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3LWM
Asym. Unit
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Asym.Unit (213 KB)
Biol.Unit 1 (206 KB)
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(1)
Title
:
STRUCTURE OF THE LARGE FRAGMENT OF THERMUS AQUATICUS DNA POLYMERASE I IN COMPLEX WITH A BLUNT-ENDED DNA AND DDATP
Authors
:
A. Marx, K. Diederichs, S. Obeid
Date
:
24 Feb 10 (Deposition) - 05 May 10 (Release) - 12 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.19
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Replication, Dna Polymerases, Dna-Binding, Dna-Directed Dna Polymerase, Amino Acid-Templating Mechanism, Nucleotidyltransferase, Transferase, Transferase-Dna Complex, Blunt-Ended Dna, Template- Independent Dna Synthesis, Terminal Deoxynucleotidyl Transferase, Template-Independent Nucleotide Addition
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Obeid, N. Blatter, R. Kranaster, A. Schnur, K. Diederichs, W. Welte A. Marx
Replication Through An Abasic Dna Lesion: Structural Basis For Adenine Selectivity
Embo J. V. 29 1738 2010
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Hetero Components
(6, 16)
Info
All Hetero Components
1a: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAa)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
3a: 2',3'-DIDEOXYADENOSINE TRIPHOSPHAT... (DDSa)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
5a: MAGNESIUM ION (MGa)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
6c: SODIUM ION (NAc)
6d: SODIUM ION (NAd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2DA
1
Mod. Nucleotide
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2
ACT
4
Ligand/Ion
ACETATE ION
3
DDS
1
Ligand/Ion
2',3'-DIDEOXYADENOSINE TRIPHOSPHATE
4
GOL
5
Ligand/Ion
GLYCEROL
5
MG
1
Ligand/Ion
MAGNESIUM ION
6
NA
4
Ligand/Ion
SODIUM ION
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Sites
(14, 14)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:46 , HOH A:166 , ARG A:587 , GLN A:613 , HIS A:639 , ARG A:659 , LYS A:663 , PHE A:667 , TYR A:671 , MG A:835 , HOH A:844 , GOL B:1 , 2DA B:112
BINDING SITE FOR RESIDUE DDS A 1
02
AC2
SOFTWARE
ARG A:313 , ASP A:551
BINDING SITE FOR RESIDUE ACT A 833
03
AC3
SOFTWARE
THR A:447 , ARG A:778
BINDING SITE FOR RESIDUE ACT A 2
04
AC4
SOFTWARE
LEU A:311 , GLU A:400 , ARG A:405
BINDING SITE FOR RESIDUE GOL A 834
05
AC5
SOFTWARE
HOH A:141 , HOH A:160 , THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 4
06
AC6
SOFTWARE
DDS A:1 , HOH A:46 , HOH A:166 , ASP A:610
BINDING SITE FOR RESIDUE MG A 835
07
AC7
SOFTWARE
GLU A:615 , TYR A:671 , ASN A:750 , GLN A:754
BINDING SITE FOR RESIDUE NA A 836
08
AC8
SOFTWARE
GLY A:510 , ARG A:741 , GLU A:745
BINDING SITE FOR RESIDUE NA A 837
09
AC9
SOFTWARE
GLU A:774
BINDING SITE FOR RESIDUE NA A 5
10
BC1
SOFTWARE
HOH A:112 , LYS A:354 , ASP A:355
BINDING SITE FOR RESIDUE NA A 6
11
BC2
SOFTWARE
HOH A:149 , ARG A:536 , LYS A:540 , DG B:107 , DG B:108 , DC B:109
BINDING SITE FOR RESIDUE GOL B 2
12
BC3
SOFTWARE
DG B:107 , DG B:108 , HOH C:9 , DC C:209
BINDING SITE FOR RESIDUE GOL B 3
13
BC4
SOFTWARE
DDS A:1 , ASP A:610 , GLU A:786 , HOH A:843 , HOH A:844 , 2DA B:112
BINDING SITE FOR RESIDUE GOL B 1
14
BC5
SOFTWARE
DG C:206 , DC C:207
BINDING SITE FOR RESIDUE ACT C 4
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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_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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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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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_3lwmA01 (A:451-830)
2a: PFAM_Taq_exonuc_3lwmA02 (A:295-420)
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Clans
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)
(
)
Families
(
)
(
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Organisms
(
)
(
)
Clan
:
no clan defined [family: DNA_pol_A]
(69)
Family
:
DNA_pol_A
(69)
Thermus aquaticus
(17)
1a
DNA_pol_A-3lwmA01
A:451-830
Clan
:
no clan defined [family: Taq-exonuc]
(17)
Family
:
Taq-exonuc
(17)
Thermus aquaticus
(17)
2a
Taq-exonuc-3lwmA02
A:295-420
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Asymmetric Unit 1
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