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3MGR
Asym. Unit
Info
Asym.Unit (251 KB)
Biol.Unit 1 (243 KB)
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(1)
Title
:
BINDING OF RUBIDIUM IONS TO THE NUCLEOSOME CORE PARTICLE
Authors
:
K. Mohideen, R. Muhammad, C. A. Davey
Date
:
07 Apr 10 (Deposition) - 16 Jun 10 (Release) - 21 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
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
:
Protein-Dna Complex, Structural Protein-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Mohideen, R. Muhammad, C. A. Davey
Perturbations In Nucleosome Structure From Heavy Metal Association.
Nucleic Acids Res. V. 38 6301 2010
[
close entry info
]
Hetero Components
(3, 23)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
2j: MANGANESE (II) ION (MNj)
2k: MANGANESE (II) ION (MNk)
2l: MANGANESE (II) ION (MNl)
2m: MANGANESE (II) ION (MNm)
2n: MANGANESE (II) ION (MNn)
3a: RUBIDIUM ION (RBa)
3b: RUBIDIUM ION (RBb)
3c: RUBIDIUM ION (RBc)
3d: RUBIDIUM ION (RBd)
3e: RUBIDIUM ION (RBe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
MN
14
Ligand/Ion
MANGANESE (II) ION
3
RB
5
Ligand/Ion
RUBIDIUM 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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
DC I:-65 , DT I:-66 , DT J:67 , DA J:68
BINDING SITE FOR RESIDUE RB J 74
02
AC2
SOFTWARE
ARG H:96 , LEU H:99
BINDING SITE FOR RESIDUE RB H 123
03
AC3
SOFTWARE
ARG D:96 , LEU D:97 , LEU D:99
BINDING SITE FOR RESIDUE RB D 123
04
AC4
SOFTWARE
DC I:-25 , DT I:-26 , DC I:-24
BINDING SITE FOR RESIDUE RB I 74
05
AC5
SOFTWARE
DT I:67 , DA I:68 , DC J:-65 , DT J:-66
BINDING SITE FOR RESIDUE RB J 75
06
AC6
SOFTWARE
DG J:61
BINDING SITE FOR RESIDUE MN J 3131
07
AC7
SOFTWARE
VAL D:45 , ASP E:77
BINDING SITE FOR RESIDUE MN E 3132
08
AC8
SOFTWARE
DT I:67 , DG J:27
BINDING SITE FOR RESIDUE MN J 3133
09
AC9
SOFTWARE
DG J:-3
BINDING SITE FOR RESIDUE MN J 3134
10
BC1
SOFTWARE
DG J:48
BINDING SITE FOR RESIDUE MN J 3135
11
BC2
SOFTWARE
DG I:48
BINDING SITE FOR RESIDUE MN I 3137
12
BC3
SOFTWARE
DG I:61
BINDING SITE FOR RESIDUE MN I 3138
13
BC4
SOFTWARE
DG J:-35 , DG J:-34
BINDING SITE FOR RESIDUE MN J 3139
14
BC5
SOFTWARE
DG I:27
BINDING SITE FOR RESIDUE MN I 3140
15
BC6
SOFTWARE
DG I:5
BINDING SITE FOR RESIDUE MN I 3141
16
BC7
SOFTWARE
DG I:-3 , DG I:-2
BINDING SITE FOR RESIDUE MN I 3142
17
BC8
SOFTWARE
DG I:-35 , DG I:-34
BINDING SITE FOR RESIDUE MN I 3143
18
BC9
SOFTWARE
DG J:5
BINDING SITE FOR RESIDUE MN J 3144
19
CC1
SOFTWARE
GLY G:44 , ALA G:45 , GLY G:46 , THR H:87 , SER H:88
BINDING SITE FOR RESIDUE CL G 3145
20
CC2
SOFTWARE
GLY C:46 , ALA C:47 , THR D:87 , SER D:88
BINDING SITE FOR RESIDUE CL D 3146
21
CC3
SOFTWARE
PRO A:121 , LYS A:122
BINDING SITE FOR RESIDUE CL A 3147
22
CC4
SOFTWARE
PRO E:121 , LYS E:122
BINDING SITE FOR RESIDUE CL E 3148
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H3_2 (A:66-74,E:66-74)
2: HISTONE_H2B (D:89-111,H:89-111)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H32_XENLA
67-75
2
A:66-74
E:66-74
2
HISTONE_H2B
PS00357
Histone H2B signature.
H2B11_XENLA
93-115
2
D:89-111
H:89-111
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d3mgrc_ (C:)
1b: SCOP_d3mgrg_ (G:)
2a: SCOP_d3mgrd_ (D:)
2b: SCOP_d3mgrh_ (H:)
3a: SCOP_d3mgra_ (A:)
3b: SCOP_d3mgre_ (E:)
4a: SCOP_d3mgrb_ (B:)
4b: SCOP_d3mgrf_ (F:)
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Class
:
All alpha proteins
(14657)
Fold
:
Histone-fold
(277)
Superfamily
:
Histone-fold
(277)
Family
:
Nucleosome core histones
(247)
Protein domain
:
Histone H2A
(45)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(34)
1a
d3mgrc_
C:
1b
d3mgrg_
G:
Protein domain
:
Histone H2B
(48)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(35)
2a
d3mgrd_
D:
2b
d3mgrh_
H:
Protein domain
:
Histone H3
(58)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(39)
3a
d3mgra_
A:
3b
d3mgre_
E:
Protein domain
:
Histone H4
(60)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(38)
4a
d3mgrb_
B:
4b
d3mgrf_
F:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Histone_3mgrH01 (H:28-98)
1b: PFAM_Histone_3mgrH02 (H:28-98)
1c: PFAM_Histone_3mgrE01 (E:57-131)
1d: PFAM_Histone_3mgrE02 (E:57-131)
1e: PFAM_Histone_3mgrF01 (F:24-93)
1f: PFAM_Histone_3mgrF02 (F:24-93)
1g: PFAM_Histone_3mgrG01 (G:17-90)
1h: PFAM_Histone_3mgrG02 (G:17-90)
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Clan
:
Histone
(49)
Family
:
Histone
(46)
Xenopus laevis (African clawed frog)
(32)
1a
Histone-3mgrH01
H:28-98
1b
Histone-3mgrH02
H:28-98
1c
Histone-3mgrE01
E:57-131
1d
Histone-3mgrE02
E:57-131
1e
Histone-3mgrF01
F:24-93
1f
Histone-3mgrF02
F:24-93
1g
Histone-3mgrG01
G:17-90
1h
Histone-3mgrG02
G:17-90
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