|
I:DT59
|
4.6
|
66.9
|
1.0
|
C1'
|
I:DA60
|
4.7
|
70.3
|
1.0
|
N1
|
I:DT59
|
4.8
|
70.3
|
1.0
|
C5'
|
J:DA282
|
4.8
|
61.7
|
1.0
|
N3
|
J:DG281
|
4.9
|
80.6
|
1.0
|
C2
|
J:DA280
|
4.9
|
68.8
|
1.0
|
N3
|
I:DT59
|
4.9
|
76.5
|
1.0
|
N3
|
J:DA282
|
5.0
|
73.0
|
1.0
|
|
Potassium binding site 4 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 4 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K431
b:97.9
occ:1.00
|
O
|
I:HOH505
|
2.1
|
79.1
|
1.0
|
O
|
J:HOH521
|
2.4
|
64.2
|
1.0
|
O
|
I:HOH542
|
2.4
|
65.3
|
1.0
|
O
|
I:HOH501
|
2.8
|
70.5
|
1.0
|
N3
|
I:DA219
|
4.1
|
87.8
|
1.0
|
O4'
|
I:DG220
|
4.2
|
80.4
|
1.0
|
C2
|
I:DA219
|
4.2
|
85.1
|
1.0
|
N3
|
I:DG220
|
4.3
|
90.4
|
1.0
|
N2
|
I:DG220
|
4.5
|
89.5
|
1.0
|
C4'
|
I:DG220
|
4.5
|
71.8
|
1.0
|
N3
|
J:DA121
|
4.6
|
87.6
|
1.0
|
O4'
|
I:DA221
|
4.7
|
88.8
|
1.0
|
O2
|
J:DT120
|
4.7
|
96.8
|
1.0
|
O4'
|
J:DA121
|
4.7
|
87.5
|
1.0
|
C2
|
I:DG220
|
4.8
|
88.2
|
1.0
|
C1'
|
I:DG220
|
4.9
|
83.1
|
1.0
|
O4'
|
J:DC122
|
4.9
|
82.6
|
1.0
|
|
Potassium binding site 5 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 5 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K432
b:100.0
occ:1.00
|
O
|
J:HOH523
|
2.4
|
84.2
|
1.0
|
O
|
J:HOH515
|
2.5
|
73.4
|
1.0
|
O
|
I:HOH507
|
2.6
|
69.2
|
1.0
|
O
|
I:HOH543
|
2.9
|
78.9
|
1.0
|
O4'
|
I:DA121
|
4.2
|
108.7
|
1.0
|
C2
|
J:DA219
|
4.5
|
86.3
|
1.0
|
N3
|
I:DA121
|
4.5
|
104.1
|
1.0
|
C4'
|
I:DA121
|
4.6
|
117.7
|
1.0
|
O4'
|
J:DA220
|
4.7
|
84.9
|
1.0
|
O4'
|
I:DC122
|
4.7
|
92.8
|
1.0
|
O2
|
I:DT120
|
4.7
|
114.7
|
1.0
|
N3
|
J:DA219
|
4.8
|
89.6
|
1.0
|
O4'
|
J:DG221
|
4.8
|
94.2
|
1.0
|
C1'
|
I:DA121
|
4.8
|
102.2
|
1.0
|
C4'
|
J:DA220
|
5.0
|
78.6
|
1.0
|
N3
|
J:DA220
|
5.0
|
91.9
|
1.0
|
O3'
|
I:DA121
|
5.0
|
113.1
|
1.0
|
|
Potassium binding site 6 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 6 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K433
b:115.0
occ:1.00
|
O
|
I:HOH535
|
3.0
|
64.5
|
1.0
|
O2
|
I:DT289
|
3.8
|
84.9
|
1.0
|
O4'
|
I:DA290
|
4.0
|
78.6
|
1.0
|
O4'
|
J:DG52
|
4.1
|
79.9
|
1.0
|
N3
|
J:DA51
|
4.3
|
77.6
|
1.0
|
C4'
|
I:DA290
|
4.4
|
82.2
|
1.0
|
C2
|
J:DA51
|
4.5
|
72.0
|
1.0
|
C4'
|
J:DG52
|
4.5
|
86.7
|
1.0
|
C1'
|
I:DA290
|
4.9
|
82.7
|
1.0
|
C2
|
I:DT289
|
4.9
|
95.6
|
1.0
|
|
Potassium binding site 7 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 7 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K434
b:110.2
occ:1.00
|
O4'
|
J:DA290
|
4.1
|
91.2
|
1.0
|
N3
|
J:DA290
|
4.5
|
95.7
|
1.0
|
O4'
|
I:DA52
|
4.5
|
96.4
|
1.0
|
C4'
|
J:DA290
|
4.7
|
88.3
|
1.0
|
C1'
|
J:DA290
|
4.7
|
86.5
|
1.0
|
O2
|
J:DT289
|
4.7
|
86.4
|
1.0
|
N2
|
I:DG51
|
4.7
|
91.4
|
1.0
|
C5'
|
I:DA52
|
4.8
|
89.5
|
1.0
|
C5'
|
J:DC291
|
4.8
|
82.7
|
1.0
|
N3
|
I:DG51
|
4.8
|
85.7
|
1.0
|
C4'
|
I:DA52
|
4.8
|
94.2
|
1.0
|
O4'
|
I:DG51
|
4.8
|
84.3
|
1.0
|
C2
|
I:DA50
|
4.9
|
76.3
|
1.0
|
O4'
|
J:DC291
|
5.0
|
85.4
|
1.0
|
|
Potassium binding site 8 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 8 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K424
b:77.5
occ:1.00
|
O
|
I:HOH513
|
2.5
|
50.9
|
1.0
|
O
|
J:HOH513
|
2.6
|
45.5
|
1.0
|
O
|
J:HOH531
|
2.6
|
50.4
|
1.0
|
O2
|
J:DT59
|
2.8
|
75.3
|
1.0
|
O4'
|
J:DA60
|
3.4
|
57.1
|
1.0
|
O
|
L:HOH210
|
3.4
|
43.8
|
1.0
|
C4'
|
J:DA60
|
3.8
|
52.4
|
1.0
|
O4'
|
I:DA282
|
3.9
|
60.9
|
1.0
|
C2
|
J:DT59
|
4.0
|
68.9
|
1.0
|
C1'
|
J:DA60
|
4.3
|
60.9
|
1.0
|
C4'
|
I:DA282
|
4.3
|
55.1
|
1.0
|
C2
|
I:DA280
|
4.4
|
59.0
|
1.0
|
N3
|
J:DA60
|
4.4
|
66.1
|
1.0
|
N2
|
I:DG281
|
4.5
|
69.7
|
1.0
|
C5'
|
J:DA60
|
4.5
|
52.2
|
1.0
|
C1'
|
J:DT59
|
4.8
|
61.5
|
1.0
|
N3
|
I:DG281
|
4.8
|
65.0
|
1.0
|
N9
|
J:DA60
|
4.8
|
66.4
|
1.0
|
O4'
|
J:DG61
|
4.8
|
54.5
|
1.0
|
N3
|
J:DT59
|
4.9
|
67.5
|
1.0
|
N1
|
J:DT59
|
4.9
|
61.5
|
1.0
|
C4
|
J:DA60
|
4.9
|
66.4
|
1.0
|
C5'
|
I:DA282
|
4.9
|
54.8
|
1.0
|
C1'
|
I:DA282
|
4.9
|
58.6
|
1.0
|
N1
|
I:DA280
|
5.0
|
67.0
|
1.0
|
|
Potassium binding site 9 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 9 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K425
b:77.5
occ:1.00
|
O
|
J:HOH509
|
2.6
|
56.5
|
1.0
|
O
|
J:HOH516
|
2.6
|
54.3
|
1.0
|
O2
|
J:DT228
|
2.6
|
92.3
|
1.0
|
O4'
|
J:DA229
|
3.4
|
76.9
|
1.0
|
C2
|
J:DT228
|
3.8
|
86.2
|
1.0
|
C4'
|
J:DA229
|
3.9
|
73.4
|
1.0
|
O4'
|
I:DA113
|
3.9
|
70.1
|
1.0
|
C2
|
I:DA111
|
4.3
|
66.3
|
1.0
|
O
|
I:HOH523
|
4.3
|
61.6
|
1.0
|
N3
|
J:DA229
|
4.4
|
89.8
|
1.0
|
C1'
|
J:DA229
|
4.4
|
80.2
|
1.0
|
C4'
|
I:DA113
|
4.5
|
66.9
|
1.0
|
C5'
|
J:DA229
|
4.5
|
71.2
|
1.0
|
N3
|
J:DT228
|
4.6
|
89.4
|
1.0
|
N2
|
I:DG112
|
4.6
|
89.2
|
1.0
|
C1'
|
J:DT228
|
4.7
|
74.1
|
1.0
|
N1
|
J:DT228
|
4.7
|
77.6
|
1.0
|
N1
|
I:DA111
|
4.8
|
73.8
|
1.0
|
O4'
|
J:DG230
|
4.9
|
54.4
|
1.0
|
N3
|
I:DG112
|
4.9
|
88.2
|
1.0
|
C1'
|
I:DA113
|
4.9
|
72.6
|
1.0
|
C4
|
J:DA229
|
4.9
|
91.4
|
1.0
|
N9
|
J:DA229
|
4.9
|
88.7
|
1.0
|
|
Potassium binding site 10 out
of 10 in 6l9z
Go back to
Potassium Binding Sites List in 6l9z
Potassium binding site 10 out
of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 10 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:K204
b:80.6
occ:1.00
|
O
|
Q:HOH304
|
2.6
|
55.4
|
1.0
|
O
|
M:ASN38
|
2.7
|
65.2
|
1.0
|
O
|
Q:ASN38
|
2.8
|
49.3
|
1.0
|
O
|
N:HOH306
|
3.1
|
44.9
|
1.0
|
C
|
M:ASN38
|
3.9
|
57.7
|
1.0
|
C
|
Q:ASN38
|
4.0
|
47.8
|
1.0
|
OG
|
R:SER78
|
4.3
|
51.6
|
1.0
|
CB
|
M:ASN38
|
4.4
|
69.2
|
1.0
|
CB
|
Q:ASN38
|
4.6
|
62.7
|
1.0
|
O
|
M:GLY37
|
4.6
|
68.9
|
1.0
|
CA
|
Q:TYR39
|
4.7
|
47.2
|
1.0
|
CA
|
M:TYR39
|
4.8
|
49.9
|
1.0
|
N
|
Q:TYR39
|
4.8
|
50.0
|
1.0
|
N
|
M:TYR39
|
4.8
|
53.4
|
1.0
|
CA
|
M:ASN38
|
4.8
|
61.9
|
1.0
|
CD1
|
M:TYR39
|
4.8
|
39.7
|
1.0
|
OG
|
N:SER78
|
4.8
|
51.0
|
1.0
|
CD1
|
Q:TYR39
|
4.9
|
42.6
|
1.0
|
CA
|
Q:ASN38
|
4.9
|
54.3
|
1.0
|
|
Reference:
D.Sharma,
C.A.Davey,
Z.Adhireksan.
Dinucleosome 338 Bp with Linker Histone H1.X To Be Published.
Page generated: Mon Aug 12 16:47:26 2024
|