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3M8R
Asym. Unit
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Asym.Unit (220 KB)
Biol.Unit 1 (213 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH TRAPPED 4'-ETHYLATED DTTP
Authors
:
K. Diederichs, A. Marx, K. Betz
Date
:
19 Mar 10 (Deposition) - 07 Jul 10 (Release) - 08 Sep 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna, Dna Polymerase, Dna Replication, Nucleotides, Modified Nucleotide, Artificial Nucleotide, Nucleotide Probes, Dna-Binding, Dna-Directed Dna Polymerase, Nucleotidyltransferase, Transferase, Transferase-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
K. Betz, F. Streckenbach, A. Schnur, T. Exner, W. Welte, K. Diederichs A. Marx
Structures Of Dna Polymerases Caught Processing Size-Augmented Nucleotide Probes.
Angew. Chem. Int. Ed. Engl. V. 49 5181 2010
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Hetero Components
(6, 11)
Info
All Hetero Components
1a: POLYETHYLENE GLYCOL (N=34) (15Pa)
1b: POLYETHYLENE GLYCOL (N=34) (15Pb)
2a: ACETATE ION (ACTa)
3a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
5a: 4'-ETHYLTHYMIDINE 5'-(TETRAHYDROGE... (HXZa)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
15P
2
Ligand/Ion
POLYETHYLENE GLYCOL (N=34)
2
ACT
1
Ligand/Ion
ACETATE ION
3
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4
GOL
4
Ligand/Ion
GLYCEROL
5
HXZ
1
Ligand/Ion
4'-ETHYLTHYMIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
6
MG
2
Ligand/Ion
MAGNESIUM 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
MG A:1 , MG A:2 , HOH A:27 , HOH A:84 , HOH A:160 , ARG A:573 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , LYS A:663 , PHE A:667 , ASP A:785 , DOC B:112 , DA C:204 , DG C:205
BINDING SITE FOR RESIDUE HXZ A 113
02
AC2
SOFTWARE
MG A:2 , HOH A:27 , HXZ A:113 , HOH A:231 , ASP A:610 , ASP A:785 , DOC B:112
BINDING SITE FOR RESIDUE MG A 1
03
AC3
SOFTWARE
MG A:1 , HXZ A:113 , ASP A:610 , TYR A:611 , ASP A:785
BINDING SITE FOR RESIDUE MG A 2
04
AC4
SOFTWARE
ACT A:7 , HOH A:49 , HOH A:55 , HOH A:226 , GLU A:315 , TRP A:318 , LEU A:552 , LEU A:560 , HIS A:561 , ASP A:578 , PRO A:579 , GOL A:834 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE 15P A 833
05
AC5
SOFTWARE
HOH A:157 , THR A:544 , PRO A:548 , LEU A:549 , PRO A:579 , ASN A:580 , ASN A:583 , 15P A:833 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 834
06
AC6
SOFTWARE
HOH A:32 , ASN A:485 , SER A:486 , ARG A:487 , ASP A:488 , HOH B:43 , HOH B:165 , DG C:211 , DT C:212 , DG C:213 , HOH C:219
BINDING SITE FOR RESIDUE GOL A 5
07
AC7
SOFTWARE
HOH A:50 , HOH A:111 , ARG A:450 , GLU A:462 , GLU A:602
BINDING SITE FOR RESIDUE 15P A 6
08
AC8
SOFTWARE
ARG A:313 , TRP A:318 , LEU A:552 , 15P A:833
BINDING SITE FOR RESIDUE ACT A 7
09
AC9
SOFTWARE
DC B:106 , DG B:107 , DG B:108 , HOH B:114 , HOH B:117 , HOH B:246 , HOH B:299 , HOH C:103 , DC C:209
BINDING SITE FOR RESIDUE GOL B 4
10
BC1
SOFTWARE
HOH C:94 , HOH C:185 , DG C:205 , DG C:206
BINDING SITE FOR RESIDUE GOL C 3
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_A (A:659-678)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPO1_THEAQ
659-678
1
A:659-678
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Exons
(0, 0)
Info
All 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, 2)
Info
All SCOP Domains
1a: SCOP_d3m8ra1 (A:294-422)
2a: SCOP_d3m8ra2 (A:423-832)
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Classes
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(
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Folds
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)
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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 prokaryotic DNA polymerase
(81)
Thermus aquaticus [TaxId: 271]
(24)
1a
d3m8ra1
A:294-422
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
:
DNA polymerase I (Klenow fragment)
(82)
Thermus aquaticus [TaxId: 271]
(24)
2a
d3m8ra2
A:423-832
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_A_3m8rA01 (A:451-830)
2a: PFAM_Taq_exonuc_3m8rA02 (A:294-420)
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Clans
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Families
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Organisms
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Clan
:
no clan defined [family: DNA_pol_A]
(69)
Family
:
DNA_pol_A
(69)
Thermus aquaticus
(17)
1a
DNA_pol_A-3m8rA01
A:451-830
Clan
:
no clan defined [family: Taq-exonuc]
(17)
Family
:
Taq-exonuc
(17)
Thermus aquaticus
(17)
2a
Taq-exonuc-3m8rA02
A:294-420
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Asym.Unit (220 KB)
Header - Asym.Unit
Biol.Unit 1 (213 KB)
Header - Biol.Unit 1
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