PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2ISO
Biol. Unit 1
Info
Asym.Unit (81 KB)
Biol.Unit 1 (76 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A DIDEOXY TERMINATED PRIMER AND 2'-DEOXYGUANOSINE 5'-BETA, GAMMA-DIFLUOROMETHYLENE TRIPHOSPHATE
Authors
:
C. A. Sucato, T. G. Upton, B. A. Kashemirov, V. Martinek, Y. Xiang, W. A. Beard
Date
:
18 Oct 06 (Deposition) - 30 Jan 07 (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, Polymerase, Leaving-Group, Transferase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Sucato, T. G. Upton, B. A. Kashemirov, V. K. Batra, V. Martinek, Y. Xiang, W. A. Beard, L. C. Pedersen, S. H. Wilson, C. E. Mckenna, J. Florian, A. Warshel, M. F. Goodman
Modifying The Beta, Gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, And The Catalytic Mechanism Of Dna Polymerase Beta.
Biochemistry V. 46 461 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
3a: 2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHO... (GFFa)
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
-1
Ligand/Ion
CHLORIDE ION
2
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3
GFF
1
Ligand/Ion
2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:190 , ASP A:192 , GFF A:338 , NA A:340 , HOH A:347
BINDING SITE FOR RESIDUE MG A 339
2
AC2
SOFTWARE
ASP A:190 , ASP A:192 , ASP A:256 , GFF A:338 , MG A:339 , DOC P:10 , HOH P:427
BINDING SITE FOR RESIDUE NA A 340
3
AC3
SOFTWARE
THR A:101 , VAL A:103 , ILE A:106 , HOH A:436 , DG P:9 , HOH P:27
BINDING SITE FOR RESIDUE NA A 341
4
AC4
SOFTWARE
LYS A:60 , LEU A:62 , VAL A:65 , HOH A:467 , DC D:3 , HOH D:364
BINDING SITE FOR RESIDUE NA A 342
5
AC5
SOFTWARE
GLN A:264 , TYR A:266 , CYS A:267 , HOH A:367
BINDING SITE FOR RESIDUE CL A 343
6
AC6
SOFTWARE
ALA A:32 , HIS A:34 , LYS A:35
BINDING SITE FOR RESIDUE CL A 344
7
AC7
SOFTWARE
LEU A:82 , ARG A:89
BINDING SITE FOR RESIDUE CL A 345
8
AC8
SOFTWARE
ASN A:294 , THR A:297 , ARG A:299
BINDING SITE FOR RESIDUE CL A 346
9
AC9
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:347 , HOH A:363 , HOH A:383 , HOH A:388 , HOH A:413 , HOH A:452 , HOH A:531 , HOH A:646 , DOC P:10 , HOH P:294 , HOH P:427 , DC T:6 , DG T:7
BINDING SITE FOR RESIDUE GFF A 338
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2isoa1 (A:10-91)
2a: SCOP_d2isoa2 (A:92-148)
3a: SCOP_d2isoa3 (A:149-335)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2isoa1
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
d2isoa2
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
d2isoa3
A:149-335
[
close SCOP info
]
CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_2isoA03 (A:149-271)
2a: CATH_2isoA04 (A:272-334)
3a: CATH_2isoA01 (A:10-91)
4a: CATH_2isoA02 (A:92-148)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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)
[unclassified]
(117)
1a
2isoA03
A:149-271
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
[unclassified]
(116)
2a
2isoA04
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)
[unclassified]
(116)
3a
2isoA01
A:10-91
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
4a
2isoA02
A:92-148
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain D
Chain P
Chain T
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (81 KB)
Header - Asym.Unit
Biol.Unit 1 (76 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2ISO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help