Potassium in PDB 7cow: 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0
Protein crystallography data
The structure of 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0, PDB code: 7cow
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)
|
49.35 /
2.86
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.215,
105.053,
171.126,
86.59,
88.95,
88.25
|
R / Rfree (%)
|
22.5 /
29.7
|
Other elements in 7cow:
The structure of 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0 also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0
(pdb code 7cow). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the
353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0, PDB code: 7cow:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
Potassium binding site 1 out
of 5 in 7cow
Go back to
Potassium Binding Sites List in 7cow
Potassium binding site 1 out
of 5 in the 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K403
b:116.8
occ:1.00
|
O2
|
I:DT237
|
2.6
|
115.1
|
1.0
|
O4'
|
I:DA238
|
3.1
|
74.3
|
1.0
|
C4'
|
I:DA238
|
3.5
|
76.8
|
1.0
|
C2
|
I:DT237
|
3.8
|
92.8
|
1.0
|
O4'
|
J:DA115
|
3.9
|
87.0
|
1.0
|
C5'
|
I:DA238
|
4.1
|
79.8
|
1.0
|
C1'
|
I:DA238
|
4.1
|
77.7
|
1.0
|
N3
|
I:DA238
|
4.3
|
91.6
|
1.0
|
C4'
|
J:DA115
|
4.3
|
78.4
|
1.0
|
C1'
|
I:DT237
|
4.3
|
89.2
|
1.0
|
N2
|
J:DG114
|
4.4
|
109.4
|
1.0
|
N1
|
I:DT237
|
4.6
|
89.0
|
1.0
|
N9
|
I:DA238
|
4.7
|
75.6
|
1.0
|
C4
|
I:DA238
|
4.8
|
80.8
|
1.0
|
N3
|
I:DT237
|
4.8
|
81.2
|
1.0
|
C5'
|
J:DA115
|
4.8
|
80.3
|
1.0
|
C3'
|
I:DA238
|
4.8
|
75.8
|
1.0
|
O4'
|
I:DG239
|
4.9
|
65.3
|
1.0
|
N3
|
J:DG114
|
4.9
|
119.9
|
1.0
|
C2
|
J:DA113
|
4.9
|
71.4
|
1.0
|
C5'
|
I:DG239
|
5.0
|
72.6
|
1.0
|
O3'
|
I:DA238
|
5.0
|
70.7
|
1.0
|
|
Potassium binding site 2 out
of 5 in 7cow
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Potassium Binding Sites List in 7cow
Potassium binding site 2 out
of 5 in the 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K404
b:110.6
occ:1.00
|
O2
|
I:DT61
|
2.7
|
152.6
|
1.0
|
O4'
|
J:DA291
|
2.8
|
103.7
|
1.0
|
C4'
|
J:DA291
|
3.6
|
99.5
|
1.0
|
C2
|
I:DT61
|
3.8
|
137.4
|
1.0
|
N2
|
J:DG290
|
3.8
|
127.3
|
1.0
|
O4'
|
I:DA62
|
3.9
|
138.1
|
1.0
|
C1'
|
J:DA291
|
4.1
|
114.4
|
1.0
|
N3
|
J:DG290
|
4.2
|
133.1
|
1.0
|
C5'
|
J:DA291
|
4.2
|
99.6
|
1.0
|
C4'
|
I:DA62
|
4.4
|
125.0
|
1.0
|
C5'
|
I:DA62
|
4.4
|
116.9
|
1.0
|
C1'
|
I:DT61
|
4.4
|
138.9
|
1.0
|
C2
|
J:DG290
|
4.5
|
130.8
|
1.0
|
N9
|
J:DA291
|
4.5
|
127.9
|
1.0
|
O4'
|
I:DT61
|
4.5
|
129.8
|
1.0
|
N3
|
J:DA291
|
4.5
|
108.5
|
1.0
|
N1
|
I:DT61
|
4.6
|
131.8
|
1.0
|
N3
|
I:DT61
|
4.7
|
132.9
|
1.0
|
C4
|
J:DA291
|
4.7
|
124.6
|
1.0
|
C3'
|
J:DA291
|
4.8
|
101.4
|
1.0
|
C2
|
J:DA289
|
4.9
|
135.1
|
1.0
|
O3'
|
J:DA291
|
4.9
|
94.7
|
1.0
|
|
Potassium binding site 3 out
of 5 in 7cow
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Potassium Binding Sites List in 7cow
Potassium binding site 3 out
of 5 in the 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K402
b:101.6
occ:1.00
|
O2
|
J:DT61
|
2.7
|
127.3
|
1.0
|
O4'
|
J:DA62
|
3.3
|
101.6
|
1.0
|
N3
|
J:DA62
|
3.6
|
132.7
|
1.0
|
N2
|
I:DG290
|
3.9
|
100.9
|
1.0
|
C2
|
J:DT61
|
3.9
|
119.4
|
1.0
|
C2
|
I:DA289
|
3.9
|
103.2
|
1.0
|
O4'
|
I:DA291
|
4.0
|
94.7
|
1.0
|
C4'
|
J:DA62
|
4.0
|
108.3
|
1.0
|
C2
|
J:DA62
|
4.2
|
135.4
|
1.0
|
N3
|
I:DG290
|
4.3
|
107.8
|
1.0
|
C4
|
J:DA62
|
4.3
|
121.2
|
1.0
|
C5'
|
J:DA62
|
4.4
|
116.2
|
1.0
|
C4'
|
I:DA291
|
4.4
|
84.0
|
1.0
|
C1'
|
J:DA62
|
4.4
|
112.0
|
1.0
|
N3
|
I:DA289
|
4.4
|
99.1
|
1.0
|
C2
|
I:DG290
|
4.5
|
101.1
|
1.0
|
C5'
|
I:DA291
|
4.6
|
84.7
|
1.0
|
N9
|
J:DA62
|
4.6
|
119.4
|
1.0
|
N3
|
J:DT61
|
4.7
|
116.8
|
1.0
|
N1
|
I:DA289
|
4.8
|
106.8
|
1.0
|
O4'
|
J:DG63
|
4.8
|
88.2
|
1.0
|
C1'
|
J:DT61
|
4.8
|
105.3
|
1.0
|
N1
|
J:DT61
|
4.9
|
113.0
|
1.0
|
O5'
|
J:DG63
|
4.9
|
92.3
|
1.0
|
|
Potassium binding site 4 out
of 5 in 7cow
Go back to
Potassium Binding Sites List in 7cow
Potassium binding site 4 out
of 5 in the 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K403
b:98.0
occ:1.00
|
O2
|
J:DT237
|
2.8
|
111.0
|
1.0
|
O4'
|
J:DA238
|
3.7
|
93.8
|
1.0
|
C2
|
J:DT237
|
4.0
|
108.6
|
1.0
|
C4'
|
J:DA238
|
4.0
|
88.3
|
1.0
|
N3
|
J:DA238
|
4.0
|
108.7
|
1.0
|
C2
|
I:DA113
|
4.1
|
94.1
|
1.0
|
C5'
|
J:DG239
|
4.1
|
107.3
|
1.0
|
O4'
|
I:DA115
|
4.2
|
90.4
|
1.0
|
C1'
|
J:DA238
|
4.2
|
94.8
|
1.0
|
O4'
|
J:DG239
|
4.2
|
95.7
|
1.0
|
C4'
|
I:DA115
|
4.6
|
91.4
|
1.0
|
C4'
|
J:DG239
|
4.6
|
95.1
|
1.0
|
N2
|
I:DG114
|
4.7
|
109.8
|
1.0
|
N3
|
I:DA113
|
4.7
|
99.9
|
1.0
|
N3
|
J:DT237
|
4.7
|
107.5
|
1.0
|
C4
|
J:DA238
|
4.7
|
99.9
|
1.0
|
N9
|
J:DA238
|
4.8
|
97.9
|
1.0
|
N3
|
I:DG114
|
4.8
|
104.6
|
1.0
|
C5'
|
I:DA115
|
4.8
|
94.4
|
1.0
|
C2
|
J:DA238
|
4.8
|
116.7
|
1.0
|
O3'
|
J:DA238
|
4.8
|
83.4
|
1.0
|
N1
|
I:DA113
|
4.9
|
97.7
|
1.0
|
N1
|
J:DT237
|
5.0
|
103.5
|
1.0
|
C5'
|
J:DA238
|
5.0
|
85.6
|
1.0
|
|
Potassium binding site 5 out
of 5 in 7cow
Go back to
Potassium Binding Sites List in 7cow
Potassium binding site 5 out
of 5 in the 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of 353 Bp Di-Nucleosome Harboring Cohesive Dna Termini with Linker Histone H1.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K404
b:134.6
occ:1.00
|
O2
|
J:DT298
|
3.1
|
182.6
|
1.0
|
O4'
|
J:DA299
|
3.5
|
139.3
|
1.0
|
O4'
|
I:DA54
|
3.8
|
162.7
|
1.0
|
N2
|
I:DG53
|
3.9
|
168.7
|
1.0
|
N3
|
I:DG53
|
3.9
|
134.3
|
1.0
|
C4'
|
J:DA299
|
4.2
|
145.1
|
1.0
|
C2
|
I:DG53
|
4.3
|
142.9
|
1.0
|
N3
|
J:DA299
|
4.3
|
130.6
|
1.0
|
C2
|
J:DT298
|
4.3
|
183.4
|
1.0
|
C4'
|
I:DA54
|
4.4
|
159.4
|
1.0
|
C1'
|
J:DA299
|
4.4
|
138.3
|
1.0
|
C2
|
I:DA52
|
4.4
|
142.7
|
1.0
|
C5'
|
I:DA54
|
4.5
|
153.4
|
1.0
|
O4'
|
I:DG53
|
4.7
|
137.4
|
1.0
|
C1'
|
J:DT298
|
4.9
|
190.5
|
1.0
|
O4'
|
J:DT298
|
4.9
|
208.1
|
1.0
|
N3
|
I:DA52
|
4.9
|
144.0
|
1.0
|
C4
|
J:DA299
|
4.9
|
133.9
|
1.0
|
C4
|
I:DG53
|
4.9
|
129.8
|
1.0
|
N9
|
J:DA299
|
5.0
|
138.2
|
1.0
|
|
Reference:
Z.Adhireksan,
D.Sharma,
C.A.Davey.
355 Bp Di-Nucleosome To Be Published.
Page generated: Mon Aug 12 18:50:03 2024
|