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3T3F
Asym. Unit
Info
Asym.Unit (216 KB)
Biol.Unit 1 (207 KB)
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(1)
Title
:
TERNARY STRUCTURE OF THE LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO AN ABASIC SITE AND DNITP
Authors
:
A. Marx, K. Diederichs, S. Obeid
Date
:
25 Jul 11 (Deposition) - 15 Feb 12 (Release) - 13 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, Abasic Site, Translesion Synthesis, A-Rule, Base Stacking, Dnitp, Nitroindol Triphosphate, Base Analogue, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Obeid, W. Welte, K. Diederichs, A. Marx
Amino Acid Templating Mechanisms In Selection Of Nucleotide Opposite Abasic Sites By A Family A Dna Polymerase.
J. Biol. Chem. V. 287 14099 2012
[
close entry info
]
Hetero Components
(7, 25)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
3a: FORMIC ACID (FMTa)
3b: FORMIC ACID (FMTb)
3c: FORMIC ACID (FMTc)
3d: FORMIC ACID (FMTd)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
6a: 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-H... (N5Pa)
7a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
FMT
4
Ligand/Ion
FORMIC ACID
4
GOL
13
Ligand/Ion
GLYCEROL
5
MG
4
Ligand/Ion
MAGNESIUM ION
6
N5P
1
Ligand/Ion
1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO-1H-INDOLE
7
NA
1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:191 , HOH A:277 , THR A:544 , TYR A:545 , PRO A:548 , PRO A:579 , ASN A:580 , ASN A:583 , HOH C:18 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 1
02
AC2
SOFTWARE
HOH A:57 , HOH A:62 , LYS A:354 , ASP A:355 , ASN A:565 , GLN A:566
BINDING SITE FOR RESIDUE GOL A 3
03
AC3
SOFTWARE
HOH A:235 , ARG A:313 , TRP A:318 , ASP A:551 , LEU A:552 , HOH C:327
BINDING SITE FOR RESIDUE GOL A 4
04
AC4
SOFTWARE
GLY A:396 , GLU A:397 , GLU A:404 , ALA A:407 , LEU A:408 , ARG A:411
BINDING SITE FOR RESIDUE GOL A 9
05
AC5
SOFTWARE
HOH A:92 , HOH A:180 , ARG A:425 , PHE A:724 , TYR A:811 , HOH A:846
BINDING SITE FOR RESIDUE GOL A 10
06
AC6
SOFTWARE
ASP A:452 , ARG A:596 , ILE A:599 , ASP A:826
BINDING SITE FOR RESIDUE GOL A 11
07
AC7
SOFTWARE
PRO A:336 , GLU A:337 , LYS A:340 , ALA A:341 , ASP A:344
BINDING SITE FOR RESIDUE GOL A 13
08
AC8
SOFTWARE
HOH A:258 , ASP A:610 , ASP A:785 , GLU A:786 , MG A:834 , N5P A:836
BINDING SITE FOR RESIDUE MG A 833
09
AC9
SOFTWARE
ASP A:610 , TYR A:611 , ASP A:785 , MG A:833 , N5P A:836
BINDING SITE FOR RESIDUE MG A 834
10
BC1
SOFTWARE
PHE A:413 , ALA A:414 , ASN A:415 , LEU A:416 , TRP A:417 , GLY A:418 , ARG A:419
BINDING SITE FOR RESIDUE NA A 835
11
BC2
SOFTWARE
HOH A:69 , HOH A:174 , HOH A:220 , HOH A:223 , HOH A:229 , HOH A:247 , HOH A:258 , HOH A:285 , 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 , MG A:833 , MG A:834 , DOC B:112 , DG C:205
BINDING SITE FOR RESIDUE N5P A 836
12
BC3
SOFTWARE
HOH A:197 , LYS A:767 , VAL A:810
BINDING SITE FOR RESIDUE FMT A 837
13
BC4
SOFTWARE
HOH A:154 , GLU A:337 , PRO A:338 , TYR A:339 , LYS A:340 , HOH A:847 , DG B:101
BINDING SITE FOR RESIDUE FMT A 2
14
BC5
SOFTWARE
HIS A:443 , THR A:447
BINDING SITE FOR RESIDUE FMT A 838
15
BC6
SOFTWARE
HOH A:264 , ARG A:349 , ASP A:371 , TRP A:417 , ARG A:435
BINDING SITE FOR RESIDUE FMT A 839
16
BC7
SOFTWARE
LYS A:508 , HOH B:40 , HOH B:75 , DC B:106 , DG B:107 , HOH B:117 , HOH B:136 , HOH B:202
BINDING SITE FOR RESIDUE GOL B 12
17
BC8
SOFTWARE
HOH B:1402 , HOH B:1403 , HOH B:1404 , HOH B:1405
BINDING SITE FOR RESIDUE MG B 1401
18
BC9
SOFTWARE
HOH C:19 , HOH C:149 , HOH C:190 , DG C:205 , DG C:206 , HOH C:217
BINDING SITE FOR RESIDUE GOL C 2
19
CC1
SOFTWARE
ASN A:485 , DG B:107 , HOH B:116 , HOH C:153 , HOH C:157 , DG C:211 , DT C:212 , HOH C:219 , HOH C:286
BINDING SITE FOR RESIDUE GOL C 5
20
CC2
SOFTWARE
HOH C:19 , HOH C:50 , DC C:207 , DG C:208
BINDING SITE FOR RESIDUE GOL C 6
21
CC3
SOFTWARE
ARG A:556 , DC B:103 , DG C:214 , DT C:215 , DC C:216
BINDING SITE FOR RESIDUE GOL C 7
22
CC4
SOFTWARE
ARG A:728 , DG C:206 , DC C:207 , HOH C:322
BINDING SITE FOR RESIDUE GOL C 8
23
CC5
SOFTWARE
HOH C:1502 , HOH C:1503 , HOH C:1504 , HOH C:1505 , HOH C:1506
BINDING SITE FOR RESIDUE MG C 1501
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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:
Select:
Label:
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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All Exon Boundaries
View:
Label:
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_d3t3fa1 (A:293-422)
2a: SCOP_d3t3fa2 (A:423-832)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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 prokaryotic DNA polymerase
(81)
Thermus aquaticus [TaxId: 271]
(24)
1a
d3t3fa1
A:293-422
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
d3t3fa2
A:423-832
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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