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2AGP
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (79 KB)
Biol.Unit 2 (79 KB)
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(1)
Title
:
FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDE SELECTION AND PYROPHOSPHOROLYSIS
Authors
:
H. Ling, W. Yang
Date
:
27 Jul 05 (Deposition) - 06 Sep 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,D (1x)
Biol. Unit 2: B,E,F (1x)
Keywords
:
Base Stacking, Fidelity, Metal Ion, Mismatch, Pyrophosphorolysis, Transferase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Vaisman, H. Ling, R. Woodgate, W. Yang
Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide Selection And Pyrophosphorolysis.
Embo J. V. 24 2957 2005
(for further references see the
PDB file header
)
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTa)
2b: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTb)
3a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
3b: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
DGT
2
Ligand/Ion
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
3
DOC
2
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4
MG
5
Ligand/Ion
MAGNESIUM ION
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:7 , PHE A:8 , ASP A:105 , DGT A:401 , MG A:403
BINDING SITE FOR RESIDUE CA A 402
2
AC2
SOFTWARE
ASP A:105 , GLU A:106 , DGT A:401 , CA A:402 , DOC C:1813
BINDING SITE FOR RESIDUE MG A 403
3
AC3
SOFTWARE
ALA A:181 , ILE A:186 , HOH A:503 , HOH A:562 , HOH A:851 , HOH A:1044 , HOH A:1229
BINDING SITE FOR RESIDUE MG A 404
4
AC4
SOFTWARE
ASP B:7 , PHE B:8 , ASP B:105 , DGT B:501
BINDING SITE FOR RESIDUE CA B 402
5
AC5
SOFTWARE
ALA B:181 , ILE B:186 , HOH B:704 , HOH B:845 , HOH B:1146
BINDING SITE FOR RESIDUE MG B 404
6
AC6
SOFTWARE
ASP B:294 , HOH B:587 , HOH B:619 , HOH E:593 , DG E:1809 , DA E:1810
BINDING SITE FOR RESIDUE MG B 407
7
AC7
SOFTWARE
ASP B:105 , GLU B:106 , DGT B:501 , HOH B:580
BINDING SITE FOR RESIDUE MG B 408
8
AC8
SOFTWARE
ASP A:7 , TYR A:10 , PHE A:11 , TYR A:12 , ALA A:44 , THR A:45 , ARG A:51 , ALA A:57 , MET A:76 , ASP A:105 , LYS A:159 , CA A:402 , MG A:403 , HOH A:528 , HOH A:738 , HOH A:797 , HOH A:819 , HOH A:920 , HOH A:1160 , HOH A:1161 , HOH A:1168 , HOH C:1240 , DOC C:1813 , DT D:1905 , DG D:1906
BINDING SITE FOR RESIDUE DGT A 401
9
AC9
SOFTWARE
ASP B:7 , TYR B:10 , PHE B:11 , TYR B:12 , ALA B:44 , THR B:45 , ARG B:51 , ASP B:105 , LYS B:159 , CA B:402 , MG B:408 , HOH B:580 , HOH B:585 , HOH B:648 , HOH B:788 , HOH B:862 , HOH B:966 , HOH B:1043 , HOH B:1057 , HOH B:1067 , HOH B:1151 , HOH F:505 , DT F:1905
BINDING SITE FOR RESIDUE DGT B 501
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:3-187,B:3-187)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
DPO4_SULSO
3-187
2
A:3-187
B:3-187
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2agpa1 (A:241-341)
1b: SCOP_d2agpb1 (B:241-341)
2a: SCOP_d2agpa2 (A:2-240)
2b: SCOP_d2agpb2 (B:2-240)
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)
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Superfamily
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Family
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(62)
Protein domain
:
DinB homolog (DBH)
(39)
Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]
(34)
1a
d2agpa1
A:241-341
1b
d2agpb1
B:241-341
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Lesion bypass DNA polymerase (Y-family), catalytic domain
(104)
Protein domain
:
DinB homolog (DBH)
(46)
Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]
(40)
2a
d2agpa2
A:2-240
2b
d2agpb2
B:2-240
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2agpA01 (A:2-10,A:78-166)
1b: CATH_2agpB01 (B:2-10,B:78-166)
2a: CATH_2agpA04 (A:244-336)
2b: CATH_2agpB04 (B:244-336)
3a: CATH_2agpA03 (A:167-233)
3b: CATH_2agpB03 (B:167-233)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.270, no name defined]
(278)
[unclassified]
(58)
1a
2agpA01
A:2-10,A:78-166
1b
2agpB01
B:2-10,B:78-166
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.100, no name defined]
(80)
[unclassified]
(29)
2a
2agpA04
A:244-336
2b
2agpB04
B:244-336
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
3a
2agpA03
A:167-233
3b
2agpB03
B:167-233
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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Asym.Unit (160 KB)
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