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5CG9
Asym. Unit
Info
Asym.Unit (113 KB)
Biol.Unit 1 (55 KB)
Biol.Unit 2 (55 KB)
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(1)
Title
:
NGTET1 IN COMPLEX WITH 5MC DNA IN SPACE GROUP P3221
Authors
:
H. Hashimoto, J. E. Pais, N. Dai, X. Zhang, Y. Zheng, X. Cheng
Date
:
09 Jul 15 (Deposition) - 09 Sep 15 (Release) - 23 Dec 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.69
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Dioxygenase, 5-Methylcytosine, Ngtet1, Oxidoreductase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Hashimoto, J. E. Pais, N. Dai, I. R. Correa, X. Zhang, Y. Zheng, X. Cheng
Structure Of Naegleria Tet-Like Dioxygenase (Ngtet1) In Complexes With A Reaction Intermediate 5-Hydroxymethylcytosine Dna.
Nucleic Acids Res. V. 43 10713 2015
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Hetero Components
(5, 11)
Info
All Hetero Components
1a: 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONO... (5CMa)
1b: 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONO... (5CMb)
2a: 2-OXOGLUTARIC ACID (AKGa)
2b: 2-OXOGLUTARIC ACID (AKGb)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
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No.
Name
Count
Type
Full Name
1
5CM
2
Mod. Nucleotide
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2
AKG
2
Ligand/Ion
2-OXOGLUTARIC ACID
3
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
4
MN
2
Ligand/Ion
MANGANESE (II) ION
5
SO4
3
Ligand/Ion
SULFATE ION
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Sites
(11, 11)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:168 , ALA A:202 , ASN A:205 , EDO D:403
binding site for residue SO4 A 401
02
AC2
SOFTWARE
ASN A:214 , ARG A:224 , HIS A:229 , ASP A:231 , LEU A:240 , TYR A:242 , LEU A:253 , HIS A:279 , VAL A:281 , ARG A:289 , VAL A:293 , MN A:403 , HOH A:501 , 5CM C:20
binding site for residue AKG A 402
03
AC3
SOFTWARE
HIS A:229 , ASP A:231 , HIS A:279 , AKG A:402 , HOH A:501
binding site for residue MN A 403
04
AC4
SOFTWARE
ASN A:175 , TYR A:201 , ASN A:205 , ASN D:175 , TYR D:201
binding site for residue SO4 D 401
05
AC5
SOFTWARE
GLU D:168 , ALA D:202 , ASN D:205 , EDO D:403
binding site for residue SO4 D 402
06
AC6
SOFTWARE
SO4 A:401 , SO4 D:402
binding site for residue EDO D 403
07
AC7
SOFTWARE
ASN D:214 , ARG D:224 , HIS D:229 , ASP D:231 , LEU D:240 , TYR D:242 , LEU D:253 , HIS D:279 , VAL D:281 , ARG D:289 , VAL D:293 , MN D:405 , HOH D:501 , 5CM F:20
binding site for residue AKG D 404
08
AC8
SOFTWARE
HIS D:229 , ASP D:231 , HIS D:279 , AKG D:404 , HOH D:501
binding site for residue MN D 405
09
AC9
SOFTWARE
DG E:8 , DA F:18 , DG F:19
binding site for residue EDO F 101
10
AD1
SOFTWARE
TYR D:141 , ASN D:147 , ARG D:224 , ASP D:234 , VAL D:293 , PHE D:295 , HIS D:297 , AKG D:404 , DG E:8 , DC E:9 , DT E:10 , DA F:18 , DG F:21 , EDO F:101
binding site for Di-nucleotide DG F 19 and 5CM F 20
11
AD2
SOFTWARE
TYR D:141 , ASN D:147 , TYR D:153 , ARG D:224 , ASP D:234 , VAL D:293 , PHE D:295 , HIS D:297 , GLN D:310 , AKG D:404 , DG E:6 , DC E:7 , DG F:19 , DC F:22
binding site for Di-nucleotide 5CM F 20 and DG F 21
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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Pfam Domains
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Asym.Unit (113 KB)
Header - Asym.Unit
Biol.Unit 1 (55 KB)
Header - Biol.Unit 1
Biol.Unit 2 (55 KB)
Header - Biol.Unit 2
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