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3OJS
Asym. Unit
Info
Asym.Unit (308 KB)
Biol.Unit 1 (299 KB)
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(1)
Title
:
SNAPSHOTS OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS PROCESSING C5 MODIFIED THYMIDINES
Authors
:
A. Marx, K. Diederichs, S. Obeid
Date
:
23 Aug 10 (Deposition) - 15 Dec 10 (Release) - 27 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, C5 Modified Nucleotide Analogs, Binding Pocket, Denron-Labeled Triphosphate, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
S. Obeid, A. Baccaro, W. Welte, K. Diederichs, A. Marx
Structural Basis For The Synthesis Of Nucleobase Modified Dna By Thermus Aquaticus Dna Polymerase.
Proc. Natl. Acad. Sci. Usa V. 107 21327 2010
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Hetero Components
(6, 19)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: TRIETHYLENE GLYCOL (PGEa)
5b: TRIETHYLENE GLYCOL (PGEb)
5c: TRIETHYLENE GLYCOL (PGEc)
5d: TRIETHYLENE GLYCOL (PGEd)
6a: 2'-DEOXY-5-[9-(3-{[4-(DIETHYLAMINO... (XJSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
GOL
8
Ligand/Ion
GLYCEROL
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
PGE
4
Ligand/Ion
TRIETHYLENE GLYCOL
6
XJS
1
Ligand/Ion
2'-DEOXY-5-[9-(3-{[4-(DIETHYLAMINO)-4-OXOBUTANOYL]AMINO}PROPYL)-18-ETHYL-5,8,14,17-TETRAOXO-4,9,13,18-TETRAAZAICOS-1-YN-1-YL]URIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
[
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Sites
(18, 18)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MG A:7 , MG A:8 , HOH A:33 , HOH A:115 , HOH A:120 , HOH A:162 , HOH A:185 , HOH A:248 , 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 , LYS A:663 , PHE A:667 , ARG A:677 , ASP A:785 , HOH A:833 , HOH B:28 , DC B:111 , DOC B:112 , GOL C:8 , HOH C:33 , HOH C:42 , DA C:204 , DG C:205 , DG C:206
BINDING SITE FOR RESIDUE XJS A 1
02
AC2
SOFTWARE
GOL A:6 , HOH A:37 , HOH A:55 , HOH A:100 , ASN A:485 , SER A:486 , ARG A:487 , ASP A:488 , DG C:211 , DT C:212
BINDING SITE FOR RESIDUE GOL A 2
03
AC3
SOFTWARE
HOH A:142 , HOH A:219 , HOH A:221 , HOH A:282 , ASP A:452 , TYR A:455 , ARG A:596 , ILE A:599 , ASP A:826
BINDING SITE FOR RESIDUE GOL A 3
04
AC4
SOFTWARE
HOH A:126 , HOH A:168 , THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , PGE C:6 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 4
05
AC5
SOFTWARE
HOH A:53 , HOH A:176 , ARG A:313 , TRP A:318 , ASP A:551 , LEU A:552
BINDING SITE FOR RESIDUE GOL A 5
06
AC6
SOFTWARE
GOL A:2 , HOH A:37 , HOH A:67 , HOH A:125 , HOH A:223 , ASN A:485 , ARG A:487 , DG B:107 , DG B:108 , DC B:109
BINDING SITE FOR RESIDUE GOL A 6
07
AC7
SOFTWARE
XJS A:1 , MG A:8 , ASP A:610 , TYR A:611 , ASP A:785
BINDING SITE FOR RESIDUE MG A 7
08
AC8
SOFTWARE
XJS A:1 , MG A:7 , HOH A:216 , ASP A:610 , ASP A:785 , HOH A:833 , DOC B:112
BINDING SITE FOR RESIDUE MG A 8
09
AC9
SOFTWARE
HOH A:188 , HOH A:198 , GLU A:462 , GLU A:466 , ARG A:593 , GLU A:825
BINDING SITE FOR RESIDUE PGE A 835
10
BC1
SOFTWARE
HOH A:58 , HOH A:183 , HOH A:220 , ARG A:425 , PHE A:724
BINDING SITE FOR RESIDUE ACT A 836
11
BC2
SOFTWARE
HOH A:152 , GLU A:742 , GLU A:745 , ARG A:746 , DA C:203
BINDING SITE FOR RESIDUE PGE A 837
12
BC3
SOFTWARE
HOH A:155 , HOH A:166 , VAL A:310 , LEU A:311 , ARG A:405
BINDING SITE FOR RESIDUE PGE A 838
13
BC4
SOFTWARE
HOH A:150 , HOH A:235 , TYR A:455
BINDING SITE FOR RESIDUE ACT A 840
14
BC5
SOFTWARE
TRP A:417 , ARG A:431 , ARG A:435
BINDING SITE FOR RESIDUE ACT A 841
15
BC6
SOFTWARE
HOH B:21 , HOH B:26 , HOH B:27 , HOH B:30 , DC B:106 , DG B:107 , DG B:108 , DC B:109 , HOH C:27 , HOH C:37 , DG C:208 , DC C:209
BINDING SITE FOR RESIDUE GOL B 7
16
BC7
SOFTWARE
GOL A:4 , HOH A:132 , ASP A:578 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE PGE C 6
17
BC8
SOFTWARE
XJS A:1 , HOH C:24 , DG C:205 , DG C:206
BINDING SITE FOR RESIDUE GOL C 8
18
BC9
SOFTWARE
ARG A:728 , DG C:206 , DC C:207
BINDING SITE FOR RESIDUE GOL C 9
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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:
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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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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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Sorry, no Info available
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_A_3ojsA01 (A:451-830)
2a: PFAM_Taq_exonuc_3ojsA02 (A:294-420)
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Clans
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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-3ojsA01
A:451-830
Clan
:
no clan defined [family: Taq-exonuc]
(17)
Family
:
Taq-exonuc
(17)
Thermus aquaticus
(17)
2a
Taq-exonuc-3ojsA02
A:294-420
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