DNA polymerase 3D structures: Difference between revisions

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Michal Harel (talk | contribs)
32,820 edits
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*DNA polymerase I
*DNA polymerase I


**[[1taq]] – TaDpo I - Thermus aquaticus<br />
**[[1taq]] – TaDpo I - ''Thermus aquaticus''<br />
**[[1jxe]] – TaDpo I Stoffel fragment 290-832<br />
**[[1jxe]] – TaDpo I Stoffel fragment 290-832<br />
**[[5ktq]] – TaDpo I Stoffel fragment + nucleotide<br />
**[[5ktq]] – TaDpo I Stoffel fragment + nucleotide<br />
Line 13: Line 13:
**[[5oxj]] – TaDpo I + DNA + GMP derivative + imidazole derivative<br />
**[[5oxj]] – TaDpo I + DNA + GMP derivative + imidazole derivative<br />
**[[3ojs]], [[3oju]], [[1tau]], [[4dle]], [[4dlg]], [[4elt]], [[4elu]], [[4elv]] - TaDpo I + DNA<br />
**[[3ojs]], [[3oju]], [[1tau]], [[4dle]], [[4dlg]], [[4elt]], [[4elu]], [[4elv]] - TaDpo I + DNA<br />
**[[4flt]], [[4flu]], [[4flv]], [[4flw]], [[4flx]], [[4fly]], [[4flz]], [[4fm0]], [[4fm1]], [[4fm2]] – PaDpo I + DNA – Pyrococcus abyssi<br />
**[[4flt]], [[4flu]], [[4flv]], [[4flw]], [[4flx]], [[4fly]], [[4flz]], [[4fm0]], [[4fm1]], [[4fm2]] – PaDpo I + DNA – ''Pyrococcus abyssi<''br />
**[[1s5j]] – SsDpo I - Sulfolobus solfataricus<br />
**[[1s5j]] – SsDpo I - ''Sulfolobus solfataricus''<br />
**[[6dsy]], [[6dsx]], [[6dsw]], [[6dsv]], [[6dsu]], [[7k5o]], [[7k5p]], [[7k5r]], [[7k5q]], [[7k5s]], [[7k5t]], [[7k5u]] - GsDpo I + DNA - Geobacillus stearothermophilus<br />
**[[6dsy]], [[6dsx]], [[6dsw]], [[6dsv]], [[6dsu]], [[7k5o]], [[7k5p]], [[7k5r]], [[7k5q]], [[7k5s]], [[7k5t]], [[7k5u]] - GsDpo I + DNA - ''Geobacillus stearothermophilus''<br />
**[[3eyz]], [[6p5c]] - GsDpo I (mutant) + DNA <br />
**[[3eyz]], [[6p5c]] - GsDpo I (mutant) + DNA <br />
**[[6mu5]], [[6mu4]], [[6ur2]], [[6ur4]] - GsDpo I + DNA + nucleotide derivative <br />
**[[6mu5]], [[6mu4]], [[6ur2]], [[6ur4]] - GsDpo I + DNA + nucleotide derivative <br />
**[[3ez5]], [[6ueu]], [[6ur9]], [[6us5]] - GsDpo I (mutant) + DNA + nucleotide <br />
**[[3ez5]], [[6ueu]], [[6ur9]], [[6us5]] - GsDpo I (mutant) + DNA + nucleotide <br />
**[[3pv8]], [[3px0]], [[3px4]], [[3px6]], [[4dqi]], [[4dqp]], [[4dqq]], [[4dqr]], [[4dqs]], [[4ds4]], [[4ds5]], [[4dse]], [[4dsf]], [[4e0d]], [[4ez6]], [[4ez9]], [[4f2r]], [[4f2s]], [[4f3o]], [[4f4k]], [[4f8r]] - GkDpo I (mutant) + DNA – Geobacillus kaustophilus<br />
**[[3pv8]], [[3px0]], [[3px4]], [[3px6]], [[4dqi]], [[4dqp]], [[4dqq]], [[4dqr]], [[4dqs]], [[4ds4]], [[4ds5]], [[4dse]], [[4dsf]], [[4e0d]], [[4ez6]], [[4ez9]], [[4f2r]], [[4f2s]], [[4f3o]], [[4f4k]], [[4f8r]] - GkDpo I (mutant) + DNA – Geobacillus kaustophilus<br />
**[[6vdc]], [[6vde]] – MsPol I – Mycobacterium smegmatis<br />
**[[6vdc]], [[6vde]] – MsPol I – ''Mycobacterium smegmatis''<br />
**[[6vdd]] - MsDpo I + DNA + nucleotide derivative <br />
**[[6vdd]] - MsDpo I + DNA + nucleotide derivative <br />
**[[7pbk]] – Dpo I – Vibrio phage<br />
**[[7pbk]] – Dpo I – Vibrio phage<br />
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*DNA polymerase I klenow fragment or Taq polymerase
*DNA polymerase I klenow fragment or Taq polymerase


**[[2kzz]], [[1d8y]], [[2kzm]] – EcDpo I - Escherichia coli<br />
**[[2kzz]], [[1d8y]], [[2kzm]] – EcDpo I - ''Escherichia coli''<br />
**[[1qsl]] - EcDpo I  + DNA<br />
**[[1qsl]] - EcDpo I  + DNA<br />
**[[1kfs]], [[1krp]], [[1ksp]], [[1kln]] - EcDpo I  (mutant) + DNA<br />
**[[1kfs]], [[1krp]], [[1ksp]], [[1kln]] - EcDpo I  (mutant) + DNA<br />
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**[[3k5n]] - EcDpo II (mutant) + DNA<br />
**[[3k5n]] - EcDpo II (mutant) + DNA<br />
**[[3k5o]], [[1q8i]] - EcDpo II (mutant) <br />
**[[3k5o]], [[1q8i]] - EcDpo II (mutant) <br />
**[[3o59]], [[5bkh]] - PhDpo II large subunit - Pyrococcus horikoshii<br />
**[[3o59]], [[5bkh]] - PhDpo II large subunit - ''Pyrococcus horikoshii<''br />
**[[2kxe]] - PhDpo II small subunit<br />
**[[2kxe]] - PhDpo II small subunit<br />
**[[1qqc]] – DeDpo II – Desulfurococcus<br />
**[[1qqc]] – DeDpo II – ''Desulfurococcus''<br />
**[[5ijl]] - PaDpo II large subunit <br />
**[[5ijl]] - PaDpo II large subunit <br />
**[[5ihe]] - PaDpo II small subunit <br />
**[[5ihe]] - PaDpo II small subunit <br />
**[[6hmf]] - PaDpo II small subunit (mutant)<br />
**[[6hmf]] - PaDpo II small subunit (mutant)<br />
**[[6hms]] - PaDpo II small+large subunits + DNA – Cryo EM <br />
**[[6hms]] - PaDpo II small+large subunits + DNA – Cryo EM <br />
**[[6knb]], [[6knc]] - TkPol II small+large subunits + PCNA + DNA - Thermococcus kodakarensis – Cryo EM <br />
**[[6knb]], [[6knc]] - TkPol II small+large subunits + PCNA + DNA - ''Thermococcus kodakarensis'' – Cryo EM <br />
**[[7rsr]], [[7rss]], [[7rsu]], [[7tqw]] - TkPol + purine derivative + DNA <br />
**[[7rsr]], [[7rss]], [[7rsu]], [[7tqw]] - TkPol + purine derivative + DNA <br />
**[[7om3]], [[7omb]], [[7omg]] - TkPol + DNA + nucleotide<br />
**[[7om3]], [[7omb]], [[7omg]] - TkPol + DNA + nucleotide<br />
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**[[2hnh]], [[2hqa]] - EcDpo III subunit alpha catalytic fragment<br />
**[[2hnh]], [[2hqa]] - EcDpo III subunit alpha catalytic fragment<br />
**[[4jom]] - EcDpo III alpha subunit catalytic fragment (mutant)<br />
**[[4jom]] - EcDpo III alpha subunit catalytic fragment (mutant)<br />
**[[5m1s]], [[5fkw]], [[5fkv]], [[5fku]] - EcDpo III (mutant) subunits + DNA – Cryo EM<br />
**[[5m1s]], [[5fkw]], [[5fkv]], [[5fku]] - EcDpo III alpha (mutant) beta, epsilon subunits + DNA – Cryo EM<br />
**[[1ok7]] - EcDpo III residues 1-366 + EcDpo IV C-terminal<br />
**[[1ok7]] - EcDpo III residues 1-366 + EcDpo IV C-terminal<br />
**[[2hpi]], [[2hpm]] - TaDpo III alpha subunit<br />
**[[2hpi]], [[2hpm]] - TaDpo III alpha subunit<br />
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**[[6dlk]] - RrDpo III beta subunit – ''Rickettsia rickettsii''<br />
**[[6dlk]] - RrDpo III beta subunit – ''Rickettsia rickettsii''<br />
**[[6d47]] - MmDpo III beta subunit – ''Mycobacterium marinum''<br />
**[[6d47]] - MmDpo III beta subunit – ''Mycobacterium marinum''<br />
**[[1jqj]], [[1jql]] - EcDpo III subunit (mutant) <br />
**[[1jqj]], [[1jql]] - EcDpo III subunit beta,delta(mutant) <br />
**[[4tr6]] - Pol III beta subunit – Bacillus subtilis<br />
**[[4tr6]] - Pol III beta subunit – Bacillus subtilis<br />
**[[3p16]], [[3rb9]], [[4tr7]] - MtPol III beta subunit <br />
**[[3p16]], [[3rb9]], [[4tr7]] - MtPol III beta subunit <br />
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**[[5c51]], [[5c52]], [[5c53]] - hDpo III gamma subunit + DNA + nucleotide<br />
**[[5c51]], [[5c52]], [[5c53]] - hDpo III gamma subunit + DNA + nucleotide<br />
**[[1njf]], [[1njg]] - EcDpo III subunit  N-terminal domains 1-2<br />
**[[1njf]], [[1njg]] - EcDpo III subunit gamma N-terminal domains 1-2<br />
**[[2gno]] - TmDpo III gamma subunit<br />
**[[2gno]] - TmDpo III gamma subunit<br />
**[[1xxh]], [[1jr3]] - EcDpo III subunit ’ <br />
**[[1xxh]], [[1jr3]] - EcDpo III subunit gamma, delta,delta’ <br />
**[[1xxi]] - EcDpo III subunit ’ + nucleotide<br />
**[[1xxi]] - EcDpo III subunit gamma, delta,delta’ + nucleotide<br />


*DNA polymerase III subunit delta
*DNA polymerase III subunit delta


**[[1jqj]], [[1jql]] - EcDpo III subunit (mutant) <br />
**[[1jqj]], [[1jql]] - EcDpo III subunit beta,delta(mutant) <br />
**[[1a5t]] - EcDpo III subunit delta’ <br />
**[[1a5t]] - EcDpo III subunit delta’ <br />
**[[1xxh]], [[1jr3]] - EcDpo III subunit ’ <br />
**[[1xxh]], [[1jr3]] - EcDpo III subunit gamma, delta,delta’ <br />
**[[1xxi]] - EcDpo III subunit ’ + nucleotide<br />
**[[1xxi]] - EcDpo III subunit gamma, delta,delta’ + nucleotide<br />
**[[3glh]] - EcDpo III subunit ’<br />
**[[3glh]] - EcDpo III subunit delta,delta’,tau<br />
**[[3glf]] - EcDpo III subunit ’ DNA<br />
**[[3glf]] - EcDpo III subunitdelta,delta’,tau + DNA<br />
**[[3gli]] - EcDpo III subunit ’ DNA<br />
**[[3gli]] - EcDpo III subunit delta,delta’,tau, zeta + DNA<br />
**[[3glg]] - EcDpo III subunit ’mutant DNA<br />
**[[3glg]] - EcDpo III subunit delta,delta’,tau(mutant) + DNA<br />


*DNA polymerase III subunit epsilon
*DNA polymerase III subunit epsilon
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**[[2gui]] – EcDpo III subunit epsilon N-terminal<br />
**[[2gui]] – EcDpo III subunit epsilon N-terminal<br />
**[[1j53]], [[1j54]] - EcDpo III subunit epsilon N-terminal exonuclease domain<br />
**[[1j53]], [[1j54]] - EcDpo III subunit epsilon N-terminal exonuclease domain<br />
**[[2ido]] - EcDpo III subunit + HOT protein<br />
**[[2ido]] - EcDpo III subunit epsilon+ HOT protein<br />
**[[4gx8]] - EcDpo III ε subunit/ EcDpo III α subunit<br />
**[[4gx8]] - EcDpo III ε subunit/ EcDpo III α subunit<br />
**[[4gx9]] - EcDpo III ε subunit/ EcDpo III α subunit (mutant)<br />
**[[4gx9]] - EcDpo III ε subunit/ EcDpo III α subunit (mutant)<br />
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