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1D5A
Asym. Unit
Info
Asym.Unit (129 KB)
Biol.Unit 1 (125 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM
Authors
:
Y. Zhao, D. Jeruzalmi, L. Leighton, R. Lasken, J. Kuriyan
Date
:
06 Oct 99 (Deposition) - 24 Mar 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Dna Polymerase, Thermostable, Exonuclease, Rbd Domain, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhao, D. Jeruzalmi, I. Moarefi, L. Leighton, R. Lasken, J. Kuriyan
Crystal Structure Of An Archaebacterial Dna Polymerase.
Structure Fold. Des. V. 7 1189 1999
(for further references see the
PDB file header
)
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Hetero Components
(2, 11)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
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
2
Ligand/Ion
MAGNESIUM ION
2
SO4
9
Ligand/Ion
SULFATE ION
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Sites
(11, 11)
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)
11: BC2 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:94 , ARG A:97 , ASP A:113
BINDING SITE FOR RESIDUE SO4 A 4004
02
AC2
SOFTWARE
TYR A:7 , GLN A:91 , PRO A:115 , PHE A:116 , HOH A:3050
BINDING SITE FOR RESIDUE SO4 A 4091
03
AC3
SOFTWARE
GLY A:131 , ARG A:335 , ARG A:482 , HOH A:3022 , HOH A:3024
BINDING SITE FOR RESIDUE SO4 A 4130
04
AC4
SOFTWARE
TYR A:405 , LYS A:406 , SER A:407 , ASN A:491 , HOH A:3061 , SO4 A:4587
BINDING SITE FOR RESIDUE SO4 A 4487
05
AC5
SOFTWARE
PHE A:545 , GLU A:580 , TYR A:583 , TYR A:594 , THR A:604
BINDING SITE FOR RESIDUE SO4 A 4606
06
AC6
SOFTWARE
LYS A:188 , HOH A:3053 , HOH A:3054
BINDING SITE FOR RESIDUE SO4 A 4730
07
AC7
SOFTWARE
LYS A:464 , LYS A:468 , ARG A:746 , HOH A:3035
BINDING SITE FOR RESIDUE SO4 A 4787
08
AC8
SOFTWARE
GLU A:609
BINDING SITE FOR RESIDUE SO4 A 4706
09
AC9
SOFTWARE
LYS A:406 , ARG A:460 , LYS A:464 , LYS A:487 , SO4 A:4487
BINDING SITE FOR RESIDUE SO4 A 4587
10
BC1
SOFTWARE
ASP A:141 , GLU A:143 , ASP A:315 , MG A:5031
BINDING SITE FOR RESIDUE MG A 5030
11
BC2
SOFTWARE
ASP A:141 , MG A:5030
BINDING SITE FOR RESIDUE MG A 5031
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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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:538-546)
;
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.
DPOL_DESST
538-546
1
A:538-546
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Exons
(0, 0)
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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_d1d5aa1 (A:1-347)
2a: SCOP_d1d5aa2 (A:348-756)
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Classes
(
)
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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
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of family B DNA polymerases
(102)
Desulfurococcus tok [TaxId: 108142]
(2)
1a
d1d5aa1
A:1-347
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)
Desulfurococcus tok [TaxId: 108142]
(2)
2a
d1d5aa2
A:348-756
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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Chain A
Asymmetric Unit 1
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Asym.Unit (129 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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