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4RPX
Biol. Unit 1
Info
Asym.Unit (81 KB)
Biol.Unit 1 (74 KB)
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(1)
Title
:
PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA CONTAINING AN 8-OXO-7,8-DIHYDRO-GUANINE (8-OXOG) AND DCTP IN THE PRESENCE OF CACL2
Authors
:
R. Vyas, Z. Suo
Date
:
31 Oct 14 (Deposition) - 15 Apr 15 (Release) - 06 May 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,D,P,T
Biol. Unit 1: A,D,P,T (1x)
Keywords
:
X-Family, Pol Beta, Transferase-Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
R. Vyas, A. J. Reed, E. J. Tokarsky, Z. Suo
Viewing Human Dna Polymerase Beta Faithfully And Unfaithfully Bypass An Oxidative Lesion By Time-Dependent Crystallography.
J. Am. Chem. Soc. V. 137 5225 2015
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPH... (8OGa)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
4c: CHLORIDE ION (CLc)
5a: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPa)
5b: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPb)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
6c: SODIUM ION (NAc)
6d: SODIUM ION (NAd)
6e: SODIUM ION (NAe)
6f: SODIUM ION (NAf)
6g: SODIUM ION (NAg)
View:
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Label:
No.
Name
Count
Type
Full Name
1
8OG
1
Mod. Nucleotide
8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2
ACT
3
Ligand/Ion
ACETATE ION
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
DCP
2
Ligand/Ion
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
6
NA
-1
Ligand/Ion
SODIUM ION
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Sites
(17, 17)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:149 , GLY A:179 , SER A:180 , ARG A:183 , SER A:188 , GLY A:189 , ASP A:190 , ASP A:192 , TYR A:271 , PHE A:272 , THR A:273 , GLY A:274 , ASP A:276 , ASN A:279 , CA A:402 , CA A:403 , HOH A:501 , HOH A:503 , HOH A:560 , HOH A:613 , DC P:10 , HOH P:201 , 8OG T:6
BINDING SITE FOR RESIDUE DCP A 401
02
AC2
SOFTWARE
ASP A:190 , ASP A:192 , ASP A:256 , DCP A:401 , DC P:10 , HOH P:201
BINDING SITE FOR RESIDUE CA A 402
03
AC3
SOFTWARE
ASP A:190 , ASP A:192 , DCP A:401 , HOH A:501
BINDING SITE FOR RESIDUE CA A 403
04
AC4
SOFTWARE
ASP A:318 , ASP A:321 , HOH A:571 , DCP D:101
BINDING SITE FOR RESIDUE NA A 404
05
AC5
SOFTWARE
THR A:101 , VAL A:103 , ILE A:106 , HOH A:504 , DG P:9 , HOH P:202
BINDING SITE FOR RESIDUE NA A 405
06
AC6
SOFTWARE
GLU A:249 , HOH A:535 , HOH A:547 , HOH A:553 , HOH A:565 , HOH A:605 , HOH A:650
BINDING SITE FOR RESIDUE NA A 406
07
AC7
SOFTWARE
LYS A:60 , LEU A:62 , VAL A:65 , HOH A:537 , DC D:3 , HOH D:202
BINDING SITE FOR RESIDUE NA A 407
08
AC8
SOFTWARE
ASP A:314 , ASP A:318 , HOH A:572 , HOH A:637 , DCP D:101
BINDING SITE FOR RESIDUE NA A 408
09
AC9
SOFTWARE
ASP A:160 , HOH A:624 , HOH A:672
BINDING SITE FOR RESIDUE NA A 409
10
BC1
SOFTWARE
ASN A:133 , HIS A:134 , HIS A:135 , HOH A:632
BINDING SITE FOR RESIDUE CL A 410
11
BC2
SOFTWARE
ASN A:294 , THR A:297 , ARG A:299
BINDING SITE FOR RESIDUE CL A 411
12
BC3
SOFTWARE
ALA A:32 , ILE A:33 , HIS A:34 , LYS A:35
BINDING SITE FOR RESIDUE CL A 412
13
BC4
SOFTWARE
ASN A:37 , ARG A:40 , ASP A:276 , ILE A:277 , HOH A:614 , HOH A:664 , 8OG T:6
BINDING SITE FOR RESIDUE ACT A 413
14
BC5
SOFTWARE
VAL A:221
BINDING SITE FOR RESIDUE ACT A 414
15
BC6
SOFTWARE
LYS A:35
BINDING SITE FOR RESIDUE ACT A 415
16
BC7
SOFTWARE
ASP A:124 , LYS A:127 , ASP A:314 , SER A:315 , LYS A:317 , ASP A:318 , ASP A:321 , NA A:404 , NA A:408 , DG D:4 , DG D:5 , DC T:2
BINDING SITE FOR RESIDUE DCP D 101
17
BC8
SOFTWARE
DG P:7 , HOH P:206 , HOH P:207 , DG T:9 , HOH T:106 , HOH T:115
BINDING SITE FOR RESIDUE NA P 101
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
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Exons
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SCOP Domains
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Asymmetric Unit 1
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