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3PV8
Asym. Unit
Info
Asym.Unit (439 KB)
Biol.Unit 1 (215 KB)
Biol.Unit 2 (220 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I LARGE FRAGMENT BOUND TO DNA AND DDTTP-DA IN CLOSED CONFORMATION
Authors
:
W. Wang, L. S. Beese
Date
:
06 Dec 10 (Deposition) - 19 Oct 11 (Release) - 09 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.52
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Dna Polymerase I, Protein-Dna Complex, Thymine-Adenine, Closed Conformation, Transferase-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
W. Wang, H. W. Hellinga, L. S. Beese
Structural Evidence For The Rare Tautomer Hypothesis Of Spontaneous Mutagenesis.
Proc. Natl. Acad. Sci. Usa V. 108 17644 2011
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTa)
1b: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE (2DTb)
2a: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Ta)
2b: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOS... (D3Tb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
View:
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No.
Name
Count
Type
Full Name
1
2DT
2
Mod. Nucleotide
3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2
D3T
2
Ligand/Ion
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
SO4
3
Ligand/Ion
SULFATE ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
D3T A:201 , ASP A:653 , TYR A:654 , ASP A:830
BINDING SITE FOR RESIDUE MG A 1
2
AC2
SOFTWARE
MG A:1 , HOH A:120 , HOH A:141 , ARG A:615 , ASP A:653 , TYR A:654 , GLN A:656 , ILE A:657 , GLU A:658 , HIS A:682 , ARG A:702 , LYS A:706 , TYR A:710 , ASP A:830 , HOH A:1311 , 2DT B:29 , HOH B:192 , DA C:3 , DA C:4
BINDING SITE FOR RESIDUE D3T A 201
3
AC3
SOFTWARE
ARG A:517 , ASN A:573 , LYS D:730
BINDING SITE FOR RESIDUE SO4 A 2
4
AC4
SOFTWARE
D3T D:202 , TYR D:654 , ASP D:830 , HOH D:1823
BINDING SITE FOR RESIDUE MG D 2
5
AC5
SOFTWARE
MG D:2 , HOH D:26 , HOH D:40 , ARG D:615 , TYR D:654 , SER D:655 , GLN D:656 , ILE D:657 , GLU D:658 , HIS D:682 , ARG D:702 , LYS D:706 , TYR D:710 , ASP D:830 , HOH D:1107 , HOH D:1690 , HOH D:1820 , HOH D:1823 , 2DT E:29 , HOH E:136 , DA F:3 , DA F:4
BINDING SITE FOR RESIDUE D3T D 202
6
AC6
SOFTWARE
MET D:299 , ALA D:300 , ARG D:343 , ARG D:677 , HOH D:1451
BINDING SITE FOR RESIDUE SO4 D 1
7
AC7
SOFTWARE
ARG D:629 , ARG D:703 , HOH D:956
BINDING SITE FOR RESIDUE SO4 D 3
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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
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Exons
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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_d3pv8a1 (A:298-468)
1b: SCOP_d3pv8d1 (D:298-468)
2a: SCOP_d3pv8a2 (A:469-876)
2b: SCOP_d3pv8d2 (D:469-876)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
automated matches
(127)
Protein domain
:
automated matches
(127)
Geobacillus kaustophilus [TaxId: 1462]
(8)
1a
d3pv8a1
A:298-468
1b
d3pv8d1
D:298-468
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
automated matches
(26)
Geobacillus kaustophilus [TaxId: 1462]
(8)
2a
d3pv8a2
A:469-876
2b
d3pv8d2
D:469-876
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CATH Domains
(0, 0)
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Pfam Domains
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (439 KB)
Header - Asym.Unit
Biol.Unit 1 (215 KB)
Header - Biol.Unit 1
Biol.Unit 2 (220 KB)
Header - Biol.Unit 2
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