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- PDB-4nm2: Structure of human DNA polymerase beta complexed with a nicked DN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nm2 | ||||||
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Title | Structure of human DNA polymerase beta complexed with a nicked DNA containing a 8BrG-G at N-1 position and G-C at N position | ||||||
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![]() | TRANSFERASE / LYASE/DNA / DNA binding / helix-turn-helix motif / polymerase fold / nucleotidyl transferase / nucleus / LYASE-DNA complex | ||||||
Function / homology | ![]() Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / response to gamma radiation / base-excision repair / spindle microtubule / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / microtubule / in utero embryonic development / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Koag, M.-C. / Min, K. / Monzingo, A.F. / Lee, S. | ||||||
![]() | ![]() Title: Structural basis for promutagenicity of 8-halogenated Guanine. Authors: Koag, M.C. / Min, K. / Lee, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m2yC ![]() 4m47C ![]() 4nlkC ![]() 4nlnC ![]() 4nlzC ![]() 4nm1C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37536.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 4948.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template |
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#3: DNA chain | Mass: 3390.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: up primer |
#4: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: down primer |
-Non-polymers , 2 types, 67 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: 14-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.524→52.812 Å / Num. all: 15453 / Num. obs: 14617 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Highest resolution: 2.524 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.828 Å2
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Refinement step | Cycle: LAST / Resolution: 2.524→52.81 Å
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