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Asym. Unit
Info
Asym.Unit (204 KB)
Biol.Unit 1 (196 KB)
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(1)
Title
:
LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH 5-(N-(10-HYDROXYDECANOYL)-AMINOPENTINYL)-2-DUTP
Authors
:
K. Bergen, A. Steck, S. Struett, A. Baccaro, W. Welte, K. Diederichs, A.
Date
:
24 Jan 12 (Deposition) - 16 May 12 (Release) - 08 Aug 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, Transferase-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
K. Bergen, A. L. Steck, S. Strutt, A. Baccaro, W. Welte, K. Diederichs, A. Marx
Structures Of Klentaq Dna Polymerase Caught While Incorporating C5-Modified Pyrimidine And C7-Modified 7-Deazapurine Nucleoside Triphosphates.
J. Am. Chem. Soc. V. 134 11840 2012
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Hetero Components
(5, 16)
Info
All Hetero Components
1a: 2'-DEOXY-5-{5-[(10-HYDROXYDECANOYL... (0L5a)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
4a: FORMIC ACID (FMTa)
4b: FORMIC ACID (FMTb)
4c: FORMIC ACID (FMTc)
4d: FORMIC ACID (FMTd)
4e: FORMIC ACID (FMTe)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
5e: MAGNESIUM ION (MGe)
5f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0L5
1
Ligand/Ion
2'-DEOXY-5-{5-[(10-HYDROXYDECANOYL)AMINO]PENT-1-YN-1-YL}URIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
4
FMT
5
Ligand/Ion
FORMIC ACID
5
MG
6
Ligand/Ion
MAGNESIUM ION
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Sites
(15, 15)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:573 , ARG A:587 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , ARG A:660 , ALA A:661 , LYS A:663 , THR A:664 , PHE A:667 , ASP A:785 , MG A:902 , MG A:903 , EDO A:906 , HOH A:1002 , HOH A:1010 , HOH A:1106 , HOH A:1161 , HOH A:1205 , HOH A:1253 , DOC B:112 , DA C:204 , DG C:205
BINDING SITE FOR RESIDUE 0L5 A 901
02
AC2
SOFTWARE
ASP A:610 , TYR A:611 , ASP A:785 , 0L5 A:901 , MG A:903
BINDING SITE FOR RESIDUE MG A 902
03
AC3
SOFTWARE
ASP A:610 , ASP A:785 , 0L5 A:901 , MG A:902 , HOH A:1160 , HOH A:1161
BINDING SITE FOR RESIDUE MG A 903
04
AC4
SOFTWARE
ARG A:313 , TRP A:318 , HOH A:1129
BINDING SITE FOR RESIDUE EDO A 904
05
AC5
SOFTWARE
HIS A:621 , HOH A:1201
BINDING SITE FOR RESIDUE MG A 905
06
AC6
SOFTWARE
ARG A:573 , GLU A:615 , GLN A:754 , ALA A:757 , ALA A:758 , HIS A:784 , 0L5 A:901 , HOH A:1159
BINDING SITE FOR RESIDUE EDO A 906
07
AC7
SOFTWARE
PRO A:579 , ASN A:580 , ASN A:583 , DC C:209
BINDING SITE FOR RESIDUE FMT A 907
08
AC8
SOFTWARE
ASN A:485 , TYR A:535
BINDING SITE FOR RESIDUE FMT A 908
09
AC9
SOFTWARE
HOH A:1058 , HOH A:1246 , HOH B:308 , FMT C:302 , HOH C:441
BINDING SITE FOR RESIDUE MG A 909
10
BC1
SOFTWARE
ARG A:593 , ASP A:826 , EDO A:911 , HOH A:1069
BINDING SITE FOR RESIDUE FMT A 910
11
BC2
SOFTWARE
ASP A:452 , ARG A:596 , FMT A:910 , HOH A:1061
BINDING SITE FOR RESIDUE EDO A 911
12
BC3
SOFTWARE
LEU A:352 , LYS A:354 , ASP A:355 , HOH A:1283
BINDING SITE FOR RESIDUE FMT A 912
13
BC4
SOFTWARE
HOH B:301 , HOH B:302 , HOH B:303 , HOH B:304 , HOH B:305 , HOH C:404
BINDING SITE FOR RESIDUE MG B 201
14
BC5
SOFTWARE
HOH A:1001 , DG C:205 , HOH C:401 , HOH C:402 , HOH C:403
BINDING SITE FOR RESIDUE MG C 301
15
BC6
SOFTWARE
ASN A:485 , SER A:486 , ARG A:487 , MG A:909 , HOH A:1157 , HOH B:308 , DG C:211 , DT C:212 , HOH C:442
BINDING SITE FOR RESIDUE FMT C 302
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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)
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SCOP Domains
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CATH Domains
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Pfam Domains
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