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2NOI
Asym. Unit
Info
Asym.Unit (66 KB)
Biol.Unit 1 (61 KB)
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(1)
Title
:
STRUCTURE OF G42A HUMAN 8-OXOGUANINE GLYCOSYLASE CROSSLINKED TO UNDAMAGED G-CONTAINING DNA
Authors
:
C. T. Radom, A. Banerjee, G. L. Verdine
Date
:
25 Oct 06 (Deposition) - 21 Nov 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
N-Glycosylase/Dna Lyase, Dna Repair, 8-Oxoguanine, Hydrolase, Lyase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. T. Radom, A. Banerjee, G. L. Verdine
Structural Characterization Of Human 8-Oxoguanine Dna Glycosylase Variants Bearing Active Site Mutations.
J. Biol. Chem. V. 282 9182 2007
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
[
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:241 , LEU A:243 , VAL A:246 , DC C:26
BINDING SITE FOR RESIDUE CA C 301
[
close Site info
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SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_024831 (G12E, chain A, )
02: VAR_009519 (R46Q, chain A, )
03: VAR_024832 (A85S, chain A, )
04: VAR_024833 (R131Q, chain A, )
05: VAR_009520 (R154H, chain A, )
06: VAR_014487 (R229Q, chain A, )
07: VAR_024834 (S232T, chain A, )
08: VAR_018890 (A288V, chain A, )
09: VAR_014488 (S320T, chain A, )
10: VAR_018891 (D322N, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_024831
G
12
E
OGG1_HUMAN
Unclassified
---
A
G
12
E
02
UniProt
VAR_009519
R
46
Q
OGG1_HUMAN
Polymorphism
104893751
A
R
46
Q
03
UniProt
VAR_024832
A
85
S
OGG1_HUMAN
Polymorphism
17050550
A
A
85
S
04
UniProt
VAR_024833
R
131
Q
OGG1_HUMAN
Unclassified
---
A
R
131
Q
05
UniProt
VAR_009520
R
154
H
OGG1_HUMAN
Polymorphism
56053615
A
R
154
H
06
UniProt
VAR_014487
R
229
Q
OGG1_HUMAN
Polymorphism
1805373
A
R
229
Q
07
UniProt
VAR_024834
S
232
T
OGG1_HUMAN
Unclassified
---
A
S
232
T
08
UniProt
VAR_018890
A
288
V
OGG1_HUMAN
Polymorphism
3219012
A
A
288
V
09
UniProt
VAR_014488
S
320
T
OGG1_HUMAN
Polymorphism
1801128
A
S
320
T
10
UniProt
VAR_018891
D
322
N
OGG1_HUMAN
Polymorphism
3219014
A
D
322
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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Exons
(7, 7)
Info
All Exons
Exon 1.1a (A:8-46)
Exon 1.2b (A:46-129 (gaps))
Exon 1.3a (A:129-189)
Exon 1.4 (A:189-249)
Exon 1.5 (A:250-300)
Exon 1.6a (A:300-316)
Exon 1.6j (A:317-323)
View:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2b
3: Boundary 1.2b/1.3a
4: Boundary 1.3a/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6a
7: Boundary 1.6a/1.6j
8: Boundary 1.6j/-
View:
Label:
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
1.1a
ENST00000344629
1a
ENSE00002157661
chr3:
9791628-9792107
480
OGG1_HUMAN
1-46
46
1
A:8-46
39
1.2b
ENST00000344629
2b
ENSE00001669842
chr3:
9792629-9792876
248
OGG1_HUMAN
46-129
84
1
A:46-129 (gaps)
84
1.3a
ENST00000344629
3a
ENSE00001644854
chr3:
9793454-9793633
180
OGG1_HUMAN
129-189
61
1
A:129-189
61
1.4
ENST00000344629
4
ENSE00001165146
chr3:
9796388-9796569
182
OGG1_HUMAN
189-249
61
1
A:189-249
61
1.5
ENST00000344629
5
ENSE00001661907
chr3:
9798155-9798305
151
OGG1_HUMAN
250-300
51
1
A:250-300
51
1.6a
ENST00000344629
6a
ENSE00001764469
chr3:
9798451-9798500
50
OGG1_HUMAN
300-316
17
1
A:300-316
17
1.6j
ENST00000344629
6j
ENSE00001651617
chr3:
9798745-9799197
453
OGG1_HUMAN
317-345
29
1
A:317-323
7
[
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]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2noia2 (A:136-323)
2a: SCOP_d2noia1 (A:8-135)
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Classes
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(
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Folds
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA-glycosylase
(77)
Superfamily
:
DNA-glycosylase
(77)
Family
:
DNA repair glycosylase, 2 C-terminal domains
(36)
Protein domain
:
8-oxoguanine glycosylase
(24)
Human (Homo sapiens) [TaxId: 9606]
(24)
1a
d2noia2
A:136-323
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
TBP-like
(289)
Superfamily
:
TATA-box binding protein-like
(70)
Family
:
DNA repair glycosylase, N-terminal domain
(35)
Protein domain
:
8-oxoguanine glycosylase
(24)
Human (Homo sapiens) [TaxId: 9606]
(24)
2a
d2noia1
A:8-135
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2noiA01 (A:8-100)
2a: CATH_2noiA02 (A:104-124,A:265-323)
3a: CATH_2noiA03 (A:136-261)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
TATA-Binding Protein
(118)
Homologous Superfamily
:
[code=3.30.310.40, no name defined]
(24)
[unclassified]
(23)
1a
2noiA01
A:8-100
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Endonuclease Iii, domain 2
(65)
Homologous Superfamily
:
Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
(65)
[unclassified]
(30)
2a
2noiA02
A:104-124,A:265-323
Topology
:
Endonuclease III; domain 1
(74)
Homologous Superfamily
:
Hypothetical protein; domain 2
(73)
[unclassified]
(31)
3a
2noiA03
A:136-261
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain C
Asymmetric Unit 1
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Asym.Unit (66 KB)
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