DNA polymerase: Difference between revisions
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== 3D Structures of DNA polymerase == | == 3D Structures of DNA polymerase == | ||
''Updated | ''Updated January 2013'' | ||
===Family A – replicative and repair Dpo=== | ===Family A – replicative and repair Dpo=== | ||
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[[1ktq]] - TaDpo I klenow fragment<br /> | [[1ktq]] - TaDpo I klenow fragment<br /> | ||
[[5ktq]] – TaDpo I + nucleotide<br /> | [[5ktq]] – TaDpo I + nucleotide<br /> | ||
[[3ojs]], [[3oju]], [[1tau]] - TaDpo I + DNA<br /> | [[3ojs]], [[3oju]], [[1tau]], [[4dle]], [[4dlg]] - TaDpo I + DNA<br /> | ||
[[3po4]], [[3po5]] - TaDpo I klenow fragment + DNA<br /> | [[3po4]], [[3po5]], [[3rtv]], [[3sv3]], [[3sv4]], [[3syz]], [[3sz2]]- TaDpo I klenow fragment + DNA<br /> | ||
[[3py8]] - TaDpo I klenow fragment (mutant) + DNA<br /> | [[3py8]] - TaDpo I klenow fragment (mutant) + DNA<br /> | ||
[[3m8r]], [[3m8s]], [[3lwl]], [[3lwm]], [[1qss]], [[1qsy]], [[1qtm]], [[2ktq]], [[3ktq]], [[4ktq]], [[3rr7]], [[3rr8]], [[3rrg]], [[3rrh]], [[3t3f]], [[4df4]], [[4df8]], [[4dfj]], [[4dfk]], [[4dfm]], [[4dfp]]- TaDpo I klenow fragment + DNA + nucleotide<br /> | [[3m8r]], [[3m8s]], [[3lwl]], [[3lwm]], [[1qss]], [[1qsy]], [[1qtm]], [[2ktq]], [[3ktq]], [[4ktq]], [[3rr7]], [[3rr8]], [[3rrg]], [[3rrh]], [[3t3f]], [[4df4]], [[4df8]], [[4dfj]], [[4dfk]], [[4dfm]], [[4dfp]]- TaDpo I klenow fragment + DNA + nucleotide<br /> | ||
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[[3cfo]] – EpDpo (mutant)<br /> | [[3cfo]] – EpDpo (mutant)<br /> | ||
[[1waf]], [[1waj]] - EpDpo + nucleotide<br /> | [[1waf]], [[1waj]] - EpDpo + nucleotide<br /> | ||
[[3nci]], [[3lds]], [[3l8b]], [[3cq8]],[[3cfp]], [[3cfr]], [[3kd1]], [[3kd5]] - EpDpo (mutant) + DNA<br /> | [[3uiq]], [[4dtj]], [[4dtm]], [[4dtn]], [[4dto]], [[4dtp]], [[4dtr]], [[4dts]], [[4dtu]], [[4dtx]], [[4du1]], [[4du3]], [[4du4]] - EpDpo + DNA<br /> | ||
[[3nci]], [[3lds]], [[3l8b]], [[3cq8]],[[3cfp]], [[3cfr]], [[3kd1]], [[3kd5]], [[4e3s]] - EpDpo (mutant) + DNA<br /> | |||
[[3ndk]], [[3ne6]], [[3ngi]], [[3nhg]], [[3nae]], [[3lzj]], [[3lzi]], [[2ozs]], [[2p5g]], [[2dy4]], [[1q9x]], [[1q9y]], [[1ig9]], [[3qep]], [[3rma]], [[3rmb]], [[3rmc]], [[3rmd]], [[3rwu]], [[3s9h]], [[3scx]], [[3si6]], [[3sjj]], [[3snn]], [[3spy]], [[3spz]], [[3sq0]], [[3sq1]], [[3sq2]], [[3sq4]], [[3sun]], [[3suo]], [[3sup]], [[3suq]], [[3tab]], [[3tae]], [[3taf]], [[3tag]]- EpDpo (mutant) + DNA + nucleotide<br /> | [[3ndk]], [[3ne6]], [[3ngi]], [[3nhg]], [[3nae]], [[3lzj]], [[3lzi]], [[2ozs]], [[2p5g]], [[2dy4]], [[1q9x]], [[1q9y]], [[1ig9]], [[3qep]], [[3rma]], [[3rmb]], [[3rmc]], [[3rmd]], [[3rwu]], [[3s9h]], [[3scx]], [[3si6]], [[3sjj]], [[3snn]], [[3spy]], [[3spz]], [[3sq0]], [[3sq1]], [[3sq2]], [[3sq4]], [[3sun]], [[3suo]], [[3sup]], [[3suq]], [[3tab]], [[3tae]], [[3taf]], [[3tag]]- EpDpo (mutant) + DNA + nucleotide<br /> | ||
[[1clq]], [[3iuq]] - EpDpo + DNA + nucleotide<br /> | [[1clq]], [[3iuq]] - EpDpo + DNA + nucleotide<br /> | ||
[[2oyq]], [[2ozm]], [[2p5o]], [[2dtu]], [[3qei]], [[3qer]], [[3qes]], [[3qet]], [[3qev]], [[3qew]], [[3qex]], [[3qnn]], [[3qno]]- EpDpo (mutant) + DNA + nucleotide analog<br /> | [[2oyq]], [[2ozm]], [[2p5o]], [[2dtu]], [[3qei]], [[3qer]], [[3qes]], [[3qet]], [[3qev]], [[3qew]], [[3qex]], [[3qnn]], [[3qno]], [[4fj5]], [[4fj7]], [[4fj8]], [[4fj9]], [[4fjg]], [[4fjh]], [[4fji]], [[4fjj]], [[4fjk]], [[4fjl]], [[4fjm]], [[4fjn]], [[4fjx]], [[4fk0]], [[4fk2]], [[4fk4]] - EpDpo (mutant) + DNA + nucleotide analog<br /> | ||
[[2atq]] – EpDpo + GP32<br /> | [[2atq]] – EpDpo + GP32<br /> | ||
[[1noy]] – T4Dpo + DNA - Enterobacteria phage T4<br /> | [[1noy]] – T4Dpo + DNA - Enterobacteria phage T4<br /> | ||
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[[2pyj]], [[2pyl]] - BpDpo (mutant) + DNA + nucleotide<br /> | [[2pyj]], [[2pyl]] - BpDpo (mutant) + DNA + nucleotide<br /> | ||
[[1xhx]] - BpDpo (mutant)<br /> | [[1xhx]] - BpDpo (mutant)<br /> | ||
[[4e2i]] – hDpo α subunit β + large T antigen<br /> | |||
[[2keb]] - hDpo αB - NMR <br /> | [[2keb]] - hDpo αB - NMR <br /> | ||
[[1n5g]], [[1k0p]], [[1k18]] - hDpo α zinc finger domain- NMR<br /> | [[1n5g]], [[1k0p]], [[1k18]] - hDpo α zinc finger domain- NMR<br /> | ||
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[[1qht]] - Dpo (mutant) – ''Thermococcus''<br /> | [[1qht]] - Dpo (mutant) – ''Thermococcus''<br /> | ||
[[1d5a]] – DeDpo – ''Desulfurococcus''<br /> | [[1d5a]] – DeDpo – ''Desulfurococcus''<br /> | ||
[[4flt]], [[4flu]], [[4flv]], [[4flw]], [[4flx]], [[4fly]], [[4flz]], [[4fm0]], [[4fm1]], [[4fm2]] – Dpo + DNA – ''Pyrococcus abyssi'' | |||
===Family C – bacterial chromosomal replicative Dpo=== | ===Family C – bacterial chromosomal replicative Dpo=== | ||
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[[3q8p]], [[3q8q]], [[3lk9]], [[3mby]], [[3isb]], [[3isc]], [[1zjm]], [[1tv9]], [[1tva]], [[1bpx]], [[1bpz]], [[1zqa]], [[1zqb]], [[1zqc]], [[1zqd]], [[1zqf]], [[1zqg]], [[1zqh]], [[1zqi]], [[1zaj]], [[1zqk]], [[1zql]], [[1zqm]], [[1zqn]], [[1zqo]], [[1zqp]], [[1zqq]], [[1zqr]], [[1zqs]], [[1zqt]], [[1zqu]], [[1zqv]], [[1zqw]], [[1zqx]], [[1zqy]], [[1zqz]], [[7ice]], [[7icf]], [[7ici]], [[7icj]], [[7icl]], [[7icm]], [[7icp]], [[7icr]], [[7ict]], [[7icu]], [[7icv]], [[8icb]], [[8icc]], [[9icj]], [[9ick]], [[9icl]], [[9icm]], [[9icp]], [[9icw]], [[9icx]], [[9icy]], [[7icg]], [[7ich]], [[7ick]], [[7icn]], [[7ico]], [[7icq]], [[7ics]], [[1zqe]] - hDpo β + DNA<br /> | [[3q8p]], [[3q8q]], [[3lk9]], [[3mby]], [[3isb]], [[3isc]], [[1zjm]], [[1tv9]], [[1tva]], [[1bpx]], [[1bpz]], [[1zqa]], [[1zqb]], [[1zqc]], [[1zqd]], [[1zqf]], [[1zqg]], [[1zqh]], [[1zqi]], [[1zaj]], [[1zqk]], [[1zql]], [[1zqm]], [[1zqn]], [[1zqo]], [[1zqp]], [[1zqq]], [[1zqr]], [[1zqs]], [[1zqt]], [[1zqu]], [[1zqv]], [[1zqw]], [[1zqx]], [[1zqy]], [[1zqz]], [[7ice]], [[7icf]], [[7ici]], [[7icj]], [[7icl]], [[7icm]], [[7icp]], [[7icr]], [[7ict]], [[7icu]], [[7icv]], [[8icb]], [[8icc]], [[9icj]], [[9ick]], [[9icl]], [[9icm]], [[9icp]], [[9icw]], [[9icx]], [[9icy]], [[7icg]], [[7ich]], [[7ick]], [[7icn]], [[7ico]], [[7icq]], [[7ics]], [[1zqe]] - hDpo β + DNA<br /> | ||
[[3jpn]], [[3jpo]], [[3jpp]], [[3jpq]], [[3jpr]], [[3jpt]], [[3jps]], [[3isd]], [[3c2k]], [[3c2l]], [[3c2m]], [[2pxi]], [[2iso]], [[2isp]], [[2i9g]], [[2fmp]], [[2fmq]], [[2fms]], [[1zjn]], [[1mq2]], [[1mq3]], [[1bpy]], [[8ica]], [[8ice]], [[8icf]], [[8icg]], [[8ich]], [[8ici]], [[8icj]], [[8ick]], [[8icl]], [[8icm]], [[8icn]], [[8ico]], [[8icp]], [[8icq]], [[8icr]], [[8ics]], [[8ict]], [[8icu]], [[8icv]], [[8icw]], [[8icx]], [[8icz]], [[9ice]], [[9icg]], [[9ich]], [[9ici]], [[9icq]], [[9ics]], [[9ict]], [[9icu]], [[9icv]], [[9icr]], [[9icn]], [[9ico]], [[8icy]], [[9ica]], [[9icb]], [[9icc]], [[9icf]] - hDpo β + DNA + nucleotide<br /> | [[3jpn]], [[3jpo]], [[3jpp]], [[3jpq]], [[3jpr]], [[3jpt]], [[3jps]], [[3isd]], [[3c2k]], [[3c2l]], [[3c2m]], [[2pxi]], [[2iso]], [[2isp]], [[2i9g]], [[2fmp]], [[2fmq]], [[2fms]], [[1zjn]], [[1mq2]], [[1mq3]], [[1bpy]], [[8ica]], [[8ice]], [[8icf]], [[8icg]], [[8ich]], [[8ici]], [[8icj]], [[8ick]], [[8icl]], [[8icm]], [[8icn]], [[8ico]], [[8icp]], [[8icq]], [[8icr]], [[8ics]], [[8ict]], [[8icu]], [[8icv]], [[8icw]], [[8icx]], [[8icz]], [[9ice]], [[9icg]], [[9ich]], [[9ici]], [[9icq]], [[9ics]], [[9ict]], [[9icu]], [[9icv]], [[9icr]], [[9icn]], [[9ico]], [[8icy]], [[9ica]], [[9icb]], [[9icc]], [[9icf]], [[4do9]], [[4doa]], [[4dob]], [[4doc]] - hDpo β + DNA + nucleotide<br /> | ||
[[2p66]] - hDpo β + DNA + nucleotide analog<br /> | [[2p66]], [[4f5n]] - hDpo β + DNA + nucleotide analog<br /> | ||
[[4f5o]], [[4f5p]], [[4f5q]], [[4f5r]] - hDpo β (mutant) + DNA + nucleotide analog<br /> | |||
[[3ogu]] - hDpo β (mutant) + DNA<br /> | [[3ogu]] - hDpo β (mutant) + DNA<br /> | ||
[[2v6z]] - hDpo β N-terminal (mutant) - NMR<br /> | [[2v6z]] - hDpo β N-terminal (mutant) - NMR<br /> | ||
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[[3pml]], [[3mdc]], [[1xsn]] - hDpo λ + DNA + nucleotide<br /> | [[3pml]], [[3mdc]], [[1xsn]] - hDpo λ + DNA + nucleotide<br /> | ||
[[3mgi]], [[3hw8]], [[3hwt]], [[3hx0]], [[2pfo]], [[2pfp]], [[2pfq]] - hDpo λ (mutant) + DNA + nucleotide<br /> | [[3mgi]], [[3hw8]], [[3hwt]], [[3hx0]], [[2pfo]], [[2pfp]], [[2pfq]] - hDpo λ (mutant) + DNA + nucleotide<br /> | ||
[[3upq]], [[3uq0]], [[3uq2]] - hDpo δ (mutant) + DNA<br /> | |||
[[4fo6]] - hDpo δ (mutant) + DNA + nucleotide analog<br /> | |||
[[2htf]], [[2dun]] - hDpo μ BRCT domain – NMR<br /> | [[2htf]], [[2dun]] - hDpo μ BRCT domain – NMR<br /> | ||
[[2ihm]] - mDpo μ catalytic domain + DNA – mouse<br /> | [[2ihm]] - mDpo μ catalytic domain + DNA – mouse<br /> | ||
[[1rpl]], [[2bpc]], [[1bpe]], [[1bpb]], [[1bpd]] - rDpo β – rat<br /> | [[1rpl]], [[2bpc]], [[1bpe]], [[1bpb]], [[1bpd]] - rDpo β – rat<br /> | ||
[[2van]], [[1jn3]] - rDpo β (mutant)<br /> | [[2van]], [[1jn3]], [[3uxo]] - rDpo β (mutant)<br /> | ||
[[1dk2]], [[1dk3]], [[1bno]], [[1bnp]] - rDpo β N-terminal – NMR<br /> | [[1dk2]], [[1dk3]], [[1bno]], [[1bnp]] - rDpo β N-terminal – NMR<br /> | ||
[[1nom]] - rDpo β C-terminal<br /> | [[1nom]] - rDpo β C-terminal<br /> | ||
[[1huo]], [[1huz]] - rDpo β + DNA<br /> | [[1huo]], [[1huz]] - rDpo β + DNA<br /> | ||
[[3uxp]], [[3v72]] - rDpo β (mutant) + DNA<br /> | |||
[[1bpe]] - rDpo β + nucleotide<br /> | [[1bpe]] - rDpo β + nucleotide<br /> | ||
[[2bpf]], [[2bpg]] - rDpo β + DNA + nucleotide<br /> | [[2bpf]], [[2bpg]] - rDpo β + DNA + nucleotide<br /> | ||
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[[2ebw]] – hRev1 BRCT domain – NMR<br /> | [[2ebw]] – hRev1 BRCT domain – NMR<br /> | ||
[[3bjy]], [[2aq4]] – yRev1 catalytic domain + DNA + nucleotide<br /> | [[3bjy]], [[2aq4]] – yRev1 catalytic domain + DNA + nucleotide<br /> | ||
[[3q8r]], [[3q8s]], [[3h4b]], [[3h4d]], [[3gv5]], [[3gv7]], [[3gv8]], [[3epg]], [[3epi]], [[2fll]], [[2fln]], [[2flp]], [[2dpi]], [[2dpj]], [[2alz]], [[1zet]], [[1t3n]] - hDpo τ + DNA + nucleotide<br /> | [[3q8r]], [[3q8s]], [[3h4b]], [[3h4d]], [[3gv5]], [[3gv7]], [[3gv8]], [[3epg]], [[3epi]], [[2fll]], [[2fln]], [[2flp]], [[2dpi]], [[2dpj]], [[2alz]], [[1zet]], [[1t3n]], [[4ebc]], [[4ebd]], [[4ebe]], [[4fs1]], [[4fs2]] - hDpo τ + DNA + nucleotide<br /> | ||
[[3ngd]], [[3osn]] - hDpo τ catalytic fragment + DNA<br /> | [[3ngd]], [[3osn]] - hDpo τ catalytic fragment + DNA<br /> | ||
[[3h40]] - hDpo τ DNA binding domain + DNA<br /> | [[3h40]] - hDpo τ DNA binding domain + DNA<br /> | ||
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[[3in5]] - hDpo κ + DNA<br /> | [[3in5]] - hDpo κ + DNA<br /> | ||
[[2w7o]], [[2w7p]], [[2oh2]], [[3pzp]] - hDpo κ + DNA + nucleotide<br /> | [[2w7o]], [[2w7p]], [[2oh2]], [[3pzp]] - hDpo κ + DNA + nucleotide<br /> | ||
[[2lsj]] - hDpo η + DNA repair protein REV1<br /> | |||
[[4ecq]], [[4ecr]], [[4ecs]], [[4ect]], [[4ecu]], [[4ecv]], [[4ecw]], [[4ecx]], [[4ecy]], [[4ecz]], [[4ed0]], [[4ed1]], [[4ed2]], [[4ed3]], [[4ed6]], [[4ed7]], [[4ed8]] - hDpo η + DNA + nucleotide<br /> | |||
[[2kwu]], [[2kwv]] - mDpo τ C-terminal + ubiquitin - NMR<br /> | [[2kwu]], [[2kwv]] - mDpo τ C-terminal + ubiquitin - NMR<br /> | ||
[[3ai4]] - mDpo τ/yEGFP<br /> | [[3ai4]] - mDpo τ/yEGFP<br /> | ||
[[1jih]] – yDpo η catalytic domain<br /> | [[1jih]] – yDpo η catalytic domain<br /> | ||
[[2lsk]] - mDpo κ + DNA repair protein REV1<br /> | |||
[[2rdi]] - SsDpo IV - ''Sulfolobus solfataricus''<br /> | [[2rdi]] - SsDpo IV - ''Sulfolobus solfataricus''<br /> | ||
[[3pr4]], [[3pr5]], [[2r8g]], [[2r8h]], [[2r8i]], [[2uvr]], [[2uvu]], [[2uvv]], [[2uvw]] - SsDpo IV (mutant) + DNA + nucleotide<br /> | [[3pr4]], [[3pr5]], [[2r8g]], [[2r8h]], [[2r8i]], [[2uvr]], [[2uvu]], [[2uvv]], [[2uvw]] - SsDpo IV (mutant) + DNA + nucleotide<br /> | ||
[[2xc9]], [[3m9m]], [[3m9n]], [[3m9o]], [[2v4q]], [[2v4r]], [[2ago]], [[1ryr]], [[1rys]], [[2w9a]], [[2w9b]], [[2w9c]], [[3gii]], [[3gij]], [[3gik]], [[3gil]], [[3gim]], [[3qz7]], [[3qz8]], [[3pvx]], [[3pw0]], [[3pw2]], [[3pw4]], [[3pw5]], [[3pw7]], [[3raq]], [[3rax]], [[3rb0]], [[3rb3]], [[3rb4]], [[3rb6]], [[3rbd]], [[3rbe]]- SsDpo IV + DNA<br /> | [[2xc9]], [[3m9m]], [[3m9n]], [[3m9o]], [[2v4q]], [[2v4r]], [[2ago]], [[1ryr]], [[1rys]], [[2w9a]], [[2w9b]], [[2w9c]], [[3gii]], [[3gij]], [[3gik]], [[3gil]], [[3gim]], [[3qz7]], [[3qz8]], [[3pvx]], [[3pw0]], [[3pw2]], [[3pw4]], [[3pw5]], [[3pw7]], [[3raq]], [[3rax]], [[3rb0]], [[3rb3]], [[3rb4]], [[3rb6]], [[3rbd]], [[3rbe]], [[4hyk]] - SsDpo IV + DNA<br /> | ||
[[2xca]], [[2xcp]], [[3khg]], [[3khh]], [[3khl]], [[3khr]], [[2w8k]], [[2w8l]], [[2rdj]], [[2v9w]], [[2va2]], [[2va3]], [[2ia6]], [[2ibk]], [[2jef]], [[2jeg]], [[2jei]], [[2jej]], [[2imw]], [[2j6s]], [[2j6t]], [[2j6u]], [[2asd]], [[2asj]], [[2asl]], [[2atl]], [[2au0]], [[2c22]], [[2c28]], [[2c2d]], [[2c2e]], [[2c2r]], [[2agp]], [[2agq]], [[2bqr]], [[2bqu]], [[2br0]], [[2bq3]], [[1s9f]], [[1s97]], [[1s0m]], [[1s0n]], [[1s0o]], [[1s10]], [[1n48]], [[1n56]], [[1jx4]], [[1jxl]], [[3t5h]], [[3t5j]], [[3t5k]], [[3t5l]], [[3v6h]], [[3v6j]], [[3v6k]] - SsDpo IV + DNA + nucleotide<br /> | [[2xca]], [[2xcp]], [[3khg]], [[3khh]], [[3khl]], [[3khr]], [[2w8k]], [[2w8l]], [[2rdj]], [[2v9w]], [[2va2]], [[2va3]], [[2ia6]], [[2ibk]], [[2jef]], [[2jeg]], [[2jei]], [[2jej]], [[2imw]], [[2j6s]], [[2j6t]], [[2j6u]], [[2asd]], [[2asj]], [[2asl]], [[2atl]], [[2au0]], [[2c22]], [[2c28]], [[2c2d]], [[2c2e]], [[2c2r]], [[2agp]], [[2agq]], [[2bqr]], [[2bqu]], [[2br0]], [[2bq3]], [[1s9f]], [[1s97]], [[1s0m]], [[1s0n]], [[1s0o]], [[1s10]], [[1n48]], [[1n56]], [[1jx4]], [[1jxl]], [[3t5h]], [[3t5j]], [[3t5k]], [[3t5l]], [[3v6h]], [[3v6j]], [[3v6k]], [[4gc6]], [[4gc7]] - SsDpo IV + DNA + nucleotide<br /> | ||
[[3fds]] – SsDpo IV + PCNA B + PCNA C<br /> | [[3fds]] – SsDpo IV + PCNA B + PCNA C<br /> | ||
[[3bq2]] – SaDpo IV + DNA – ''Sulfolobus acidocaldarius''<br /> | [[3bq2]] – SaDpo IV + DNA – ''Sulfolobus acidocaldarius''<br /> | ||
[[3bq1]] - SaDpo IV + DNA + nucleotide<br /> | [[3bq1]], [[4f4w]], [[4f4x]], [[4f4y]], [[4f4z]], [[4f50]] - SaDpo IV + DNA + nucleotide<br /> | ||
[[3bq0]] - SaDpo IV + DNA<br /> | [[3bq0]] - SaDpo IV + DNA<br /> | ||
[[4dez]] – Dpo IV – ''Mycobacterium smegmatis'' | |||
===Prokaryotic Pol I – DNA repair=== | ===Prokaryotic Pol I – DNA repair=== | ||
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[[3eyz]] - GsDpo I (mutant) + DNA <br /> | [[3eyz]] - GsDpo I (mutant) + DNA <br /> | ||
[[3ez5]] - GsDpo I (mutant) + DNA + nucleotide <br /> | [[3ez5]] - GsDpo I (mutant) + DNA + nucleotide <br /> | ||
[[3pv8]], [[3px0]], [[3px4]], [[3px6]] - GkDpo I (mutant) + DNA – ''Geobacillus kaustophilus'' | [[3pv8]], [[3px0]], [[3px4]], [[3px6]], [[4dqi]], [[4dqp]], [[4dqq]], [[4dqr]], [[4dqs]], [[4ds4]], [[4ds5]], [[4dse]], [[4dsf]], [[4e0d]] - GkDpo I (mutant) + DNA – ''Geobacillus kaustophilus'' | ||
===Prokaryotic Pol II – DNA repair=== | ===Prokaryotic Pol II – DNA repair=== | ||
