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3OJU
Asym. Unit
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Asym.Unit (303 KB)
Biol.Unit 1 (295 KB)
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(1)
Title
:
SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS PROCESSING C5 MODIFIED THYMIDIES
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
:
2.00
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, C5 Modified Nucleotide Analogs, Binding Pocket, Spin- Labeled Triphosphate, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
(5, 21)
Info
All Hetero Components
1a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: TRIETHYLENE GLYCOL (PGEa)
4b: TRIETHYLENE GLYCOL (PGEb)
4c: TRIETHYLENE GLYCOL (PGEc)
4d: TRIETHYLENE GLYCOL (PGEd)
4e: TRIETHYLENE GLYCOL (PGEe)
4f: TRIETHYLENE GLYCOL (PGEf)
4g: TRIETHYLENE GLYCOL (PGEg)
4h: TRIETHYLENE GLYCOL (PGEh)
4i: TRIETHYLENE GLYCOL (PGEi)
4j: TRIETHYLENE GLYCOL (PGEj)
4k: TRIETHYLENE GLYCOL (PGEk)
5a: 2'-DEOXY-5-[(1-HYDROXY-2,2,5,5-TET... (SSJa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2
GOL
6
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
PGE
11
Ligand/Ion
TRIETHYLENE GLYCOL
5
SSJ
1
Ligand/Ion
2'-DEOXY-5-[(1-HYDROXY-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYNYL]URIDINE 5'-(TETRAHYDROGENTRIPHOSPHATE)
[
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MG A:2 , MG A:3 , HOH A:33 , HOH A:70 , HOH A:126 , 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 , THR A:664 , PHE A:667 , ASP A:785 , DC B:111 , DOC B:112 , DA C:204 , DG C:205
BINDING SITE FOR RESIDUE SSJ A 1
02
AC2
SOFTWARE
SSJ A:1 , ASP A:610 , TYR A:611 , ASP A:785
BINDING SITE FOR RESIDUE MG A 2
03
AC3
SOFTWARE
SSJ A:1 , HOH A:33 , ASP A:610 , ASP A:785
BINDING SITE FOR RESIDUE MG A 3
04
AC4
SOFTWARE
HOH A:163 , LYS A:354 , ASP A:355 , ASN A:565 , GLN A:566
BINDING SITE FOR RESIDUE GOL A 4
05
AC5
SOFTWARE
THR A:544 , PRO A:579 , ASN A:580 , ASN A:583 , HOH C:22 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 5
06
AC6
SOFTWARE
GOL A:9 , HOH A:157 , ASN A:485 , DG B:107 , DG C:211 , DT C:212
BINDING SITE FOR RESIDUE GOL A 6
07
AC7
SOFTWARE
GLU A:347 , ARG A:349 , GLY A:370 , ASP A:371
BINDING SITE FOR RESIDUE PGE A 7
08
AC8
SOFTWARE
GLU A:745 , ARG A:746
BINDING SITE FOR RESIDUE PGE A 8
09
AC9
SOFTWARE
GOL A:6 , ASN A:485 , SER A:486 , ARG A:487 , ASP A:488 , HOH B:31 , DG C:211 , DT C:212 , DG C:213
BINDING SITE FOR RESIDUE GOL A 9
10
BC1
SOFTWARE
HOH A:42 , HOH A:131 , LYS A:767 , ARG A:771 , VAL A:810
BINDING SITE FOR RESIDUE PGE A 10
11
BC2
SOFTWARE
ASP A:371 , ARG A:435
BINDING SITE FOR RESIDUE PGE A 11
12
BC3
SOFTWARE
ARG A:313 , GLU A:315 , TRP A:318 , LEU A:552
BINDING SITE FOR RESIDUE PGE A 12
13
BC4
SOFTWARE
GLY A:396 , GLU A:397 , GLU A:404 , ARG A:411
BINDING SITE FOR RESIDUE PGE A 13
14
BC5
SOFTWARE
SER A:460 , LYS A:542
BINDING SITE FOR RESIDUE PGE A 14
15
BC6
SOFTWARE
ARG A:425 , TRP A:428 , PHE A:724
BINDING SITE FOR RESIDUE GOL A 15
16
BC7
SOFTWARE
THR A:447 , ARG A:778
BINDING SITE FOR RESIDUE PGE A 16
17
BC8
SOFTWARE
GLY A:479
BINDING SITE FOR RESIDUE PGE A 17
18
BC9
SOFTWARE
HOH A:124 , LYS A:508 , THR A:509 , GLU A:734 , ALA A:735
BINDING SITE FOR RESIDUE PGE A 18
19
CC1
SOFTWARE
ARG A:728 , MET A:747 , PGE C:2 , DG C:206 , DC C:207
BINDING SITE FOR RESIDUE GOL C 1
20
CC2
SOFTWARE
GOL C:1 , HOH C:31 , DG C:205 , DG C:206 , DC C:207
BINDING SITE FOR RESIDUE PGE C 2
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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:
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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
All Exons
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3ojua1 (A:294-422)
2a: SCOP_d3ojua2 (A:423-832)
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Protein Domains
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(
)
Organisms
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(
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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
d3ojua1
A:294-422
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
d3ojua2
A:423-832
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CATH Domains
(0, 0)
Info
all 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_3ojuA01 (A:451-830)
2a: PFAM_Taq_exonuc_3ojuA02 (A:294-420)
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Clans
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Families
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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-3ojuA01
A:451-830
Clan
:
no clan defined [family: Taq-exonuc]
(17)
Family
:
Taq-exonuc
(17)
Thermus aquaticus
(17)
2a
Taq-exonuc-3ojuA02
A:294-420
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