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4ELV
Asym. Unit
Info
Asym.Unit (208 KB)
Biol.Unit 1 (200 KB)
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(1)
Title
:
SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS PROCESSING MODIFIED PYRIMIDINES
Authors
:
A. Marx, K. Diederichs, S. Obeid
Date
:
11 Apr 12 (Deposition) - 24 Apr 13 (Release) - 24 Apr 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, Modified Nucleotides, A Family, Dna Synthesis, Rigid Linker, Elongation Of Modified Dna, Non-Natural Nucleotide, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Obeid, H. Bu Kamp, W. Welte, K. Diederichs, A. Marx
Snapshot Of The Large Fragment Of Dna Polymerase I From Thermus Aquaticus Processing Modified Pyrimidines
To Be Published
[
close entry info
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Hetero Components
(7, 13)
Info
All Hetero Components
1a: [[(2S,5R)-5-[4-AZANYL-5-[2-(4-ETHY... (0R7a)
2a: [(2S,5R)-5-{4-AMINO-5-[(4-ETHYNYLP... (0R8a)
3a: CALCIUM ION (CAa)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
7a: TRIETHYLENE GLYCOL (PGEa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
0R7
1
Ligand/Ion
[[(2S,5R)-5-[4-AZANYL-5-[2-(4-ETHYNYLPHENYL)ETHYNYL]-2-OXIDANYLIDENE-PYRIMIDIN-1-YL]OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE
2
0R8
1
Mod. Nucleotide
[(2S,5R)-5-{4-AMINO-5-[(4-ETHYNYLPHENYL)ETHYNYL]-2-OXOPYRIMIDIN-1(2H)-YL}TETRAHYDROFURAN-2-YL]METHYLDIHYDROGEN PHOSPHATE
3
CA
1
Ligand/Ion
CALCIUM ION
4
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
5
GOL
4
Ligand/Ion
GLYCEROL
6
MG
3
Ligand/Ion
MAGNESIUM ION
7
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
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Sites
(12, 12)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:610 , GLU A:786 , 0R7 A:902 , HOH A:1019 , HOH A:1048 , HOH A:1129 , HOH A:1196
BINDING SITE FOR RESIDUE MG A 901
02
AC2
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:901 , CA A:908 , HOH A:1045 , HOH A:1080 , HOH A:1196 , HOH A:1200 , HOH A:1207 , HOH A:1231 , 0R8 B:112 , DG C:204 , DG C:205
BINDING SITE FOR RESIDUE 0R7 A 902
03
AC3
SOFTWARE
THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , HOH A:1090 , HOH A:1155 , DC C:209 , DC C:210 , HOH C:405
BINDING SITE FOR RESIDUE GOL A 903
04
AC4
SOFTWARE
ASP A:371 , TRP A:417 , ARG A:431 , ARG A:435
BINDING SITE FOR RESIDUE PGE A 904
05
AC5
SOFTWARE
ARG A:425 , LEU A:723 , PHE A:724 , GLU A:774 , TYR A:811 , HOH A:1160 , HOH A:1239
BINDING SITE FOR RESIDUE GOL A 905
06
AC6
SOFTWARE
ASP A:452 , TYR A:455 , ARG A:593 , ARG A:596 , ILE A:599 , HOH A:1110
BINDING SITE FOR RESIDUE GOL A 906
07
AC7
SOFTWARE
LEU A:311 , GLU A:400 , ARG A:405
BINDING SITE FOR RESIDUE EDO A 907
08
AC8
SOFTWARE
ASP A:610 , TYR A:611 , ASP A:785 , 0R7 A:902
BINDING SITE FOR RESIDUE CA A 908
09
AC9
SOFTWARE
HOH B:335 , HOH B:336 , HOH B:337 , HOH B:338 , HOH C:437 , HOH C:444
BINDING SITE FOR RESIDUE MG B 201
10
BC1
SOFTWARE
DG C:205 , DG C:206 , HOH C:404 , HOH C:426 , HOH C:429
BINDING SITE FOR RESIDUE GOL C 301
11
BC2
SOFTWARE
DG C:214 , HOH C:439 , HOH C:440 , HOH C:441 , HOH C:442 , HOH C:443
BINDING SITE FOR RESIDUE MG C 302
12
BC3
SOFTWARE
ALA A:570 , ARG A:728 , DG C:206 , DC C:207
BINDING SITE FOR RESIDUE EDO C 303
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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Exons
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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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