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4DFM
Asym. Unit
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Asym.Unit (202 KB)
Biol.Unit 1 (195 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN TERNARY COMPLEX WITH 5-(AMINOPENTINYL)-2-DCTP
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
:
1.89
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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, 12)
Info
All Hetero Components
1a: 5-(5-AMINOPENT-1-YN-1-YL)-2'-DEOXY... (0L6a)
2a: 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHO... (DDGa)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
4a: FORMIC ACID (FMTa)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0L6
1
Ligand/Ion
5-(5-AMINOPENT-1-YN-1-YL)-2'-DEOXYCYTIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
2
DDG
1
Mod. Nucleotide
2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
3
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
4
FMT
1
Ligand/Ion
FORMIC ACID
5
MG
4
Ligand/Ion
MAGNESIUM 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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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
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 , ARG A:660 , LYS A:663 , PHE A:667 , ASP A:785 , MG A:902 , MG A:903 , EDO A:906 , HOH A:1001 , HOH A:1004 , HOH A:1006 , HOH A:1190 , DDG B:112 , DG C:204
BINDING SITE FOR RESIDUE 0L6 A 901
02
AC2
SOFTWARE
ASP A:610 , TYR A:611 , ASP A:785 , 0L6 A:901 , MG A:903
BINDING SITE FOR RESIDUE MG A 902
03
AC3
SOFTWARE
ASP A:610 , ASP A:785 , 0L6 A:901 , MG A:902 , HOH A:1001 , HOH A:1002
BINDING SITE FOR RESIDUE MG A 903
04
AC4
SOFTWARE
GLU A:337 , PRO A:338 , TYR A:339 , LYS A:340 , HOH A:1184 , DG B:101
BINDING SITE FOR RESIDUE FMT A 904
05
AC5
SOFTWARE
HOH A:1191 , HOH A:1192 , HOH A:1193 , HOH A:1194 , HOH B:321 , HOH C:328
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 , 0L6 A:901
BINDING SITE FOR RESIDUE EDO A 906
07
AC7
SOFTWARE
LEU A:352 , LYS A:354 , ASP A:355 , GLN A:566 , HOH A:1016 , HOH A:1028
BINDING SITE FOR RESIDUE EDO A 907
08
AC8
SOFTWARE
GLY A:396 , GLU A:397 , GLU A:404 , LEU A:408 , ARG A:411 , HOH A:1156
BINDING SITE FOR RESIDUE EDO A 908
09
AC9
SOFTWARE
THR A:544 , TYR A:545 , ASN A:580 , ASN A:583 , HOH A:1112 , DC C:209 , HOH C:326
BINDING SITE FOR RESIDUE EDO A 909
10
BC1
SOFTWARE
ASP A:452 , ARG A:593 , ARG A:596 , ASP A:826
BINDING SITE FOR RESIDUE EDO A 910
11
BC2
SOFTWARE
HOH B:302 , HOH B:304 , HOH B:308 , HOH B:319 , HOH C:318
BINDING SITE FOR RESIDUE MG B 201
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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)
;
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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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Asymmetric Unit 1
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Asym.Unit (202 KB)
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