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1HD7
Asym. Unit
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Asym.Unit (55 KB)
Biol.Unit 1 (49 KB)
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(1)
Title
:
A SECOND DIVALENT METAL ION IN THE ACTIVE SITE OF A NEW CRYSTAL FORM OF HUMAN APURINIC/APYRIDINIMIC ENDONUCLEASE, APE1, AND ITS IMPLICATIONS FOR THE CATALYTIC MECHANISM
Authors
:
P. T. Beernink, B. W. Segelke, B. Rupp
Date
:
09 Nov 00 (Deposition) - 16 Feb 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Dna Repair, Endonuclease, Ape1, Hap1, Ref-1
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. T. Beernink, B. W. Segelke, M. Z. Hadi, J. P. Erzberger, D. M. Wilson Iii, B. Rupp
Two Divalent Metal Ions In The Active Site Of A New Crystal Form Of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications For The Catalytic Mechanism
J. Mol. Biol. V. 307 1023 2001
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: LEAD (II) ION (PBa)
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Label:
No.
Name
Count
Type
Full Name
1
PB
1
Ligand/Ion
LEAD (II) ION
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:70 , GLU A:96 , HOH A:2069 , HOH A:2079 , HOH A:2282 , HOH A:2283
BINDING SITE FOR RESIDUE PB A1319
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SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_013455 (Q51H, chain A, )
2: VAR_014823 (I64V, chain A, )
3: VAR_019790 (D148E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_013455
Q
51
H
APEX1_HUMAN
Polymorphism
1048945
A
Q
51
H
2
UniProt
VAR_014823
I
64
V
APEX1_HUMAN
Polymorphism
2307486
A
I
64
V
3
UniProt
VAR_019790
D
148
E
APEX1_HUMAN
Polymorphism
1130409
A
D
148
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: AP_NUCLEASE_F1_4 (A:62-318)
2: AP_NUCLEASE_F1_1 (A:89-98)
3: AP_NUCLEASE_F1_2 (A:251-267)
4: AP_NUCLEASE_F1_3 (A:277-288)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AP_NUCLEASE_F1_4
PS51435
AP endonucleases family 1 profile.
APEX1_HUMAN
62-318
1
A:62-318
2
AP_NUCLEASE_F1_1
PS00726
AP endonucleases family 1 signature 1.
APEX1_HUMAN
89-98
1
A:89-98
3
AP_NUCLEASE_F1_2
PS00727
AP endonucleases family 1 signature 2.
APEX1_HUMAN
251-267
1
A:251-267
4
AP_NUCLEASE_F1_3
PS00728
AP endonucleases family 1 signature 3.
APEX1_HUMAN
277-288
1
A:277-288
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Exons
(3, 3)
Info
All Exons
Exon 1.3a (A:44-82)
Exon 1.4 (A:83-147 (gaps))
Exon 1.5a (A:147-318)
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All Exon Boundaries
1: Boundary 1.2/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1c
ENST00000398030
1c
ENSE00001531237
chr14:
20923400-20923497
98
APEX1_HUMAN
-
0
0
-
-
1.2
ENST00000398030
2
ENSE00000889014
chr14:
20923737-20923862
126
APEX1_HUMAN
1-20
20
0
-
-
1.3a
ENST00000398030
3a
ENSE00000652723
chr14:
20924073-20924260
188
APEX1_HUMAN
20-82
63
1
A:44-82
39
1.4
ENST00000398030
4
ENSE00000652726
chr14:
20924827-20925019
193
APEX1_HUMAN
83-147
65
1
A:83-147 (gaps)
65
1.5a
ENST00000398030
5a
ENSE00001842242
chr14:
20925150-20925895
746
APEX1_HUMAN
147-318
172
1
A:147-318
172
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1hd7a_ (A:)
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)
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)
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)
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)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNase I-like
(70)
Superfamily
:
DNase I-like
(70)
Family
:
DNase I-like
(31)
Protein domain
:
DNA repair endonuclease Hap1
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1hd7a_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1hd7A00 (A:44-318)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Deoxyribonuclease I; Chain A
(35)
Homologous Superfamily
:
[code=3.60.10.10, no name defined]
(35)
Human (Homo sapiens)
(8)
1a
1hd7A00
A:44-318
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Pfam Domains
(0, 0)
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all PFAM domains
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Chain A
Asymmetric Unit 1
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