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4IEM
Asym. Unit
Info
Asym.Unit (413 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (104 KB)
Biol.Unit 3 (107 KB)
Biol.Unit 4 (105 KB)
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(1)
Title
:
HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE (APE1) WITH PRODUCT DNA AND MG2+
Authors
:
S. E. Tsutakawa, C. D. Mol, A. S. Arvai, J. A. Tainer
Date
:
13 Dec 12 (Deposition) - 23 Jan 13 (Release) - 10 Apr 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.39
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,E,F,G (1x)
Biol. Unit 2: B,H,I,J (1x)
Biol. Unit 3: C,K,L,M (1x)
Biol. Unit 4: D,N,O,P (1x)
Keywords
:
Metalloprotein, Dna Damage, Dna Repair, Base Excision Repair, Protein-Dna, Ref1, Nuclease, Hydrolase, Lyase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. E. Tsutakawa, D. S. Shin, C. D. Mol, T. Izumi, A. S. Arvai, A. K. Mantha B. Szczesny, I. N. Ivanov, D. J. Hosfield, B. Maiti, M. E. Pique, K. A. Frankel, K. Hitomi, R. P. Cunningham, S. Mitra, J. A. Tainer
Conserved Structural Chemistry For Incision Activity In Structurally Non-Homologous Apurinic/Apyrimidinic Endonuclease Ape1 And Endonuclease Iv Dna Repair Enzymes.
J. Biol. Chem. V. 288 8445 2013
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Hetero Components
(3, 20)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
1b: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRb)
1c: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRc)
1d: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
3i: SODIUM ION (NAi)
View:
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Label:
No.
Name
Count
Type
Full Name
1
3DR
4
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
MG
7
Ligand/Ion
MAGNESIUM ION
3
NA
9
Ligand/Ion
SODIUM ION
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Sites
(16, 16)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:641 , DC E:505 , DG G:518 , DT G:519 , HOH G:606
BINDING SITE FOR RESIDUE MG A 501
02
AC2
SOFTWARE
GLU A:96 , HOH A:601 , HOH A:602 , HOH A:603 , DC E:505 , 3DR F:506
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
DT L:509 , DT M:515
BINDING SITE FOR RESIDUE MG A 503
04
AC4
SOFTWARE
TYR A:269 , MET A:270 , MET A:271 , ASN A:272 , DG G:518
BINDING SITE FOR RESIDUE NA A 504
05
AC5
SOFTWARE
LEU A:44 , TYR A:45
BINDING SITE FOR RESIDUE NA A 505
06
AC6
SOFTWARE
GLU B:96 , HOH B:502 , HOH B:503 , DC H:505 , 3DR I:506 , HOH I:601
BINDING SITE FOR RESIDUE MG B 401
07
AC7
SOFTWARE
ASP B:47 , TYR B:257 , SER B:298 , LYS B:299
BINDING SITE FOR RESIDUE NA B 402
08
AC8
SOFTWARE
ARG B:185 , ASP B:189 , VAL B:213 , GLU B:236
BINDING SITE FOR RESIDUE NA B 403
09
AC9
SOFTWARE
ASP B:189 , ARG B:193 , LEU B:243
BINDING SITE FOR RESIDUE NA B 404
10
BC1
SOFTWARE
GLU C:96 , HOH C:601 , HOH C:602 , DC K:505 , HOH K:701 , 3DR L:506
BINDING SITE FOR RESIDUE MG C 401
11
BC2
SOFTWARE
ASP C:70 , HOH C:614 , HOH C:668 , DC K:505 , HOH K:701 , DG M:518 , DT M:519
BINDING SITE FOR RESIDUE MG C 402
12
BC3
SOFTWARE
GLU D:96 , HOH D:501 , HOH D:502 , DC N:505 , HOH N:701 , 3DR O:506
BINDING SITE FOR RESIDUE MG D 401
13
BC4
SOFTWARE
ASN D:222 , DT O:509
BINDING SITE FOR RESIDUE NA D 402
14
BC5
SOFTWARE
DT E:503 , DA E:504
BINDING SITE FOR RESIDUE NA E 601
15
BC6
SOFTWARE
DC F:510
BINDING SITE FOR RESIDUE NA F 601
16
BC7
SOFTWARE
DT N:503 , DA N:504
BINDING SITE FOR RESIDUE NA N 601
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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 (413 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
Biol.Unit 2 (104 KB)
Header - Biol.Unit 2
Biol.Unit 3 (107 KB)
Header - Biol.Unit 3
Biol.Unit 4 (105 KB)
Header - Biol.Unit 4
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