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2PXI
Asym. Unit
Info
Asym.Unit (79 KB)
Biol.Unit 1 (75 KB)
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(1)
Title
:
TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A DIDEOXY TERMINATED PRIMER AND 2'-DEOXYGUANOSINE 5'-BETA, GAMMA-MONOFLUOROMETHYLENE TRIPHOSPHATE
Authors
:
C. E. Mckenna, V. K. Batra, W. A. Beard, L. C. Pedersen, S. H. Wilson
Date
:
14 May 07 (Deposition) - 08 Jan 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,D,P,T
Biol. Unit 1: A,D,P,T (1x)
Keywords
:
Nucleotidyl Transferase, Dna Polymerase, Chiral Interaction, Stereoselectivity, Lyase, Transferase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. E. Mckenna, B. A. Kashemirov, T. G. Upton, V. K. Batra, M. F. Goodman, L. C. Pedersen, W. A. Beard, S. H. Wilson
(R)-Beta, Gamma-Fluoromethylene-Dgtp-Dna Ternary Complex With Dna Polymerase Beta.
J. Am. Chem. Soc. V. 129 15412 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 11)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
3a: 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUO... (GFHa)
4a: MAGNESIUM ION (MGa)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
5
Ligand/Ion
CHLORIDE ION
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
GFH
1
Ligand/Ion
2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
NA
3
Ligand/Ion
SODIUM ION
[
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]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:190 , ASP A:192 , GFH A:338 , NA A:340 , HOH A:348
BINDING SITE FOR RESIDUE MG A 339
02
AC2
SOFTWARE
ASP A:190 , ASP A:192 , ASP A:256 , GFH A:338 , MG A:339 , DOC P:10
BINDING SITE FOR RESIDUE NA A 340
03
AC3
SOFTWARE
THR A:101 , VAL A:103 , ILE A:106 , HOH A:484 , DG P:9 , HOH P:11
BINDING SITE FOR RESIDUE NA A 341
04
AC4
SOFTWARE
LYS A:60 , LEU A:62 , VAL A:65 , HOH A:380 , DC D:3
BINDING SITE FOR RESIDUE NA A 342
05
AC5
SOFTWARE
GLN A:264 , TYR A:266 , CYS A:267 , VAL A:313 , HOH A:456
BINDING SITE FOR RESIDUE CL A 343
06
AC6
SOFTWARE
ALA A:32 , HIS A:34 , LYS A:35
BINDING SITE FOR RESIDUE CL A 344
07
AC7
SOFTWARE
LYS A:81 , LEU A:82 , ARG A:89
BINDING SITE FOR RESIDUE CL A 345
08
AC8
SOFTWARE
ASN A:294 , THR A:297 , ARG A:299
BINDING SITE FOR RESIDUE CL A 346
09
AC9
SOFTWARE
PRO A:330 , LYS A:331
BINDING SITE FOR RESIDUE CL A 347
10
BC1
SOFTWARE
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 , ARG A:283 , MG A:339 , NA A:340 , HOH A:348 , HOH A:350 , HOH A:374 , HOH A:386 , HOH A:394 , HOH A:400 , HOH A:447 , DOC P:10 , DC T:6 , DG T:7
BINDING SITE FOR RESIDUE GFH A 338
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_018881 (P242R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_018881
P
242
R
DPOLB_HUMAN
Polymorphism
3136797
A
P
242
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (A:179-198)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_X
PS00522
DNA polymerase family X signature.
DPOLB_HUMAN
179-198
1
A:179-198
[
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]
Exons
(14, 14)
Info
All Exons
Exon 1.1b (A:10-21)
Exon 1.2a (A:21-40)
Exon 1.4a (A:40-62)
Exon 1.5a (A:63-87)
Exon 1.6 (A:88-107)
Exon 1.7 (A:107-124)
Exon 1.9b (A:124-141)
Exon 1.10b (A:141-159)
Exon 1.11a (A:160-184)
Exon 1.13b (A:184-207)
Exon 1.14 (A:208-236)
Exon 1.15d (A:237-258)
Exon 1.16b (A:258-305)
Exon 1.18c (A:305-335)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2a
03: Boundary 1.2a/1.4a
04: Boundary 1.4a/1.5a
05: Boundary 1.5a/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.9b
08: Boundary 1.9b/1.10b
09: Boundary 1.10b/1.11a
10: Boundary 1.11a/1.13b
11: Boundary 1.13b/1.14
12: Boundary 1.14/1.15d
13: Boundary 1.15d/1.16b
14: Boundary 1.16b/1.18c
15: Boundary 1.18c/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000265421
1b
ENSE00002128274
chr8:
42195973-42196203
231
DPOLB_HUMAN
1-21
21
1
A:10-21
12
1.2a
ENST00000265421
2a
ENSE00001090262
chr8:
42196530-42196587
58
DPOLB_HUMAN
21-40
20
1
A:21-40
20
1.4a
ENST00000265421
4a
ENSE00001090263
chr8:
42202471-42202537
67
DPOLB_HUMAN
40-62
23
1
A:40-62
23
1.5a
ENST00000265421
5a
ENSE00001090267
chr8:
42206534-42206608
75
DPOLB_HUMAN
63-87
25
1
A:63-87
25
1.6
ENST00000265421
6
ENSE00001090266
chr8:
42207525-42207583
59
DPOLB_HUMAN
88-107
20
1
A:88-107
20
1.7
ENST00000265421
7
ENSE00001090264
chr8:
42210037-42210086
50
DPOLB_HUMAN
107-124
18
1
A:107-124
18
1.9b
ENST00000265421
9b
ENSE00000692498
chr8:
42213034-42213085
52
DPOLB_HUMAN
124-141
18
1
A:124-141
18
1.10b
ENST00000265421
10b
ENSE00000692500
chr8:
42214687-42214741
55
DPOLB_HUMAN
141-159
19
1
A:141-159
19
1.11a
ENST00000265421
11a
ENSE00000692501
chr8:
42214838-42214910
73
DPOLB_HUMAN
160-184
25
1
A:160-184
25
1.13b
ENST00000265421
13b
ENSE00000692502
chr8:
42218813-42218883
71
DPOLB_HUMAN
184-207
24
1
A:184-207
24
1.14
ENST00000265421
14
ENSE00000692503
chr8:
42220130-42220216
87
DPOLB_HUMAN
208-236
29
1
A:208-236
29
1.15d
ENST00000265421
15d
ENSE00000430961
chr8:
42226789-42226853
65
DPOLB_HUMAN
237-258
22
1
A:237-258
22
1.16b
ENST00000265421
16b
ENSE00000692505
chr8:
42227367-42227506
140
DPOLB_HUMAN
258-305
48
1
A:258-305
48
1.18c
ENST00000265421
18c
ENSE00002135820
chr8:
42229081-42229326
246
DPOLB_HUMAN
305-335
31
1
A:305-335
31
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2pxia1 (A:10-91)
2a: SCOP_d2pxia2 (A:92-148)
3a: SCOP_d2pxia3 (A:149-335)
View:
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Classes
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Folds
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Superfamilies
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(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
DNA polymerase beta, N-terminal domain-like
(205)
Family
:
DNA polymerase beta, N-terminal domain-like
(183)
Protein domain
:
DNA polymerase beta, N-terminal (8 kD)-domain
(156)
Human (Homo sapiens) [TaxId: 9606]
(141)
1a
d2pxia1
A:10-91
Superfamily
:
PsbU/PolX domain-like
(218)
Family
:
DNA polymerase beta-like, second domain
(190)
Protein domain
:
DNA polymerase beta
(164)
Human (Homo sapiens) [TaxId: 9606]
(141)
2a
d2pxia2
A:92-148
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nucleotidyltransferase
(287)
Superfamily
:
Nucleotidyltransferase
(287)
Family
:
DNA polymerase beta-like
(218)
Protein domain
:
DNA polymerase beta, catalytic (31 kD) fragment
(164)
Human (Homo sapiens) [TaxId: 9606]
(141)
3a
d2pxia3
A:149-335
[
close SCOP info
]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_2pxiA03 (A:149-271)
2a: CATH_2pxiA04 (A:272-334)
3a: CATH_2pxiA01 (A:12-91)
4a: CATH_2pxiA02 (A:92-148)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta Polymerase; domain 2
(187)
Homologous Superfamily
:
Beta Polymerase, domain 2
(183)
Human (Homo sapiens)
(22)
1a
2pxiA03
A:149-271
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
Human (Homo sapiens)
(21)
2a
2pxiA04
A:272-334
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.110, no name defined]
(150)
Human (Homo sapiens)
(21)
3a
2pxiA01
A:12-91
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
Human (Homo sapiens)
(34)
4a
2pxiA02
A:92-148
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_DNA_pol_lambd_f_2pxiA01 (A:97-148)
View:
Select:
Label:
Clans
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(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DNA_pol_lambd_f]
(69)
Family
:
DNA_pol_lambd_f
(69)
Homo sapiens (Human)
(55)
1a
DNA_pol_lambd_f-2pxiA01
A:97-148
[
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]
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Backbone
Sidechain
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Protein & NOT PROSITE
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Chain P
Chain T
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