Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48398.68 
• Atom Count: 3280 
• Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

3MBY

Ternary complex of DNA Polymerase BETA with template base A and 8oxodGTP in the active site with a dideoxy terminated primer

• DOI: 10.2210/pdb3MBY/pdb
• NDB: NA0492

• Classification: Transferase Lyase/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2010-03-26 Released: 2010-06-09 
• Deposition Author(s): Batra, V.K., Beard, W.A., Hou, E.W., Pedersen, L.C., Prasad, R., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.246 
• R-Value Work: 0.190 

Literature

Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site.

Batra, V.K., Beard, W.A., Hou, E.W., Pedersen, L.C., Prasad, R., Wilson, S.H.

(2010) Nat.Struct.Mol.Biol. 17: 889-890

• PubMed: 20526335 
• DOI: 10.1038/nsmb.1852


• PubMed Abstract: 
  

The major product of oxidative base damage is 8-oxo-7,8-dihydro-2'-deoxyguanine (8odG). The coding potential of this lesion is modulated by its glycosidic torsion angle that controls whether its Watson-Crick or Hoogsteen edge is used for base pairing. The 2.0-A structure of DNA polymerase (pol) beta bound with 8odGTP opposite template adenine indicates that the modified nucleotide assumes the mutagenic syn conformation and that the nonmutagenic anti conformation would be incompatible with efficient DNA synthesis.

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Organizational Affiliation: 

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase beta	A	335	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens) Go to Gene View: POLB Go to UniProtKB:  P06746

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	T	16	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')	P	10	N/A

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (5'-D(P*GP*TP*CP*GP*G)-3')	D	5	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
8DG	A	8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 BUZOGVVQWCXXDP-VPENINKCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DOC	P	DNA LINKING	C9 H14 N3 O6 P		DC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.246 
• R-Value Work: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 50.830	α = 90.00
b = 80.030	β = 107.70
c = 55.420	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
CNS	refinement
HKL-2000	data scaling
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-26 
• Released Date: 2010-06-09 
• Deposition Author(s): Batra, V.K., Beard, W.A., Hou, E.W., Pedersen, L.C., Prasad, R., Wilson, S.H.

Revision History 

• Version 1.0: 2010-06-09
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance