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5JRG
Asym. Unit
Info
Asym.Unit (256 KB)
Biol.Unit 1 (247 KB)
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Title
:
CRYSTAL STRUCTURE OF THE NUCLEOSOME CONTAINING THE DNA WITH TETRAHYDROFURAN (THF)
Authors
:
A. Osakabe, Y. Arimura, N. Horikoshi, H. Kurumizaka
Date
:
06 May 16 (Deposition) - 08 Mar 17 (Release) - 08 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Histone Fold, Dna Binding, Nucleus, Chromatin Formation, Nucleosome, Ap-Site, Dna Binding Protein-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Osakabe, Y. Arimura, S. Matsumoto, N. Horikoshi, K. Sugasawa, H. Kurumizaka
Polymorphism Of Apyrimidinic Dna Structures In The Nucleosome
Sci Rep V. 7 41783 2017
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Hetero Components
(3, 21)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
1b: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
3e: MANGANESE (II) ION (MNe)
3f: MANGANESE (II) ION (MNf)
3g: MANGANESE (II) ION (MNg)
3h: MANGANESE (II) ION (MNh)
3i: MANGANESE (II) ION (MNi)
3j: MANGANESE (II) ION (MNj)
3k: MANGANESE (II) ION (MNk)
3l: MANGANESE (II) ION (MNl)
3m: MANGANESE (II) ION (MNm)
3n: MANGANESE (II) ION (MNn)
3o: MANGANESE (II) ION (MNo)
View:
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Label:
No.
Name
Count
Type
Full Name
1
3DR
2
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
MN
15
Ligand/Ion
MANGANESE (II) ION
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Sites
(22, 22)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:121 , LYS A:122
binding site for residue CL A 201
02
AC2
SOFTWARE
GLY C:46 , ALA C:47 , THR D:90 , SER D:91
binding site for residue CL C 201
03
AC3
SOFTWARE
ASP E:77 , HOH E:3110
binding site for residue MN E 3001
04
AC4
SOFTWARE
PRO E:121 , LYS E:122
binding site for residue CL E 3002
05
AC5
SOFTWARE
GLY G:44 , ALA G:45 , GLY G:46 , ALA G:47 , THR H:90 , SER H:91 , HOH I:337
binding site for residue CL G 2001
06
AC6
SOFTWARE
DT I:135
binding site for residue MN I 201
07
AC7
SOFTWARE
DG I:120
binding site for residue MN I 203
08
AC8
SOFTWARE
DG I:99 , HOH I:310 , HOH I:342 , HOH I:348 , HOH J:315
binding site for residue MN I 204
09
AC9
SOFTWARE
DG I:96 , DG I:97 , HOH I:339
binding site for residue MN I 205
10
AD1
SOFTWARE
DG I:39 , DG I:40 , HOH I:306 , DC J:106
binding site for residue MN I 206
11
AD2
SOFTWARE
DA I:132 , DG I:133 , HOH I:325
binding site for residue MN I 207
12
AD3
SOFTWARE
DG I:68 , HOH I:347
binding site for residue MN I 208
13
AD4
SOFTWARE
DG J:120 , HOH J:326 , HOH J:344
binding site for residue MN J 201
14
AD5
SOFTWARE
DG J:39 , DG J:40 , HOH J:336
binding site for residue MN J 202
15
AD6
SOFTWARE
DG J:133
binding site for residue MN J 203
16
AD7
SOFTWARE
DG J:99
binding site for residue MN J 204
17
AD8
SOFTWARE
DG J:68
binding site for residue MN J 205
18
AD9
SOFTWARE
DT J:37
binding site for residue MN J 206
19
AE1
SOFTWARE
ARG G:11 , DC I:115 , DT I:118 , DA J:29 , DA J:30 , DG J:31
binding site for Di-nucleotide DT I 116 and 3DR I 117
20
AE2
SOFTWARE
DT I:116 , DT I:119 , DA J:27 , DA J:28
binding site for Di-nucleotide 3DR I 117 and DT I 118
21
AE3
SOFTWARE
DA I:29 , DA I:30 , DG I:31 , DC J:115 , DT J:118
binding site for Di-nucleotide DT J 116 and 3DR J 117
22
AE4
SOFTWARE
DA I:28 , DA I:29 , DA I:30 , DT J:116 , DT J:119
binding site for Di-nucleotide 3DR J 117 and DT J 118
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (256 KB)
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