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3SV3
Asym. Unit
Info
Asym.Unit (306 KB)
Biol.Unit 1 (297 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 THE ARTIFICIAL BASE PAIR DNAM-D5SICSTP
Authors
:
K. Betz, K. Diederichs, A. Marx
Date
:
12 Jul 11 (Deposition) - 06 Jun 12 (Release) - 12 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, Artificial Base Pair, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Betz, D. A. Malyshev, T. Lavergne, W. Welte, K. Diederichs, T. J. Dwyer, P. Ordoukhanian, F. E. Romesberg, A. Marx
Klentaq Polymerase Replicates Unnatural Base Pairs By Inducing A Watson-Crick Geometry.
Nat. Chem. Biol. V. 8 612 2012
[
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Hetero Components
(6, 29)
Info
All Hetero Components
1a: 2-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-H... (5SIa)
1b: 2-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-H... (5SIb)
2a: (1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METH... (BMNa)
3a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
4a: FORMIC ACID (FMTa)
4b: FORMIC ACID (FMTb)
4c: FORMIC ACID (FMTc)
4d: FORMIC ACID (FMTd)
4e: FORMIC ACID (FMTe)
4f: FORMIC ACID (FMTf)
4g: FORMIC ACID (FMTg)
4h: FORMIC ACID (FMTh)
4i: FORMIC ACID (FMTi)
4j: FORMIC ACID (FMTj)
4k: FORMIC ACID (FMTk)
4l: FORMIC ACID (FMTl)
4m: FORMIC ACID (FMTm)
4n: FORMIC ACID (FMTn)
4o: FORMIC ACID (FMTo)
4p: FORMIC ACID (FMTp)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
6e: MAGNESIUM ION (MGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5SI
2
Ligand/Ion
2-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-6-METHYLISOQUINOLINE-1(2H)-THIONE
2
BMN
1
Mod. Nucleotide
(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL
3
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4
FMT
16
Ligand/Ion
FORMIC ACID
5
GOL
4
Ligand/Ion
GLYCEROL
6
MG
5
Ligand/Ion
MAGNESIUM ION
[
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Sites
(27, 27)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:153 , HOH A:154 , HOH A:170 , GLN A:633 , ARG A:801 , LYS A:804 , GLU A:805 , LEU A:813 , ALA A:814 , PRO A:816 , MG A:834 , MG A:842 , HOH A:901 , HOH A:905 , HOH A:906
BINDING SITE FOR RESIDUE 5SI A 1
02
AC2
SOFTWARE
HOH A:169 , HOH A:191 , ARG A:573 , ASP A:610 , TYR A:611 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , LYS A:663 , THR A:664 , PHE A:667 , ASP A:785 , MG A:836 , MG A:837 , HOH A:893 , HOH B:49 , DOC B:112 , DG C:205
BINDING SITE FOR RESIDUE 5SI A 833
03
AC3
SOFTWARE
5SI A:1 , HOH A:153 , HOH A:154 , HOH A:170
BINDING SITE FOR RESIDUE MG A 834
04
AC4
SOFTWARE
THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , HOH A:871 , HOH A:882 , HOH C:95 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 835
05
AC5
SOFTWARE
HOH A:155 , ARG A:313 , TRP A:318 , ASP A:551 , LEU A:552
BINDING SITE FOR RESIDUE GOL A 2
06
AC6
SOFTWARE
GLU A:337 , LYS A:340
BINDING SITE FOR RESIDUE FMT A 8
07
AC7
SOFTWARE
HIS A:443 , THR A:447
BINDING SITE FOR RESIDUE FMT A 9
08
AC8
SOFTWARE
ASP A:610 , TYR A:611 , ASP A:785 , 5SI A:833 , MG A:837
BINDING SITE FOR RESIDUE MG A 836
09
AC9
SOFTWARE
HOH A:163 , ASP A:610 , ASP A:785 , 5SI A:833 , MG A:836 , HOH A:855 , DOC B:112
BINDING SITE FOR RESIDUE MG A 837
10
BC1
SOFTWARE
ILE A:823 , GLY A:824 , GLU A:825 , SER A:829
BINDING SITE FOR RESIDUE FMT A 838
11
BC2
SOFTWARE
PRO A:792 , LYS A:793 , GLU A:794 , ARG A:795
BINDING SITE FOR RESIDUE FMT A 839
12
BC3
SOFTWARE
HOH A:42
BINDING SITE FOR RESIDUE FMT A 840
13
BC4
SOFTWARE
LEU A:311 , GLU A:400 , ARG A:405
BINDING SITE FOR RESIDUE FMT A 841
14
BC5
SOFTWARE
5SI A:1 , HOH A:901 , HOH A:902 , HOH A:903 , HOH A:904 , HOH A:905
BINDING SITE FOR RESIDUE MG A 842
15
BC6
SOFTWARE
ASP A:488 , LYS A:511 , HOH A:852 , DC B:106 , DT C:212 , FMT C:217
BINDING SITE FOR RESIDUE FMT A 843
16
BC7
SOFTWARE
GLU A:708 , ARG A:715 , HOH A:908
BINDING SITE FOR RESIDUE FMT A 844
17
BC8
SOFTWARE
HOH A:89 , HOH A:90 , HOH A:106 , ASN A:485 , DG B:107
BINDING SITE FOR RESIDUE FMT A 845
18
BC9
SOFTWARE
ARG A:746
BINDING SITE FOR RESIDUE FMT A 846
19
CC1
SOFTWARE
TYR A:455 , ARG A:596
BINDING SITE FOR RESIDUE FMT A 847
20
CC2
SOFTWARE
HOH B:2 , HOH B:3 , HOH B:4 , HOH B:5 , HOH B:6 , HOH C:222
BINDING SITE FOR RESIDUE MG B 1
21
CC3
SOFTWARE
HOH C:41 , DG C:205 , DG C:206
BINDING SITE FOR RESIDUE GOL C 3
22
CC4
SOFTWARE
ARG A:728 , DG C:206 , DC C:207
BINDING SITE FOR RESIDUE FMT C 4
23
CC5
SOFTWARE
HOH C:135 , DC C:207 , DG C:208
BINDING SITE FOR RESIDUE FMT C 6
24
CC6
SOFTWARE
HOH C:35 , DG C:213 , DG C:214
BINDING SITE FOR RESIDUE FMT C 1
25
CC7
SOFTWARE
HOH A:90 , HOH A:121 , ARG A:487 , FMT A:843 , HOH A:852 , HOH C:8 , DG C:211 , DT C:212
BINDING SITE FOR RESIDUE FMT C 217
26
CC8
SOFTWARE
DC B:104 , HOH C:36 , DC C:210 , DG C:211 , DT C:212
BINDING SITE FOR RESIDUE GOL C 218
27
CC9
SOFTWARE
ARG A:556 , DC B:103 , DT C:215 , DC C:216
BINDING SITE FOR RESIDUE FMT C 219
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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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all CATH domains
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Pfam Domains
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Asymmetric Unit 1
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