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2NQJ
Asym. Unit
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Asym.Unit (112 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (49 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV (ENDO IV) E261Q MUTANT BOUND TO DAMAGED DNA
Authors
:
E. D. Garcin-Hosfield, D. J. Hosfield, J. A. Tainer
Date
:
31 Oct 06 (Deposition) - 06 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C,D (1x)
Biol. Unit 2: B (1x)
Keywords
:
Tim_barrel, Trinuclear Zinc Site, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. D. Garcin, D. J. Hosfield, S. A. Desai, B. J. Haas, M. Bjoras, R. P. Cunningham, J. A. Tainer
Dna Apurinic-Apyrimidinic Site Binding And Excision By Endonuclease Iv.
Nat. Struct. Mol. Biol. V. 15 515 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
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No.
Name
Count
Type
Full Name
1
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
ZN
4
Ligand/Ion
ZINC ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:69 , HIS A:109 , GLU A:145 , ZN A:352 , 3DR C:307
BINDING SITE FOR RESIDUE ZN A 351
2
AC2
SOFTWARE
GLU A:145 , ASP A:179 , HIS A:182 , HIS A:216 , GLN A:261 , ZN A:351 , 3DR C:307
BINDING SITE FOR RESIDUE ZN A 352
3
AC3
SOFTWARE
HIS A:182 , ASP A:229 , HIS A:231 , DC C:306 , 3DR C:307
BINDING SITE FOR RESIDUE ZN A 353
4
AC4
SOFTWARE
HIS B:182 , ASP B:229 , HIS B:231 , DG C:315
BINDING SITE FOR RESIDUE ZN B 403
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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
(4, 8)
Info
All PROSITE Patterns/Profiles
1: AP_NUCLEASE_F2_4 (A:1-279,B:1-279)
2: AP_NUCLEASE_F2_1 (A:69-77,B:69-77)
3: AP_NUCLEASE_F2_2 (A:175-182,B:175-182)
4: AP_NUCLEASE_F2_3 (A:215-231,B:215-231)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AP_NUCLEASE_F2_4
PS51432
AP endonucleases family 2 profile.
END4_ECOLI
1-280
2
A:1-279
B:1-279
2
AP_NUCLEASE_F2_1
PS00729
AP endonucleases family 2 signature 1.
END4_ECOLI
69-77
2
A:69-77
B:69-77
3
AP_NUCLEASE_F2_2
PS00730
AP endonucleases family 2 signature 2.
END4_ECOLI
175-182
2
A:175-182
B:175-182
4
AP_NUCLEASE_F2_3
PS00731
AP endonucleases family 2 signature 3.
END4_ECOLI
215-231
2
A:215-231
B:215-231
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Exons
(0, 0)
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2nqja_ (A:)
1b: SCOP_d2nqjb_ (B:)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Xylose isomerase-like
(125)
Family
:
Endonuclease IV
(8)
Protein domain
:
Endonuclease IV
(6)
Escherichia coli [TaxId: 562]
(5)
1a
d2nqja_
A:
1b
d2nqjb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2nqjA00 (A:1-279)
1b: CATH_2nqjB00 (B:1-279)
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)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Divalent-metal-dependent TIM barrel enzymes
(98)
[unclassified]
(4)
1a
2nqjA00
A:1-279
1b
2nqjB00
B:1-279
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_AP_endonuc_2_2nqjB01 (B:19-239)
1b: PFAM_AP_endonuc_2_2nqjB02 (B:19-239)
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Clan
:
TIM_barrel
(694)
Family
:
AP_endonuc_2
(72)
Escherichia coli (strain K12)
(5)
1a
AP_endonuc_2-2nqjB01
B:19-239
1b
AP_endonuc_2-2nqjB02
B:19-239
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Asym.Unit (112 KB)
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