Chlorine 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:
Chlorine Binding Sites:
The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine where determined in the
Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 7xx7:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Chlorine binding site 1 out
of 8 in 7xx7
Go back to
Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
A:Cl201
b:110.2
occ:1.00
|
N
|
A:LYS122
|
3.0
|
73.6
|
1.0
|
CD
|
A:PRO121
|
3.4
|
76.4
|
1.0
|
N
|
A:PRO121
|
3.5
|
74.8
|
1.0
|
CB
|
A:LYS122
|
3.6
|
74.4
|
1.0
|
CG
|
A:LYS122
|
3.6
|
75.6
|
1.0
|
CB
|
A:PRO121
|
3.7
|
75.3
|
1.0
|
CA
|
A:LYS122
|
3.9
|
73.0
|
1.0
|
C
|
A:PRO121
|
3.9
|
73.9
|
1.0
|
CA
|
A:PRO121
|
3.9
|
74.2
|
1.0
|
CB
|
A:MET120
|
3.9
|
75.2
|
1.0
|
CG
|
A:PRO121
|
3.9
|
76.3
|
1.0
|
CD
|
A:LYS122
|
4.0
|
77.8
|
1.0
|
C
|
A:MET120
|
4.3
|
73.3
|
1.0
|
CA
|
A:MET120
|
4.7
|
73.4
|
1.0
|
SD
|
A:MET120
|
4.7
|
79.6
|
1.0
|
CG
|
A:MET120
|
4.9
|
77.1
|
1.0
|
|
Chlorine binding site 2 out
of 8 in 7xx7
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Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
C:Cl203
b:102.3
occ:1.00
|
N
|
C:GLY46
|
3.0
|
87.0
|
1.0
|
N
|
D:SER91
|
3.3
|
68.8
|
1.0
|
CA
|
C:GLY46
|
3.4
|
85.4
|
1.0
|
C
|
C:GLY44
|
3.5
|
85.4
|
1.0
|
N
|
C:ALA47
|
3.5
|
80.5
|
1.0
|
N
|
C:ALA45
|
3.6
|
87.7
|
1.0
|
CA
|
D:THR90
|
3.6
|
70.0
|
1.0
|
CA
|
C:GLY44
|
3.6
|
84.6
|
1.0
|
CB
|
D:THR90
|
3.7
|
70.5
|
1.0
|
C
|
D:THR90
|
3.9
|
69.5
|
1.0
|
C
|
C:GLY46
|
3.9
|
83.5
|
1.0
|
O
|
C:GLY44
|
4.0
|
84.4
|
1.0
|
OG
|
D:SER91
|
4.1
|
68.1
|
1.0
|
C
|
C:ALA45
|
4.1
|
87.6
|
1.0
|
CB
|
D:SER91
|
4.2
|
68.2
|
1.0
|
OP1
|
J:DG38
|
4.2
|
100.2
|
1.0
|
CG2
|
D:THR90
|
4.3
|
71.0
|
1.0
|
CA
|
D:SER91
|
4.3
|
68.4
|
1.0
|
CA
|
C:ALA45
|
4.4
|
87.5
|
1.0
|
CA
|
C:ALA47
|
4.6
|
77.7
|
1.0
|
CB
|
C:ALA47
|
4.6
|
77.2
|
1.0
|
N
|
C:GLY44
|
4.7
|
83.4
|
1.0
|
O
|
D:ILE89
|
4.8
|
72.4
|
1.0
|
OG1
|
D:THR90
|
4.9
|
71.0
|
1.0
|
N
|
D:THR90
|
4.9
|
70.3
|
1.0
|
|
Chlorine binding site 3 out
of 8 in 7xx7
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Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
E:Cl201
b:93.8
occ:1.00
|
N
|
E:LYS122
|
3.2
|
72.0
|
1.0
|
CG
|
E:LYS122
|
3.6
|
78.4
|
1.0
|
CD
|
E:PRO121
|
3.6
|
69.2
|
1.0
|
CB
|
E:LYS122
|
3.6
|
76.3
|
1.0
|
N
|
E:PRO121
|
3.7
|
68.3
|
1.0
|
CB
|
E:PRO121
|
3.9
|
69.1
|
1.0
|
CD
|
E:LYS122
|
3.9
|
82.5
|
1.0
|
CA
|
E:LYS122
|
4.0
|
73.2
|
1.0
|
C
|
E:PRO121
|
4.0
|
69.5
|
1.0
|
CB
|
E:MET120
|
4.0
|
72.5
|
1.0
|
CA
|
E:PRO121
|
4.1
|
68.2
|
1.0
|
CG
|
E:PRO121
|
4.1
|
69.4
|
1.0
|
CE
|
E:LYS122
|
4.4
|
84.8
|
1.0
|
C
|
E:MET120
|
4.4
|
68.0
|
1.0
|
NZ
|
E:LYS122
|
4.6
|
87.9
|
1.0
|
SD
|
E:MET120
|
4.8
|
81.3
|
1.0
|
CA
|
E:MET120
|
4.9
|
69.0
|
1.0
|
|
Chlorine binding site 4 out
of 8 in 7xx7
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Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
G:Cl204
b:86.2
occ:1.00
|
N
|
G:GLY46
|
3.1
|
75.5
|
1.0
|
N
|
H:SER91
|
3.3
|
69.6
|
1.0
|
CA
|
G:GLY46
|
3.5
|
74.1
|
1.0
|
C
|
G:GLY44
|
3.6
|
79.6
|
1.0
|
N
|
G:ALA45
|
3.6
|
79.9
|
1.0
|
N
|
G:ALA47
|
3.6
|
70.6
|
1.0
|
CA
|
H:THR90
|
3.6
|
70.2
|
1.0
|
CB
|
H:THR90
|
3.6
|
70.8
|
1.0
|
CA
|
G:GLY44
|
3.7
|
80.2
|
1.0
|
C
|
H:THR90
|
4.0
|
69.7
|
1.0
|
C
|
G:GLY46
|
4.0
|
71.8
|
1.0
|
OG
|
H:SER91
|
4.1
|
71.7
|
1.0
|
O
|
G:GLY44
|
4.1
|
77.1
|
1.0
|
C
|
G:ALA45
|
4.2
|
77.1
|
1.0
|
CG2
|
H:THR90
|
4.2
|
72.0
|
1.0
|
OP1
|
I:DG38
|
4.2
|
100.1
|
1.0
|
CB
|
H:SER91
|
4.3
|
70.1
|
1.0
|
CA
|
H:SER91
|
4.4
|
68.8
|
1.0
|
CA
|
G:ALA45
|
4.5
|
79.1
|
1.0
|
CA
|
G:ALA47
|
4.7
|
69.2
|
1.0
|
CB
|
G:ALA47
|
4.7
|
69.5
|
1.0
|
N
|
G:GLY44
|
4.7
|
81.0
|
1.0
|
OG1
|
H:THR90
|
4.9
|
70.0
|
1.0
|
O
|
H:ILE89
|
4.9
|
69.0
|
1.0
|
N
|
H:THR90
|
5.0
|
69.1
|
1.0
|
|
Chlorine binding site 5 out
of 8 in 7xx7
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Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
K:Cl201
b:91.0
occ:1.00
|
N
|
K:LYS122
|
3.0
|
47.8
|
1.0
|
CD
|
K:PRO121
|
3.3
|
48.4
|
1.0
|
N
|
K:PRO121
|
3.4
|
47.6
|
1.0
|
CB
|
K:PRO121
|
3.6
|
48.1
|
1.0
|
CB
|
K:LYS122
|
3.6
|
49.1
|
1.0
|
CG
|
K:LYS122
|
3.7
|
49.8
|
1.0
|
CA
|
K:PRO121
|
3.8
|
47.7
|
1.0
|
C
|
K:PRO121
|
3.8
|
47.3
|
1.0
|
CG
|
K:PRO121
|
3.8
|
48.5
|
1.0
|
CA
|
K:LYS122
|
3.9
|
48.1
|
1.0
|
CB
|
K:MET120
|
4.0
|
48.5
|
1.0
|
CD
|
K:LYS122
|
4.1
|
51.4
|
1.0
|
C
|
K:MET120
|
4.2
|
47.1
|
1.0
|
CE
|
K:LYS122
|
4.7
|
53.0
|
1.0
|
CA
|
K:MET120
|
4.7
|
47.4
|
1.0
|
SD
|
K:MET120
|
4.9
|
51.8
|
1.0
|
O
|
K:PRO121
|
4.9
|
46.6
|
1.0
|
O
|
K:MET120
|
5.0
|
46.7
|
1.0
|
|
Chlorine binding site 6 out
of 8 in 7xx7
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Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
M:Cl201
b:67.0
occ:1.00
|
N
|
M:GLY46
|
3.2
|
55.1
|
1.0
|
N
|
N:SER91
|
3.3
|
52.5
|
1.0
|
CA
|
M:GLY46
|
3.6
|
54.2
|
1.0
|
CB
|
N:THR90
|
3.7
|
52.0
|
1.0
|
CA
|
N:THR90
|
3.7
|
51.4
|
1.0
|
N
|
M:ALA47
|
3.8
|
50.5
|
1.0
|
C
|
M:GLY44
|
3.8
|
57.1
|
1.0
|
N
|
M:ALA45
|
3.8
|
57.2
|
1.0
|
CA
|
M:GLY44
|
3.9
|
58.0
|
1.0
|
OG
|
N:SER91
|
4.0
|
54.5
|
1.0
|
C
|
N:THR90
|
4.0
|
51.4
|
1.0
|
C
|
M:GLY46
|
4.2
|
52.3
|
1.0
|
OP1
|
T:DG38
|
4.2
|
80.0
|
1.0
|
CB
|
N:SER91
|
4.2
|
53.5
|
1.0
|
CG2
|
N:THR90
|
4.2
|
52.6
|
1.0
|
C
|
M:ALA45
|
4.3
|
55.9
|
1.0
|
O
|
M:GLY44
|
4.3
|
56.9
|
1.0
|
CA
|
N:SER91
|
4.4
|
52.7
|
1.0
|
CA
|
M:ALA45
|
4.6
|
56.8
|
1.0
|
OG1
|
N:THR90
|
4.8
|
51.7
|
1.0
|
CA
|
M:ALA47
|
4.9
|
48.5
|
1.0
|
N
|
M:GLY44
|
4.9
|
58.0
|
1.0
|
CB
|
M:ALA47
|
5.0
|
48.1
|
1.0
|
|
Chlorine binding site 7 out
of 8 in 7xx7
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Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
O:Cl201
b:77.3
occ:1.00
|
N
|
O:LYS122
|
3.4
|
46.4
|
1.0
|
CD
|
O:PRO121
|
3.5
|
47.1
|
1.0
|
N
|
O:PRO121
|
3.7
|
46.3
|
1.0
|
CG
|
O:LYS122
|
3.8
|
48.4
|
1.0
|
CB
|
O:LYS122
|
3.9
|
47.8
|
1.0
|
CB
|
O:PRO121
|
3.9
|
46.7
|
1.0
|
CB
|
O:MET120
|
4.0
|
47.9
|
1.0
|
CG
|
O:PRO121
|
4.0
|
47.1
|
1.0
|
CD
|
O:LYS122
|
4.1
|
50.0
|
1.0
|
CA
|
O:PRO121
|
4.1
|
45.9
|
1.0
|
C
|
O:PRO121
|
4.2
|
45.8
|
1.0
|
CA
|
O:LYS122
|
4.2
|
46.4
|
1.0
|
C
|
O:MET120
|
4.5
|
45.9
|
1.0
|
CE
|
O:LYS122
|
4.6
|
50.8
|
1.0
|
SD
|
O:MET120
|
4.7
|
51.3
|
1.0
|
CA
|
O:MET120
|
4.8
|
46.5
|
1.0
|
CG
|
O:MET120
|
4.9
|
49.0
|
1.0
|
|
Chlorine binding site 8 out
of 8 in 7xx7
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Chlorine Binding Sites List in 7xx7
Chlorine 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 Chlorine with other atoms in the Cl 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
|
Q:Cl204
b:74.2
occ:1.00
|
N
|
Q:GLY46
|
3.2
|
59.8
|
1.0
|
N
|
R:SER91
|
3.2
|
54.4
|
1.0
|
CB
|
R:THR90
|
3.5
|
56.0
|
1.0
|
CA
|
R:THR90
|
3.5
|
55.5
|
1.0
|
CA
|
Q:GLY46
|
3.6
|
59.3
|
1.0
|
N
|
Q:ALA47
|
3.6
|
56.6
|
1.0
|
C
|
Q:GLY44
|
3.6
|
59.9
|
1.0
|
CA
|
Q:GLY44
|
3.7
|
60.4
|
1.0
|
N
|
Q:ALA45
|
3.7
|
60.8
|
1.0
|
C
|
R:THR90
|
3.9
|
54.7
|
1.0
|
OG
|
R:SER91
|
4.0
|
56.0
|
1.0
|
C
|
Q:GLY46
|
4.1
|
57.6
|
1.0
|
CG2
|
R:THR90
|
4.1
|
56.7
|
1.0
|
O
|
Q:GLY44
|
4.1
|
58.3
|
1.0
|
CB
|
R:SER91
|
4.2
|
54.4
|
1.0
|
C
|
Q:ALA45
|
4.3
|
60.2
|
1.0
|
CA
|
R:SER91
|
4.3
|
53.4
|
1.0
|
OP1
|
S:DG38
|
4.3
|
79.7
|
1.0
|
CA
|
Q:ALA45
|
4.6
|
60.8
|
1.0
|
CA
|
Q:ALA47
|
4.7
|
55.3
|
1.0
|
CB
|
Q:ALA47
|
4.7
|
55.4
|
1.0
|
OG1
|
R:THR90
|
4.7
|
55.2
|
1.0
|
N
|
Q:GLY44
|
4.7
|
59.7
|
1.0
|
N
|
R:THR90
|
4.9
|
55.1
|
1.0
|
O
|
R:ILE89
|
4.9
|
56.3
|
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: Wed Jul 26 15:10:56 2023
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