Equivalence class DNA_4.0_24656.1 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2VS7|1|B+ 2VS7|1|C (rep) | 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*CP*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3', 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3' | Desulfurococcus mucosus | The crystal structure of I-DmoI in complex with DNA and Ca | X-ray diffraction | 2.05 | 50 | 2008-11-11 | |||
| 2 | 2VS7|1|E+ 2VS7|1|F | 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*CP*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3', 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3' | Desulfurococcus mucosus | The crystal structure of I-DmoI in complex with DNA and Ca | X-ray diffraction | 2.05 | 50 | 2008-11-11 | |||
| 3 | 2VS7|1|H+ 2VS7|1|I | 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP *CP*TP*TP*AP*CP*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3', 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3' | Desulfurococcus mucosus | The crystal structure of I-DmoI in complex with DNA and Ca | X-ray diffraction | 2.05 | 50 | 2008-11-11 | |||
| 4 | 2V6E|1|C+ 2V6E|1|E+ 2V6E|1|D+ 2V6E|1|F | TELRL | Ravinvirus N15 | protelomerase TelK complexed with substrate DNA | X-ray diffraction | 3.2 | 88 | 2007-10-02 | |||
| 5 | 1R7M|1|C+ 1R7M|1|D | 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3', 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3' | The homing endonuclease I-SceI bound to its DNA recognition region | X-ray diffraction | 2.25 | 48 | 2004-10-26 | ||||
| 6 | 1R7M|1|E+ 1R7M|1|F | 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3', 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3' | The homing endonuclease I-SceI bound to its DNA recognition region | X-ray diffraction | 2.25 | 48 | 2004-10-26 | ||||
| 7 | 3C0X|1|D+ 3C0X|1|B+ 3C0X|1|C | DNA (5'-D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)-3'), DNA (5'-D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3'), DNA (5'-D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3') | I-SceI in complex with a top nicked DNA substrate | X-ray diffraction | 2.3 | 48 | 2008-05-06 | ||||
| 8 | 3OOR|1|C+ 3OOR|1|D | 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*CP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3', 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3' | I-SceI mutant (K86R/G100T)complexed with C/G+4 DNA substrate | X-ray diffraction | 2.5 | 48 | 2010-11-17 | ||||
| 9 | 2O93|1|A+ 2O93|1|B | kappaB enhancer element, DNA 25-mer | Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element | X-ray diffraction | 3.05 | 50 | 2007-06-19 | ||||
| 10 | 3OOL|1|C+ 3OOL|1|D | 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*CP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3', 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3' | I-SceI complexed with C/G+4 DNA substrate | X-ray diffraction | 2.3 | 48 | 2010-11-17 | ||||
| 11 | 1SKW|1|T+ 1SKW|1|P | 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3' | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template | X-ray diffraction | 2.3 | 18 | 2004-07-06 | ||||
| 12 | 1SL1|1|T+ 1SL1|1|P | 5'-D(*CP*CP*C*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*TP*(2DA))-3' | Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | X-ray diffraction | 2.2 | 19 | 2004-07-06 | ||||
| 13 | 1SL2|1|T+ 1SL2|1|P | 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*TP*(2DA))-3' | Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide | X-ray diffraction | 2.3 | 19 | 2004-07-06 | ||||
| 14 | 1SKS|1|T+ 1SKS|1|P | 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3' | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | X-ray diffraction | 2.3 | 23 | 2004-07-06 | ||||
| 15 | 2JA7|1|5+ 2JA7|1|4+ 2JA7|1|6 | 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TTP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3', 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3', 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' | synthetic construct | CPD lesion containing RNA Polymerase II elongation complex C | X-ray diffraction | 3.8 | 35 | 2007-02-20 | |||
| 16 | 2JA7|1|2+ 2JA7|1|1+ 2JA7|1|3 | 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TTP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3', 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3', 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' | synthetic construct | CPD lesion containing RNA Polymerase II elongation complex C | X-ray diffraction | 3.8 | 35 | 2007-02-20 | |||
| 17 | 2QFJ|1|C | DNA (5'-D(*DTP*DCP*DGP*DGP*DGP*DAP*DTP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DTP*DTP*DGP*DTP*DGP*DTP*DTP*DAP*DTP*DT)-3') | Crystal Structure of First Two RRM Domains of FIR Bound to ssDNA from a Portion of FUSE | X-ray diffraction | 2.1 | 4 | 2008-03-04 | ||||
| 18 | 2JA5|1|T+ 2JA5|1|P | 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TTP*TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3', 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' | synthetic construct | CPD lesion containing RNA Polymerase II elongation complex A | X-ray diffraction | 3.8 | 21 | 2007-02-20 | |||
| 19 | 1SL0|1|T+ 1SL0|1|P | 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3' | Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide | X-ray diffraction | 3.2 | 21 | 2004-07-06 | ||||
| 20 | 2P6R|1|X+ 2P6R|1|Y | 25-MER, 5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3' | Crystal structure of superfamily 2 helicase Hel308 in complex with unwound DNA | X-ray diffraction | 3 | 40 | 2007-06-12 | ||||
| 21 | 1SL0|1|U+ 1SL0|1|Q | 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3' | Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide | X-ray diffraction | 3.2 | 21 | 2004-07-06 | ||||
| 22 | 2JA8|1|T+ 2JA8|1|P | 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TP*TTP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3', 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*AP*UP)-3' | synthetic construct | CPD lesion containing RNA Polymerase II elongation complex D | X-ray diffraction | 3.8 | 29 | 2007-02-20 | |||
| 23 | 2O4I|1|D | 5'-D(*GP*CP*TP*AP*GP*GP*CP*AP*GP*GP*AP*AP*CP*CP*CP*CP*TP*CP*CP*TP*CP*CP*CP*CP*T)-3' | Structure of TREX1 in complex with DNA | X-ray diffraction | 3.5 | 4 | 2007-03-13 | ||||
| 24 | 2O4I|1|C | 5'-D(*GP*CP*TP*AP*GP*GP*CP*AP*GP*GP*AP*AP*CP*CP*CP*CP*TP*CP*CP*TP*CP*CP*CP*CP*T)-3' | Structure of TREX1 in complex with DNA | X-ray diffraction | 3.5 | 4 | 2007-03-13 | ||||
| 25 | 1SAX|1|C+ 1SAX|1|D | 5'-d(CAAAATTACAACTGTAATATCGGAG)-3', 5'-d(GCTCCGATATTACAGTTGTAATTTT)-3' | Three-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA | X-ray diffraction | 2.8 | 50 | 2004-04-27 | ||||
| 26 | 1Z63|1|C+ 1Z63|1|D | 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3', 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3' | Sulfolobus solfataricus SWI2/SNF2 ATPase core in complex with dsDNA | X-ray diffraction | 3 | 39 | 2005-05-17 | ||||
| 27 | 1Z63|1|E+ 1Z63|1|F | 5'-D(*AP*AP*AP*AP*AP*A*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP*AP*AP*AP*A)-3', 5'-D(*TP*TP*TP*TP*TP*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*TP*TP*TP*TP*TP*T)-3' | Sulfolobus solfataricus SWI2/SNF2 ATPase core in complex with dsDNA | X-ray diffraction | 3 | 39 | 2005-05-17 | ||||
| 28 | 2JA6|1|T+ 2JA6|1|P | 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TTP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3', 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' | synthetic construct | CPD lesion containing RNA Polymerase II elongation complex B | X-ray diffraction | 4 | 29 | 2007-02-20 |
Release history
| Release | 0.6 |
|---|---|
| Date | 2011-03-05 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.
| #S | View | PDB | Title | Method | Resolution | #NTs | NAKB NA annotation | NAKB protein annotation |
|---|---|---|---|---|---|---|---|---|
| 1 | 2VS7|1|B+ 2VS7|1|C | The crystal structure of I-DmoI in complex with DNA and Ca | X-RAY DIFFRACTION | 2.05 | 50 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 2 | 2VS7|1|H+ 2VS7|1|I | The crystal structure of I-DmoI in complex with DNA and Ca | X-RAY DIFFRACTION | 2.05 | 50 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 3 | 2VS7|1|E+ 2VS7|1|F | The crystal structure of I-DmoI in complex with DNA and Ca | X-RAY DIFFRACTION | 2.05 | 50 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 4 | 2O4I|1|C | Structure of TREX1 in complex with DNA | X-RAY DIFFRACTION | 3.5 | 4 | enzyme,hydrolase,nuclease | ||
| 5 | 2O4I|1|D | Structure of TREX1 in complex with DNA | X-RAY DIFFRACTION | 3.5 | 4 | enzyme,hydrolase,nuclease | ||
| 6 | 1R7M|1|C+ 1R7M|1|D | The homing endonuclease I-SceI bound to its DNA recognition region | X-RAY DIFFRACTION | 2.25 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 7 | 3OOL|1|C+ 3OOL|1|D | I-SceI complexed with C/G+4 DNA substrate | X-RAY DIFFRACTION | 2.3 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 8 | 3OOR|1|C+ 3OOR|1|D | I-SceI mutant (K86R/G100T)complexed with C/G+4 DNA substrate | X-RAY DIFFRACTION | 2.5 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 9 | 1R7M|1|E+ 1R7M|1|F | The homing endonuclease I-SceI bound to its DNA recognition region | X-RAY DIFFRACTION | 2.25 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 10 | 3C0X|1|D+ 3C0X|1|B+ 3C0X|1|C | I-SceI in complex with a top nicked DNA substrate | X-RAY DIFFRACTION | 2.3 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 11 | 2O93|1|A+ 2O93|1|B | Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element | X-RAY DIFFRACTION | 3.05 | 50 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 12 | 2V6E|1|C+ 2V6E|1|E+ 2V6E|1|D+ 2V6E|1|F | protelomerase TelK complexed with substrate DNA | X-RAY DIFFRACTION | 3.2 | 88 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 13 | 1SAX|1|C+ 1SAX|1|D | Three-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA | X-RAY DIFFRACTION | 2.8 | 50 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 14 | 1Z63|1|E+ 1Z63|1|F | Sulfolobus solfataricus SWI2/SNF2 ATPase core in complex with dsDNA | X-RAY DIFFRACTION | 3 | 39 | B-form double helix,double helix,structure | enzyme,helicase,hydrolase | |
| 15 | 1SL2|1|T+ 1SL2|1|P | Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide | X-RAY DIFFRACTION | 2.3 | 19 | B-form double helix,double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 16 | 1Z63|1|C+ 1Z63|1|D | Sulfolobus solfataricus SWI2/SNF2 ATPase core in complex with dsDNA | X-RAY DIFFRACTION | 3 | 39 | B-form double helix,double helix,structure | enzyme,helicase,hydrolase | |
| 17 | 1SKS|1|T+ 1SKS|1|P | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | X-RAY DIFFRACTION | 2.3 | 23 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 18 | 1SKW|1|T+ 1SKW|1|P | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template | X-RAY DIFFRACTION | 2.3 | 18 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 19 | 1SL0|1|T+ 1SL0|1|P | Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide | X-RAY DIFFRACTION | 3.2 | 21 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 20 | 1SL0|1|U+ 1SL0|1|Q | Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide | X-RAY DIFFRACTION | 3.2 | 21 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 21 | 1SL1|1|T+ 1SL1|1|P | Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | X-RAY DIFFRACTION | 2.2 | 19 | double helix,structure | enzyme,oxidoreductase,polymerase,transferase | |
| 22 | 2P6R|1|X+ 2P6R|1|Y | Crystal structure of superfamily 2 helicase Hel308 in complex with unwound DNA | X-RAY DIFFRACTION | 3 | 40 | enzyme,helicase,hydrolase | ||
| 23 | 2JA6|1|T+ 2JA6|1|P | CPD lesion containing RNA Polymerase II elongation complex B | X-RAY DIFFRACTION | 4 | 29 | enzyme,polymerase,transferase | ||
| 24 | 2JA7|1|5+ 2JA7|1|4+ 2JA7|1|6 | CPD lesion containing RNA Polymerase II elongation complex C | X-RAY DIFFRACTION | 3.8 | 35 | enzyme,polymerase,transferase | ||
| 25 | 2JA7|1|2+ 2JA7|1|1+ 2JA7|1|3 | CPD lesion containing RNA Polymerase II elongation complex C | X-RAY DIFFRACTION | 3.8 | 35 | enzyme,polymerase,transferase | ||
| 26 | 2JA5|1|T+ 2JA5|1|P | CPD lesion containing RNA Polymerase II elongation complex A | X-RAY DIFFRACTION | 3.8 | 21 | A-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 27 | 2QFJ|1|C | Crystal Structure of First Two RRM Domains of FIR Bound to ssDNA from a Portion of FUSE | X-RAY DIFFRACTION | 2.1 | 4 | post-transcriptional,regulatory,splicing | ||
| 28 | 2JA8|1|T+ 2JA8|1|P | CPD lesion containing RNA Polymerase II elongation complex D | X-RAY DIFFRACTION | 3.8 | 29 | enzyme,polymerase,transferase |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.
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