Calcium in PDB 7xx5: Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Protein crystallography data
The structure of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 7xx5
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)
|
46.57 /
3.19
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.071,
101.736,
218.399,
90,
103.52,
90
|
R / Rfree (%)
|
20.3 /
25.9
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
(pdb code 7xx5). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the
Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 7xx5:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 13 in 7xx5
Go back to
Calcium Binding Sites List in 7xx5
Calcium binding site 1 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca201
b:129.7
occ:1.00
|
OE1
|
G:GLU64
|
2.9
|
144.7
|
1.0
|
CD
|
G:GLU64
|
3.6
|
127.3
|
1.0
|
OE1
|
G:GLU61
|
3.9
|
114.9
|
1.0
|
OE2
|
G:GLU64
|
3.9
|
121.4
|
1.0
|
CG1
|
H:VAL48
|
4.2
|
121.6
|
1.0
|
CB
|
G:GLU64
|
4.5
|
114.3
|
1.0
|
O
|
G:ALA60
|
4.6
|
123.5
|
1.0
|
CG
|
G:GLU64
|
4.6
|
121.2
|
1.0
|
CB
|
G:ALA60
|
4.8
|
113.0
|
1.0
|
CD
|
G:GLU61
|
4.8
|
122.8
|
1.0
|
C
|
G:ALA60
|
4.9
|
116.0
|
1.0
|
|
Calcium binding site 2 out
of 13 in 7xx5
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Calcium Binding Sites List in 7xx5
Calcium binding site 2 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca101
b:112.1
occ:1.00
|
O6
|
J:DG51
|
2.5
|
153.1
|
1.0
|
O6
|
I:DG-52
|
3.4
|
155.5
|
1.0
|
C6
|
J:DG51
|
3.7
|
151.6
|
1.0
|
N7
|
J:DG50
|
3.8
|
140.6
|
1.0
|
N4
|
I:DC-51
|
4.0
|
164.0
|
1.0
|
O6
|
J:DG50
|
4.2
|
139.8
|
1.0
|
C6
|
I:DG-52
|
4.3
|
163.2
|
1.0
|
N4
|
J:DC52
|
4.3
|
153.2
|
1.0
|
N7
|
J:DG51
|
4.4
|
162.2
|
1.0
|
C5
|
J:DG51
|
4.4
|
150.9
|
1.0
|
C5
|
J:DG50
|
4.4
|
137.1
|
1.0
|
C6
|
J:DG50
|
4.6
|
138.8
|
1.0
|
N7
|
I:DG-52
|
4.7
|
175.8
|
1.0
|
C8
|
J:DG50
|
4.7
|
144.8
|
1.0
|
N1
|
J:DG51
|
4.8
|
147.9
|
1.0
|
C5
|
I:DG-52
|
4.8
|
168.2
|
1.0
|
|
Calcium binding site 3 out
of 13 in 7xx5
Go back to
Calcium Binding Sites List in 7xx5
Calcium binding site 3 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca102
b:113.3
occ:1.00
|
O6
|
I:DG51
|
2.9
|
149.6
|
1.0
|
O6
|
J:DG-52
|
3.3
|
138.9
|
1.0
|
N7
|
I:DG50
|
3.5
|
158.5
|
1.0
|
N7
|
I:DG51
|
3.8
|
161.0
|
1.0
|
C6
|
I:DG51
|
3.9
|
164.9
|
1.0
|
C5
|
I:DG50
|
4.2
|
156.3
|
1.0
|
C6
|
J:DG-52
|
4.2
|
146.0
|
1.0
|
C5
|
I:DG51
|
4.2
|
165.3
|
1.0
|
O6
|
I:DG50
|
4.2
|
138.2
|
1.0
|
C8
|
I:DG50
|
4.3
|
168.1
|
1.0
|
N4
|
I:DC52
|
4.4
|
147.8
|
1.0
|
N4
|
J:DC-51
|
4.4
|
142.4
|
1.0
|
C6
|
I:DG50
|
4.4
|
153.8
|
1.0
|
C5
|
J:DG-52
|
5.0
|
145.7
|
1.0
|
|
Calcium binding site 4 out
of 13 in 7xx5
Go back to
Calcium Binding Sites List in 7xx5
Calcium binding site 4 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca103
b:120.8
occ:1.00
|
N7
|
I:DG-34
|
3.8
|
154.9
|
1.0
|
C8
|
I:DG-34
|
4.5
|
156.5
|
1.0
|
C5
|
I:DG-34
|
4.9
|
153.7
|
1.0
|
O6
|
I:DG-34
|
4.9
|
153.8
|
1.0
|
|
Calcium binding site 5 out
of 13 in 7xx5
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Calcium Binding Sites List in 7xx5
Calcium binding site 5 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Ca101
b:119.1
occ:1.00
|
O6
|
J:DG-2
|
3.0
|
141.9
|
1.0
|
N7
|
J:DG-3
|
3.3
|
141.2
|
1.0
|
O6
|
J:DG-3
|
3.8
|
154.4
|
1.0
|
C5
|
J:DG-3
|
4.0
|
146.2
|
1.0
|
C6
|
J:DG-2
|
4.1
|
150.5
|
1.0
|
C8
|
J:DG-3
|
4.2
|
141.6
|
1.0
|
C6
|
J:DG-3
|
4.3
|
150.9
|
1.0
|
N7
|
J:DG-2
|
4.6
|
155.6
|
1.0
|
C5
|
J:DG-2
|
4.7
|
154.5
|
1.0
|
O4
|
I:DT1
|
5.0
|
167.3
|
1.0
|
N4
|
I:DC2
|
5.0
|
177.9
|
1.0
|
|
Calcium binding site 6 out
of 13 in 7xx5
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Calcium Binding Sites List in 7xx5
Calcium binding site 6 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Ca201
b:96.9
occ:1.00
|
OE1
|
Q:GLU91
|
3.1
|
138.2
|
1.0
|
OE2
|
Q:GLU91
|
3.2
|
127.7
|
1.0
|
CD
|
Q:GLU91
|
3.6
|
127.3
|
1.0
|
|
Calcium binding site 7 out
of 13 in 7xx5
Go back to
Calcium Binding Sites List in 7xx5
Calcium binding site 7 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Ca202
b:116.5
occ:1.00
|
O
|
Q:ASN89
|
2.5
|
84.9
|
1.0
|
C
|
Q:ASN89
|
3.7
|
75.8
|
1.0
|
CA
|
Q:ASP90
|
4.6
|
86.3
|
1.0
|
N
|
Q:ASP90
|
4.6
|
81.5
|
1.0
|
CB
|
Q:ASN89
|
4.6
|
74.1
|
1.0
|
CA
|
Q:ASN89
|
4.7
|
71.8
|
1.0
|
|
Calcium binding site 8 out
of 13 in 7xx5
Go back to
Calcium Binding Sites List in 7xx5
Calcium binding site 8 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Ca203
b:115.5
occ:1.00
|
O
|
Q:GLY22
|
3.6
|
89.8
|
1.0
|
CE
|
R:LYS116
|
4.2
|
116.7
|
1.0
|
NZ
|
R:LYS116
|
4.2
|
124.8
|
1.0
|
OE1
|
R:GLU113
|
4.8
|
104.3
|
1.0
|
C
|
Q:GLY22
|
4.8
|
93.0
|
1.0
|
OE2
|
Q:GLU56
|
5.0
|
88.6
|
1.0
|
|
Calcium binding site 9 out
of 13 in 7xx5
Go back to
Calcium Binding Sites List in 7xx5
Calcium binding site 9 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ca101
b:107.3
occ:1.00
|
O6
|
T:DG-52
|
2.8
|
120.6
|
1.0
|
O6
|
S:DG51
|
3.1
|
114.5
|
1.0
|
N4
|
T:DC-51
|
3.7
|
138.1
|
1.0
|
C6
|
T:DG-52
|
3.7
|
128.0
|
1.0
|
N4
|
S:DC52
|
4.1
|
120.1
|
1.0
|
C6
|
S:DG51
|
4.1
|
117.5
|
1.0
|
O6
|
S:DG50
|
4.2
|
110.9
|
1.0
|
N7
|
S:DG51
|
4.3
|
135.3
|
1.0
|
N7
|
S:DG50
|
4.3
|
134.6
|
1.0
|
C5
|
T:DG-52
|
4.5
|
131.5
|
1.0
|
C6
|
S:DG50
|
4.6
|
120.9
|
1.0
|
C5
|
S:DG51
|
4.6
|
124.4
|
1.0
|
N7
|
T:DG-52
|
4.6
|
139.6
|
1.0
|
C5
|
S:DG50
|
4.6
|
126.0
|
1.0
|
N1
|
T:DG-52
|
4.6
|
125.5
|
1.0
|
C4
|
T:DC-51
|
5.0
|
135.7
|
1.0
|
|
Calcium binding site 10 out
of 13 in 7xx5
Go back to
Calcium Binding Sites List in 7xx5
Calcium binding site 10 out
of 13 in the Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ca102
b:112.7
occ:1.00
|
O6
|
S:DG-40
|
3.6
|
147.0
|
1.0
|
O6
|
S:DG-41
|
3.7
|
135.3
|
1.0
|
N4
|
T:DC40
|
4.1
|
116.3
|
1.0
|
N7
|
S:DG-41
|
4.3
|
136.9
|
1.0
|
C6
|
S:DG-41
|
4.5
|
131.3
|
1.0
|
C7
|
S:DT-42
|
4.6
|
126.3
|
1.0
|
C6
|
S:DG-40
|
4.7
|
152.2
|
1.0
|
C5
|
S:DG-41
|
4.7
|
130.9
|
1.0
|
N6
|
T:DA39
|
4.9
|
129.4
|
1.0
|
|
Reference:
Z.Adhireksan,
B.Qiuye,
P.L.Lee,
D.Sharma,
S.Padavattan,
C.A.Davey.
Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (Sticky-169A Dna Fragment) To Be Published.
Page generated: Wed Jul 26 12:36:44 2023
|