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- PDB-8icn: DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8icn | ||||||
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Title | DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF ATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) | ||||||
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![]() | TRANSFERASE/DNA / ![]() ![]() ![]() ![]() | ||||||
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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pelletier, H. / Sawaya, M.R. | ||||||
![]() | ![]() Title: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #1: ![]() Title: Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates Authors: Sawaya, M.R. / Rawson, T. / Wilson, S.H. / Kraut, J. / Pelletier, H. #2: ![]() Title: The Role of Thumb Movement and Template Bending in Polymerase Fidelity Authors: Pelletier, H. #3: ![]() Title: Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J. #4: ![]() Title: Characterization of the Metal Ion-Binding HHH Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis Authors: Pelletier, H. / Sawaya, M.R. #6: ![]() Title: Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP Authors: Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J. #7: ![]() Title: Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism Authors: Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.5 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zqtC ![]() 7iceC ![]() 7icfC ![]() 7icgC ![]() 7ichC ![]() 7iciC ![]() 7icjC ![]() 7ickC ![]() 7iclC ![]() 7icmC ![]() 7icnC ![]() 7icoC ![]() 7icpC ![]() 7icqC ![]() 7icrC ![]() 7icsC ![]() 7ictC ![]() 7icuC ![]() 7icvC ![]() 8icjC ![]() 8ickC ![]() 8iclC ![]() 8icmC ![]() 8icoC ![]() 8icpC ![]() 8icqC ![]() 8icrC ![]() 8icsC ![]() 8ictC ![]() 8icuC ![]() 8icvC ![]() 8icwC ![]() 8icxC ![]() 8icyC ![]() 9icfC ![]() 9ickC ![]() 9icnC ![]() 9icoC ![]() 9icpC ![]() 9icqC ![]() 9icrC ![]() 9icsC ![]() 9ictC ![]() 9icuC ![]() 9icvC ![]() 8icbS C: citing same article ( S: Starting model for refinement |
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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
-DNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 2434.643 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2425.629 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 38241.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 140 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MN / | ||||
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#5: Chemical | #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
-Details
Compound details | A POSSIBLE PHYSIOLOGICAL SUBSTRATE FOR POL BETA IS A DNA GAP, WHERE THE LENGTH OF THE GAP CAN RANGE ...A POSSIBLE PHYSIOLOGI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.4 % |
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Crystal grow![]() | pH: 6.5 Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE ...Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Mar 18, 1995 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 11624 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rsym value: 0.043 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.3 % / Rsym value: 0.139 / % possible all: 85 |
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Processing
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Refinement | Method to determine structure![]() Starting model: 8ICB Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
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Solvent computation | Solvent model: MOEWS / Bsol: 566.4 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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