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4DFJ
Asym. Unit
Info
Asym.Unit (206 KB)
Biol.Unit 1 (199 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 5-(AMINOPENTINYL)-DTTP
Authors
:
K. Bergen, A. Steck, S. Struett, A. Baccaro, W. Welte, K. Diederichs, A.
Date
:
23 Jan 12 (Deposition) - 16 May 12 (Release) - 08 Aug 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, 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
(6, 21)
Info
All Hetero Components
1a: 5-(5-AMINOPENT-1-YN-1-YL)-2'-DEOXY... (0KLa)
2a: CHLORIDE ION (CLa)
3a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
5a: FORMIC ACID (FMTa)
5b: FORMIC ACID (FMTb)
5c: FORMIC ACID (FMTc)
5d: FORMIC ACID (FMTd)
5e: FORMIC ACID (FMTe)
5f: FORMIC ACID (FMTf)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
6e: MAGNESIUM ION (MGe)
6f: MAGNESIUM ION (MGf)
6g: MAGNESIUM ION (MGg)
6h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0KL
1
Ligand/Ion
5-(5-AMINOPENT-1-YN-1-YL)-2'-DEOXYURIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
2
CL
1
Ligand/Ion
CHLORIDE ION
3
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
5
FMT
6
Ligand/Ion
FORMIC ACID
6
MG
8
Ligand/Ion
MAGNESIUM ION
[
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Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:610 , ASP A:785 , MG A:902 , 0KL A:903 , HOH A:1011 , HOH A:1026
BINDING SITE FOR RESIDUE MG A 901
02
AC2
SOFTWARE
ASP A:610 , TYR A:611 , ASP A:785 , MG A:901 , 0KL A:903
BINDING SITE FOR RESIDUE MG A 902
03
AC3
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 , THR A:664 , PHE A:667 , ASP A:785 , MG A:901 , MG A:902 , FMT A:904 , HOH A:1013 , HOH A:1020 , HOH A:1026 , HOH A:1050 , DOC B:112 , CL B:203 , DA C:204 , DG C:205
BINDING SITE FOR RESIDUE 0KL A 903
04
AC4
SOFTWARE
ARG A:573 , GLU A:615 , ALA A:757 , 0KL A:903
BINDING SITE FOR RESIDUE FMT A 904
05
AC5
SOFTWARE
SER A:383 , THR A:385 , THR A:386 , HOH A:1038
BINDING SITE FOR RESIDUE MG A 905
06
AC6
SOFTWARE
ARG A:771 , HOH A:1089 , HOH A:1150
BINDING SITE FOR RESIDUE MG A 906
07
AC7
SOFTWARE
THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , DC C:209
BINDING SITE FOR RESIDUE EDO A 907
08
AC8
SOFTWARE
ARG A:425 , TRP A:428 , PHE A:724
BINDING SITE FOR RESIDUE FMT A 908
09
AC9
SOFTWARE
HIS A:621 , ARG A:771 , GLU A:774 , MET A:775 , MG A:912
BINDING SITE FOR RESIDUE EDO A 909
10
BC1
SOFTWARE
LYS A:508 , GLU A:734 , ALA A:735
BINDING SITE FOR RESIDUE FMT A 910
11
BC2
SOFTWARE
ASP A:488 , HOH A:1090 , DT C:212 , DG C:213 , MG C:302
BINDING SITE FOR RESIDUE EDO A 911
12
BC3
SOFTWARE
HIS A:621 , LEU A:723 , EDO A:909
BINDING SITE FOR RESIDUE MG A 912
13
BC4
SOFTWARE
GLU A:347 , ARG A:349 , GLY A:370 , ASP A:371 , ARG A:435
BINDING SITE FOR RESIDUE FMT A 913
14
BC5
SOFTWARE
ARG A:313 , GLU A:315 , ASP A:578 , HOH A:1084
BINDING SITE FOR RESIDUE FMT A 914
15
BC6
SOFTWARE
LYS A:508 , DC B:106 , DG B:107 , HOH B:303 , HOH B:323
BINDING SITE FOR RESIDUE FMT B 201
16
BC7
SOFTWARE
HOH B:302 , HOH B:303 , HOH B:304 , HOH B:305 , HOH C:401
BINDING SITE FOR RESIDUE MG B 202
17
BC8
SOFTWARE
0KL A:903 , DC B:111 , DOC B:112 , HOH B:301
BINDING SITE FOR RESIDUE CL B 203
18
BC9
SOFTWARE
DG C:213 , DG C:214
BINDING SITE FOR RESIDUE EDO C 301
19
CC1
SOFTWARE
EDO A:911 , HOH A:1090 , HOH A:1143 , HOH A:1144 , DG C:211 , DT C:212
BINDING SITE FOR RESIDUE MG C 302
20
CC2
SOFTWARE
HOH B:306 , DG C:205 , HOH C:402 , HOH C:403 , HOH C:404
BINDING SITE FOR RESIDUE MG C 303
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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
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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
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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 (206 KB)
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