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1S5J
Asym. Unit
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Asym.Unit (132 KB)
Biol.Unit 1 (127 KB)
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(1)
Title
:
INSIGHT IN DNA REPLICATION: THE CRYSTAL STRUCTURE OF DNA POLYMERASE B1 FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS
Authors
:
C. Savino, L. Federici, V. Nastopoulos, K. A. Johnson, F. M. Pisani, M. Rossi, D. Tsernoglou
Date
:
21 Jan 04 (Deposition) - 09 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Dna Polymerase, Replication, Disulfide Bonds, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Savino, L. Federici, K. A. Johnson, B. Vallone, V. Nastopoulos, M. Rossi, F. M. Pisani, D. Tsernoglou
Insights Into Dna Replication: The Crystal Structure Of Dna Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Structure V. 12 2001 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
SO4
9
Ligand/Ion
SULFATE ION
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:138 , ARG A:142 , LYS A:157 , TYR A:158 , HOH A:1019 , HOH A:1030 , HOH A:1068 , HOH A:1073
BINDING SITE FOR RESIDUE SO4 A 883
02
AC2
SOFTWARE
ARG A:574 , LYS A:579 , LYS A:603 , HOH A:968 , HOH A:1136
BINDING SITE FOR RESIDUE SO4 A 884
03
AC3
SOFTWARE
ILE A:50 , PHE A:52 , LYS A:72 , GLU A:221
BINDING SITE FOR RESIDUE SO4 A 885
04
AC4
SOFTWARE
ALA A:516 , SER A:517 , ASN A:607 , HOH A:968 , HOH A:1132
BINDING SITE FOR RESIDUE SO4 A 886
05
AC5
SOFTWARE
LYS A:87 , ARG A:136 , LYS A:247
BINDING SITE FOR RESIDUE SO4 A 887
06
AC6
SOFTWARE
ARG A:142 , ARG A:145 , HOH A:1010 , HOH A:1057
BINDING SITE FOR RESIDUE SO4 A 888
07
AC7
SOFTWARE
TRP A:41 , GLU A:43 , LYS A:76 , ILE A:77
BINDING SITE FOR RESIDUE SO4 A 889
08
AC8
SOFTWARE
GLU A:276 , PHE A:289 , ASN A:290 , THR A:291 , GLU A:294
BINDING SITE FOR RESIDUE SO4 A 890
09
AC9
SOFTWARE
TYR A:152 , GLU A:475 , LYS A:479
BINDING SITE FOR RESIDUE SO4 A 891
10
BC1
SOFTWARE
ASP A:231 , GLU A:233 , ASP A:413
BINDING SITE FOR RESIDUE MG A 892
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:653-661)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_B
PS00116
DNA polymerase family B signature.
DPOL1_SULSO
653-661
1
A:653-661
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1s5ja1 (A:40-449)
2a: SCOP_d1s5ja2 (A:450-864)
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Classes
(
)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of family B DNA polymerases
(102)
Sulfolobus solfataricus [TaxId: 2287]
(1)
1a
d1s5ja1
A:40-449
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
:
Family B DNA polymerase
(100)
Sulfolobus solfataricus [TaxId: 2287]
(1)
2a
d1s5ja2
A:450-864
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_1s5jA01 (A:450-864)
2a: PFAM_DNA_pol_B_exo1_1s5jA02 (A:72-382)
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Clans
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)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
DNA_pol_B-like
(44)
Family
:
DNA_pol_B
(38)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
1a
DNA_pol_B-1s5jA01
A:450-864
Clan
:
RNase_H
(288)
Family
:
DNA_pol_B_exo1
(38)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(1)
2a
DNA_pol_B_exo1-1s5jA02
A:72-382
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Chain A
Asymmetric Unit 1
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Asym.Unit (132 KB)
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