Potassium in PDB 7xx7: Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
Protein crystallography data
The structure of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 7xx7
was solved by
Z.Adhireksan,
B.Qiuye,
P.L.Lee,
D.Sharma,
S.Padavattan,
C.A.Davey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.83 /
2.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.852,
102.111,
216.179,
90,
96.34,
90
|
R / Rfree (%)
|
22.1 /
25.9
|
Other elements in 7xx7:
The structure of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
(pdb code 7xx7). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the
Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 7xx7:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Potassium binding site 1 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 1 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K204
b:112.5
occ:1.00
|
O
|
G:ASN38
|
2.7
|
75.1
|
1.0
|
O
|
C:ASN38
|
3.1
|
81.7
|
1.0
|
C
|
G:ASN38
|
3.9
|
76.8
|
1.0
|
C
|
C:ASN38
|
4.3
|
80.4
|
1.0
|
OG
|
H:SER78
|
4.4
|
68.9
|
1.0
|
OG
|
D:SER78
|
4.6
|
80.3
|
1.0
|
CA
|
G:TYR39
|
4.6
|
71.4
|
1.0
|
CB
|
G:ASN38
|
4.6
|
83.2
|
1.0
|
CD1
|
G:TYR39
|
4.7
|
64.7
|
1.0
|
N
|
G:TYR39
|
4.7
|
74.3
|
1.0
|
O
|
G:GLY37
|
4.8
|
86.3
|
1.0
|
CB
|
C:ASN38
|
4.8
|
86.2
|
1.0
|
CA
|
G:ASN38
|
5.0
|
81.4
|
1.0
|
|
Potassium binding site 2 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 2 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K109
b:101.5
occ:1.00
|
O2
|
I:DT-26
|
2.9
|
88.3
|
1.0
|
O4'
|
I:DA-25
|
3.5
|
80.6
|
1.0
|
O4'
|
J:DA28
|
3.6
|
82.5
|
1.0
|
C4'
|
I:DA-25
|
3.9
|
79.0
|
1.0
|
C4'
|
J:DA28
|
4.0
|
78.9
|
1.0
|
C2
|
I:DT-26
|
4.1
|
88.3
|
1.0
|
C1'
|
I:DA-25
|
4.4
|
81.5
|
1.0
|
N3
|
I:DA-25
|
4.5
|
85.1
|
1.0
|
C5'
|
I:DA-25
|
4.5
|
81.0
|
1.0
|
C2
|
J:DA26
|
4.5
|
86.6
|
1.0
|
N2
|
J:DG27
|
4.6
|
91.9
|
1.0
|
C5'
|
J:DA28
|
4.6
|
77.9
|
1.0
|
C1'
|
J:DA28
|
4.7
|
83.2
|
1.0
|
C1'
|
I:DT-26
|
4.8
|
88.3
|
1.0
|
O4'
|
I:DG-24
|
4.9
|
84.0
|
1.0
|
N3
|
J:DG27
|
5.0
|
92.2
|
1.0
|
N1
|
I:DT-26
|
5.0
|
87.9
|
1.0
|
N3
|
I:DT-26
|
5.0
|
89.6
|
1.0
|
|
Potassium binding site 3 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 3 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K110
b:128.8
occ:1.00
|
O
|
J:HOH204
|
2.6
|
105.0
|
1.0
|
O4'
|
I:DA36
|
3.9
|
120.3
|
1.0
|
O4'
|
J:DA-33
|
4.2
|
114.4
|
1.0
|
C4'
|
I:DA36
|
4.4
|
120.8
|
1.0
|
C1'
|
I:DA36
|
4.4
|
119.4
|
1.0
|
N3
|
I:DA36
|
4.5
|
117.1
|
1.0
|
C4'
|
J:DA-33
|
4.5
|
111.6
|
1.0
|
C5'
|
J:DA-33
|
4.6
|
107.8
|
1.0
|
O2
|
I:DT35
|
4.7
|
123.6
|
1.0
|
C5'
|
I:DC37
|
4.8
|
115.3
|
1.0
|
N2
|
J:DG-34
|
4.9
|
115.4
|
1.0
|
|
Potassium binding site 4 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 4 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K110
b:116.7
occ:1.00
|
O2
|
J:DT-26
|
2.8
|
99.0
|
1.0
|
O4'
|
J:DA-25
|
3.5
|
83.8
|
1.0
|
O4'
|
I:DA28
|
3.8
|
81.1
|
1.0
|
C4'
|
J:DA-25
|
3.9
|
80.6
|
1.0
|
C2
|
J:DT-26
|
4.0
|
94.9
|
1.0
|
C4'
|
I:DA28
|
4.2
|
79.4
|
1.0
|
C2
|
I:DA26
|
4.4
|
85.0
|
1.0
|
N2
|
I:DG27
|
4.4
|
86.2
|
1.0
|
C1'
|
J:DA-25
|
4.5
|
85.1
|
1.0
|
C5'
|
J:DA-25
|
4.5
|
80.8
|
1.0
|
N3
|
J:DA-25
|
4.6
|
99.2
|
1.0
|
C1'
|
J:DT-26
|
4.7
|
89.5
|
1.0
|
C5'
|
I:DA28
|
4.8
|
80.1
|
1.0
|
N3
|
I:DG27
|
4.8
|
87.7
|
1.0
|
C1'
|
I:DA28
|
4.9
|
81.5
|
1.0
|
N1
|
J:DT-26
|
4.9
|
93.4
|
1.0
|
N3
|
J:DT-26
|
4.9
|
96.0
|
1.0
|
|
Potassium binding site 5 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 5 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:K202
b:104.1
occ:1.00
|
O
|
Q:ASN38
|
2.7
|
56.7
|
1.0
|
O
|
M:ASN38
|
3.0
|
61.4
|
1.0
|
C
|
Q:ASN38
|
4.0
|
56.2
|
1.0
|
C
|
M:ASN38
|
4.2
|
60.0
|
1.0
|
OG
|
N:SER78
|
4.4
|
54.7
|
1.0
|
CB
|
Q:ASN38
|
4.4
|
59.9
|
1.0
|
OG
|
R:SER78
|
4.5
|
52.3
|
1.0
|
CA
|
Q:TYR39
|
4.8
|
53.1
|
1.0
|
O
|
Q:GLY37
|
4.8
|
58.0
|
1.0
|
CA
|
M:TYR39
|
4.8
|
57.0
|
1.0
|
N
|
Q:TYR39
|
4.8
|
54.4
|
1.0
|
CB
|
M:ASN38
|
4.9
|
63.9
|
1.0
|
CA
|
Q:ASN38
|
4.9
|
58.5
|
1.0
|
CD1
|
Q:TYR39
|
4.9
|
48.7
|
1.0
|
N
|
M:TYR39
|
5.0
|
58.7
|
1.0
|
|
Potassium binding site 6 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 6 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:K116
b:110.0
occ:1.00
|
O2
|
S:DT-26
|
3.0
|
72.2
|
1.0
|
O4'
|
S:DA-25
|
3.6
|
57.4
|
1.0
|
O4'
|
T:DA28
|
3.8
|
61.8
|
1.0
|
C4'
|
S:DA-25
|
3.9
|
55.2
|
1.0
|
C2
|
S:DT-26
|
4.1
|
70.6
|
1.0
|
C4'
|
T:DA28
|
4.2
|
59.2
|
1.0
|
C2
|
T:DA26
|
4.3
|
65.9
|
1.0
|
N2
|
T:DG27
|
4.5
|
65.7
|
1.0
|
C1'
|
S:DA-25
|
4.5
|
57.6
|
1.0
|
C5'
|
S:DA-25
|
4.6
|
56.3
|
1.0
|
N3
|
S:DA-25
|
4.6
|
62.2
|
1.0
|
C5'
|
T:DA28
|
4.7
|
58.6
|
1.0
|
C1'
|
S:DT-26
|
4.8
|
66.4
|
1.0
|
N3
|
T:DG27
|
4.9
|
65.8
|
1.0
|
O4'
|
S:DG-24
|
4.9
|
55.0
|
1.0
|
C1'
|
T:DA28
|
4.9
|
62.3
|
1.0
|
N1
|
T:DA26
|
5.0
|
66.8
|
1.0
|
N3
|
T:DA26
|
5.0
|
66.6
|
1.0
|
|
Potassium binding site 7 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 7 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:K117
b:124.4
occ:1.00
|
O
|
T:HOH211
|
2.6
|
107.7
|
1.0
|
O
|
T:HOH206
|
2.6
|
92.7
|
1.0
|
O
|
T:HOH219
|
2.7
|
93.7
|
1.0
|
N3
|
S:DA36
|
4.0
|
96.2
|
1.0
|
O4'
|
S:DA36
|
4.1
|
106.4
|
1.0
|
C1'
|
S:DA36
|
4.4
|
102.6
|
1.0
|
O2
|
S:DT35
|
4.5
|
101.4
|
1.0
|
O4'
|
S:DC37
|
4.7
|
86.4
|
1.0
|
C2
|
T:DA-35
|
4.7
|
78.3
|
1.0
|
C5'
|
S:DC37
|
4.7
|
91.0
|
1.0
|
C2
|
S:DA36
|
4.7
|
94.0
|
1.0
|
C4'
|
S:DA36
|
4.8
|
107.8
|
1.0
|
N2
|
T:DG-34
|
4.8
|
91.0
|
1.0
|
N3
|
T:DA-35
|
4.8
|
77.0
|
1.0
|
O4'
|
T:DA-33
|
4.8
|
90.5
|
1.0
|
C4
|
S:DA36
|
4.8
|
97.7
|
1.0
|
C4'
|
S:DC37
|
4.9
|
86.6
|
1.0
|
N3
|
T:DG-34
|
5.0
|
84.8
|
1.0
|
|
Potassium binding site 8 out
of 8 in 7xx7
Go back to
Potassium Binding Sites List in 7xx7
Potassium binding site 8 out
of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)
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 Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:K108
b:101.0
occ:1.00
|
O2
|
T:DT-26
|
2.9
|
70.0
|
1.0
|
O4'
|
T:DA-25
|
3.6
|
64.8
|
1.0
|
O4'
|
S:DA28
|
3.7
|
60.4
|
1.0
|
C4'
|
T:DA-25
|
3.9
|
62.5
|
1.0
|
C2
|
T:DT-26
|
4.1
|
69.4
|
1.0
|
C4'
|
S:DA28
|
4.1
|
57.0
|
1.0
|
O
|
P:HOH203
|
4.2
|
68.9
|
1.0
|
O
|
T:HOH210
|
4.3
|
70.7
|
1.0
|
N2
|
S:DG27
|
4.4
|
62.6
|
1.0
|
C2
|
S:DA26
|
4.4
|
68.8
|
1.0
|
C5'
|
T:DA-25
|
4.5
|
64.2
|
1.0
|
C1'
|
T:DA-25
|
4.5
|
64.8
|
1.0
|
N3
|
T:DA-25
|
4.7
|
66.6
|
1.0
|
C5'
|
S:DA28
|
4.7
|
56.6
|
1.0
|
C1'
|
T:DT-26
|
4.7
|
69.5
|
1.0
|
C1'
|
S:DA28
|
4.8
|
59.9
|
1.0
|
N3
|
S:DG27
|
4.8
|
63.2
|
1.0
|
N1
|
T:DT-26
|
4.9
|
69.8
|
1.0
|
N3
|
T:DT-26
|
5.0
|
71.4
|
1.0
|
|
Reference:
Z.Adhireksan,
B.Qiuye,
P.L.Lee,
D.Sharma,
S.Padavattan,
C.A.Davey.
Diversity in Linker Histone-Nucleosome Interactions Between and Within Variants To Be Published.
Page generated: Thu Jul 27 18:05:24 2023
|