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3MGQ
Asym. Unit
Info
Asym.Unit (253 KB)
Biol.Unit 1 (245 KB)
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(1)
Title
:
BINDING OF NICKEL 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
:
2.65
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
(2, 51)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: NICKEL (II) ION (NIa)
2aa: NICKEL (II) ION (NIaa)
2ab: NICKEL (II) ION (NIab)
2ac: NICKEL (II) ION (NIac)
2ad: NICKEL (II) ION (NIad)
2ae: NICKEL (II) ION (NIae)
2af: NICKEL (II) ION (NIaf)
2ag: NICKEL (II) ION (NIag)
2ah: NICKEL (II) ION (NIah)
2ai: NICKEL (II) ION (NIai)
2aj: NICKEL (II) ION (NIaj)
2ak: NICKEL (II) ION (NIak)
2al: NICKEL (II) ION (NIal)
2am: NICKEL (II) ION (NIam)
2an: NICKEL (II) ION (NIan)
2ao: NICKEL (II) ION (NIao)
2ap: NICKEL (II) ION (NIap)
2aq: NICKEL (II) ION (NIaq)
2ar: NICKEL (II) ION (NIar)
2as: NICKEL (II) ION (NIas)
2at: NICKEL (II) ION (NIat)
2au: NICKEL (II) ION (NIau)
2b: NICKEL (II) ION (NIb)
2c: NICKEL (II) ION (NIc)
2d: NICKEL (II) ION (NId)
2e: NICKEL (II) ION (NIe)
2f: NICKEL (II) ION (NIf)
2g: NICKEL (II) ION (NIg)
2h: NICKEL (II) ION (NIh)
2i: NICKEL (II) ION (NIi)
2j: NICKEL (II) ION (NIj)
2k: NICKEL (II) ION (NIk)
2l: NICKEL (II) ION (NIl)
2m: NICKEL (II) ION (NIm)
2n: NICKEL (II) ION (NIn)
2o: NICKEL (II) ION (NIo)
2p: NICKEL (II) ION (NIp)
2q: NICKEL (II) ION (NIq)
2r: NICKEL (II) ION (NIr)
2s: NICKEL (II) ION (NIs)
2t: NICKEL (II) ION (NIt)
2u: NICKEL (II) ION (NIu)
2v: NICKEL (II) ION (NIv)
2w: NICKEL (II) ION (NIw)
2x: NICKEL (II) ION (NIx)
2y: NICKEL (II) ION (NIy)
2z: NICKEL (II) ION (NIz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
NI
47
Ligand/Ion
NICKEL (II) ION
[
close Hetero Component info
]
Sites
(49, 49)
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)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL D:45 , ASP E:77
BINDING SITE FOR RESIDUE NI E 136
02
AC2
SOFTWARE
DG I:-28 , DT I:67 , DG J:27
BINDING SITE FOR RESIDUE NI J 74
03
AC3
SOFTWARE
DG I:61
BINDING SITE FOR RESIDUE NI I 74
04
AC4
SOFTWARE
DG I:-3
BINDING SITE FOR RESIDUE NI I 75
05
AC5
SOFTWARE
DG J:48
BINDING SITE FOR RESIDUE NI J 75
06
AC6
SOFTWARE
DG J:-3
BINDING SITE FOR RESIDUE NI J 76
07
AC7
SOFTWARE
DG J:61
BINDING SITE FOR RESIDUE NI J 77
08
AC8
SOFTWARE
GLU D:102 , HIS D:106 , HIS F:18
BINDING SITE FOR RESIDUE NI D 123
09
AC9
SOFTWARE
DG I:48
BINDING SITE FOR RESIDUE NI I 76
10
BC1
SOFTWARE
HIS H:79
BINDING SITE FOR RESIDUE NI H 123
11
BC2
SOFTWARE
DA I:26 , DG I:27
BINDING SITE FOR RESIDUE NI I 77
12
BC3
SOFTWARE
DG J:8
BINDING SITE FOR RESIDUE NI J 78
13
BC4
SOFTWARE
DG I:-56
BINDING SITE FOR RESIDUE NI I 78
14
BC5
SOFTWARE
DG J:-6
BINDING SITE FOR RESIDUE NI J 79
15
BC6
SOFTWARE
GLU H:102 , LYS H:105 , HIS H:106
BINDING SITE FOR RESIDUE NI H 124
16
BC7
SOFTWARE
DA J:29 , DG J:30
BINDING SITE FOR RESIDUE NI J 80
17
BC8
SOFTWARE
DG J:-56
BINDING SITE FOR RESIDUE NI J 81
18
BC9
SOFTWARE
HIS D:79
BINDING SITE FOR RESIDUE NI D 124
19
CC1
SOFTWARE
DG I:-35 , DG I:-34 , NI I:86
BINDING SITE FOR RESIDUE NI I 80
20
CC2
SOFTWARE
DG J:5
BINDING SITE FOR RESIDUE NI J 82
21
CC3
SOFTWARE
DA I:29
BINDING SITE FOR RESIDUE NI I 81
22
CC4
SOFTWARE
DG J:71
BINDING SITE FOR RESIDUE NI J 83
23
CC5
SOFTWARE
DG I:24 , DG I:25 , NI I:89
BINDING SITE FOR RESIDUE NI I 82
24
CC6
SOFTWARE
DG J:-35 , DG J:-34
BINDING SITE FOR RESIDUE NI J 84
25
CC7
SOFTWARE
DG J:24 , DG J:25
BINDING SITE FOR RESIDUE NI J 85
26
CC8
SOFTWARE
DG I:71
BINDING SITE FOR RESIDUE NI I 83
27
CC9
SOFTWARE
DG I:64 , DG I:65
BINDING SITE FOR RESIDUE NI I 84
28
DC1
SOFTWARE
DA J:-70
BINDING SITE FOR RESIDUE NI J 86
29
DC2
SOFTWARE
HIS H:46
BINDING SITE FOR RESIDUE NI H 125
30
DC3
SOFTWARE
DG J:-34
BINDING SITE FOR RESIDUE NI J 87
31
DC4
SOFTWARE
DG I:-15 , DG J:14
BINDING SITE FOR RESIDUE NI J 88
32
DC5
SOFTWARE
DG I:-6
BINDING SITE FOR RESIDUE NI I 85
33
DC6
SOFTWARE
DG I:-34 , NI I:80
BINDING SITE FOR RESIDUE NI I 86
34
DC7
SOFTWARE
DG I:58 , DC I:59 , NI I:91 , DG J:-59
BINDING SITE FOR RESIDUE NI I 87
35
DC8
SOFTWARE
ASP F:24
BINDING SITE FOR RESIDUE NI F 103
36
DC9
SOFTWARE
ASP A:77
BINDING SITE FOR RESIDUE NI A 136
37
EC1
SOFTWARE
DA J:-19
BINDING SITE FOR RESIDUE NI J 89
38
EC2
SOFTWARE
DG J:52
BINDING SITE FOR RESIDUE NI J 90
39
EC3
SOFTWARE
ASP C:90
BINDING SITE FOR RESIDUE NI C 120
40
EC4
SOFTWARE
DG I:52
BINDING SITE FOR RESIDUE NI I 88
41
EC5
SOFTWARE
DC I:-30 , DA J:-70
BINDING SITE FOR RESIDUE NI J 91
42
EC6
SOFTWARE
ASP G:90
BINDING SITE FOR RESIDUE NI G 120
43
EC7
SOFTWARE
DG I:24 , DG I:25 , NI I:82
BINDING SITE FOR RESIDUE NI I 89
44
EC8
SOFTWARE
DT I:57 , NI I:87
BINDING SITE FOR RESIDUE NI I 91
45
EC9
SOFTWARE
DG J:64 , DG J:65
BINDING SITE FOR RESIDUE NI J 105
46
FC1
SOFTWARE
GLY G:44 , GLY G:46 , ALA G:47 , THR H:87 , SER H:88
BINDING SITE FOR RESIDUE CL G 3145
47
FC2
SOFTWARE
GLY C:46 , ALA C:47 , THR D:87 , SER D:88
BINDING SITE FOR RESIDUE CL C 3146
48
FC3
SOFTWARE
PRO A:121 , LYS A:122
BINDING SITE FOR RESIDUE CL A 3147
49
FC4
SOFTWARE
PRO E:121 , LYS E:122
BINDING SITE FOR RESIDUE CL E 3148
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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_d3mgqc_ (C:)
1b: SCOP_d3mgqg_ (G:)
2a: SCOP_d3mgqd_ (D:)
2b: SCOP_d3mgqh_ (H:)
3a: SCOP_d3mgqa_ (A:)
3b: SCOP_d3mgqe_ (E:)
4a: SCOP_d3mgqb_ (B:)
4b: SCOP_d3mgqf_ (F:)
View:
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Classes
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)
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)
Folds
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)
(
)
Superfamilies
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d3mgqc_
C:
1b
d3mgqg_
G:
Protein domain
:
Histone H2B
(48)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(35)
2a
d3mgqd_
D:
2b
d3mgqh_
H:
Protein domain
:
Histone H3
(58)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(39)
3a
d3mgqa_
A:
3b
d3mgqe_
E:
Protein domain
:
Histone H4
(60)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(38)
4a
d3mgqb_
B:
4b
d3mgqf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Histone_3mgqH01 (H:28-98)
1b: PFAM_Histone_3mgqH02 (H:28-98)
1c: PFAM_Histone_3mgqE01 (E:57-131)
1d: PFAM_Histone_3mgqE02 (E:57-131)
1e: PFAM_Histone_3mgqF01 (F:24-93)
1f: PFAM_Histone_3mgqF02 (F:24-93)
1g: PFAM_Histone_3mgqG01 (G:17-90)
1h: PFAM_Histone_3mgqG02 (G:17-90)
View:
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Clans
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(
)
Organisms
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)
(
)
Clan
:
Histone
(49)
Family
:
Histone
(46)
Xenopus laevis (African clawed frog)
(32)
1a
Histone-3mgqH01
H:28-98
1b
Histone-3mgqH02
H:28-98
1c
Histone-3mgqE01
E:57-131
1d
Histone-3mgqE02
E:57-131
1e
Histone-3mgqF01
F:24-93
1f
Histone-3mgqF02
F:24-93
1g
Histone-3mgqG01
G:17-90
1h
Histone-3mgqG02
G:17-90
[
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]
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Asym.Unit (253 KB)
Header - Asym.Unit
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