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4ELU
Asym. Unit
Info
Asym.Unit (209 KB)
Biol.Unit 1 (202 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) - 27 Mar 13 (Release) - 27 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Dna Polymerase, Modified Nucleotides, A Family, Dna Synthesis, Rigid Linker, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Obeid, H. Busskamp, W. Welte, K. Diederichs, A. Marx
Interactions Of Non-Polar And "Click-Able" Nucleotides In The Confines Of A Dna Polymerase Active Site.
Chem. Commun. (Camb. ) V. 48 8320 2012
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Hetero Components
(6, 22)
Info
All Hetero Components
1a: 2'-DEOXY-5-[(4-ETHYNYLPHENYL)ETHYN... (0R6a)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
3a: 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHO... (DDGa)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
6a: TRIETHYLENE GLYCOL (PGEa)
6b: TRIETHYLENE GLYCOL (PGEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0R6
1
Ligand/Ion
2'-DEOXY-5-[(4-ETHYNYLPHENYL)ETHYNYL]CYTIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
2
ACT
4
Ligand/Ion
ACETATE ION
3
DDG
1
Mod. Nucleotide
2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4
GOL
11
Ligand/Ion
GLYCEROL
5
MG
3
Ligand/Ion
MAGNESIUM ION
6
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
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Sites
(21, 21)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
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 , MG A:902 , MG A:903 , HOH A:1001 , HOH A:1011 , HOH A:1030 , HOH A:1050 , HOH A:1063 , HOH A:1126 , DDG B:112 , GOL B:204 , DG C:204
BINDING SITE FOR RESIDUE 0R6 A 901
02
AC2
SOFTWARE
ASP A:610 , TYR A:611 , ASP A:785 , 0R6 A:901 , MG A:903
BINDING SITE FOR RESIDUE MG A 902
03
AC3
SOFTWARE
ASP A:610 , ASP A:785 , 0R6 A:901 , MG A:902 , HOH A:1001 , HOH A:1003 , DDG B:112
BINDING SITE FOR RESIDUE MG A 903
04
AC4
SOFTWARE
ARG A:660 , LYS A:663 , LYS A:831 , HOH A:1050 , HOH A:1126 , HOH A:1305 , DDG B:112
BINDING SITE FOR RESIDUE GOL A 904
05
AC5
SOFTWARE
THR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , HOH A:1108 , HOH A:1248 , DC C:209 , DC C:210
BINDING SITE FOR RESIDUE GOL A 905
06
AC6
SOFTWARE
THR A:447 , ARG A:559 , ARG A:778
BINDING SITE FOR RESIDUE PGE A 906
07
AC7
SOFTWARE
ASP A:452 , TYR A:455 , ARG A:596 , ASP A:826
BINDING SITE FOR RESIDUE GOL A 907
08
AC8
SOFTWARE
ASP A:371 , TRP A:417 , ARG A:435
BINDING SITE FOR RESIDUE ACT A 908
09
AC9
SOFTWARE
PRO A:501 , ALA A:521 , GLU A:694
BINDING SITE FOR RESIDUE GOL A 909
10
BC1
SOFTWARE
GLN A:489 , ARG A:492 , VAL A:493 , GLU A:497
BINDING SITE FOR RESIDUE ACT A 910
11
BC2
SOFTWARE
ARG A:313 , TRP A:318 , LEU A:552 , HOH A:1046
BINDING SITE FOR RESIDUE GOL A 911
12
BC3
SOFTWARE
TRP A:645 , MET A:646 , PHE A:647 , GLY A:648 , ILE A:684
BINDING SITE FOR RESIDUE GOL A 912
13
BC4
SOFTWARE
ARG A:425 , TRP A:428 , HOH A:1028
BINDING SITE FOR RESIDUE ACT A 913
14
BC5
SOFTWARE
GLU A:337 , PRO A:338 , TYR A:339 , LYS A:340 , DG B:101
BINDING SITE FOR RESIDUE PGE B 201
15
BC6
SOFTWARE
HOH B:327 , HOH B:329 , HOH B:330 , HOH B:331 , HOH C:440
BINDING SITE FOR RESIDUE MG B 202
16
BC7
SOFTWARE
LYS A:540 , HOH A:1292 , DG B:107 , DG B:108 , DC B:109 , HOH B:312 , HOH B:314 , DC C:210 , HOH C:403
BINDING SITE FOR RESIDUE GOL B 203
17
BC8
SOFTWARE
ARG A:587 , THR A:664 , 0R6 A:901 , DC B:111 , DDG B:112 , HOH B:325 , DG C:204
BINDING SITE FOR RESIDUE GOL B 204
18
BC9
SOFTWARE
DC C:207 , DG C:208 , HOH C:410 , HOH C:429 , HOH C:434 , HOH C:440
BINDING SITE FOR RESIDUE ACT C 301
19
CC1
SOFTWARE
ARG A:728 , DG C:206 , DC C:207 , HOH C:417
BINDING SITE FOR RESIDUE GOL C 302
20
CC2
SOFTWARE
DC B:103 , DG C:213 , DG C:214
BINDING SITE FOR RESIDUE GOL C 303
21
CC3
SOFTWARE
DC C:205 , DG C:206 , HOH C:402 , HOH C:407 , HOH C:419
BINDING SITE FOR RESIDUE GOL C 304
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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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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Asymmetric Unit 1
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Asym.Unit (209 KB)
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Header - Biol.Unit 1
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