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Dioxygenase 3D structures

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Line 94: Line 94:
**[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
**[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
**[[4zhn]] – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide<br />
**[[4zhn]] – EcAlkb (mutant) + Co+2 + oxoglutarate + trinucleotide<br />
 +
**[[6ypv]] – EcAlkb + Fe+3 + oxoglutarate <br />
**[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
**[[2fd8]] – EcAlkb (mutant) + Fe+2 + oxoglutarate <br />
 +
**[[6y0q]] – EcAlkb + Fe+3 + oxoglutarate + pyrimidine derivative<br />
**[[6f9p]] – FlAlkb + Re+2 - ''Flavobacterium''<br />
**[[6f9p]] – FlAlkb + Re+2 - ''Flavobacterium''<br />
**[[6exf]] – FlAlkb + Fe+3 + lysine <br />
**[[6exf]] – FlAlkb + Fe+3 + lysine <br />
Line 167: Line 169:
**[[6kun]] – DAO + oxoglutarate – rice<br />
**[[6kun]] – DAO + oxoglutarate – rice<br />
 +
 +
* Iron/α-ketoglutarate-dependent dioxygenase (AsqJ)
 +
 +
**[[5dav]] – AnAsqJ + Ni+2 + cyclopeptin – ''Aspergillus nidulans''<br />
 +
**[[5oa4]], [[5oa7]], [[5oa8]], [[6eoz]] – AnAsqJ (mutant) + Ni+2 + cyclopeptin <br />
 +
**[[5dap]] – AnAsqJ + Ni+2 + oxoglutarate<br />
 +
**[[5daq]], [[5daw]], [[5dax]], [[5y7r]], [[5y7t]] – AnAsqJ + Fe+3 + cyclopeptin + oxoglutarate<br />
 +
**[[6k0e]] – AnAsqJ + Fe+3 + O2 + cyclopeptin + oxoglutarate<br />
 +
**[[6k0f]] – AnAsqJ + Fe+3 + H2O2 + cyclopeptin + oxoglutarate<br />
 +
**[[6jzm]], [[6k30]], [[6kd9]] – AnAsqJ + Fe+3 + cyclopeptin + succinate<br />
*Leucoanthocyanidin dioxygenase (LACD)
*Leucoanthocyanidin dioxygenase (LACD)
Line 290: Line 302:
**[[4pw8]] - hTDO + Co+2 <br />
**[[4pw8]] - hTDO + Co+2 <br />
-
**[[5tia]], [[5ti9]] – hTDO + heme + tryptophan <br />
+
**[[5tia]], [[5ti9]] – hTDO + heme + Trp <br />
**[[6pyy]], [[6pyz]], [[6vbn]] – hTDO + heme + inhibitor<br />
**[[6pyy]], [[6pyz]], [[6vbn]] – hTDO + heme + inhibitor<br />
-
**[[6a4i]] – hTDO + heme + tryptophan + inhibitor<br />
+
**[[6a4i]] – hTDO + heme + Trp + inhibitor<br />
 +
**[[6ud5]] – hTDO + heme + Trp + CO<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
**[[1yw0]] – XcTDO + Mg – ''Xanthomonas campestris''<br />
**[[2nw7]] – XcTDO + heme <br />
**[[2nw7]] – XcTDO + heme <br />
**[[4hka]] – TDO + heme – ''Drosophila melanogaster''<br />
**[[4hka]] – TDO + heme – ''Drosophila melanogaster''<br />
-
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + tryptophan <br />
+
**[[3bk9]], [[3e08]] – XcTDO (mutant) + heme + Trp <br />
-
**[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + tryptophan derivative<br />
+
**[[2nw8]], [[2nw9]] – XcTDO + heme + Mn + Trp derivative<br />
**[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
**[[2nox]] – CmTDO + heme – ''Cupriavidus metallidurans''<br />
Line 321: Line 334:
**[[4xf3]] – rCysDO (mutant) + Fe+3 + inhibitor + cysteine<br />
**[[4xf3]] – rCysDO (mutant) + Fe+3 + inhibitor + cysteine<br />
**[[2q4s]], [[2atf]] – mCysDO + Ni+2 <br />
**[[2q4s]], [[2atf]] – mCysDO + Ni+2 <br />
 +
**[[6xb9]] – AvCysDO + Fe+3 + hydroxyl propionic acid – ''Azotobacter vinelandii'' <br />
 +
**[[7kov]] – AvCysDO + Fe+3 + SCN<br />
*4-hydroxyphenylpyruvate dioxygenase (HPPD)
*4-hydroxyphenylpyruvate dioxygenase (HPPD)
Line 329: Line 344:
**[[1t47]] – HPPD + Fe+2 – ''Streptomyces avermitilis''<br />
**[[1t47]] – HPPD + Fe+2 – ''Streptomyces avermitilis''<br />
**[[3zgj]] – HPPD + Co+2 + mandelic acid – ''Streptomyces coelicolor''<br />
**[[3zgj]] – HPPD + Co+2 + mandelic acid – ''Streptomyces coelicolor''<br />
-
**[[1sqd]], [[1sp9]] – AtHPPD + Fe+3 <br />
+
**[[1sqd]], [[1sp9]], [[6j63]] – AtHPPD + Fe+3 <br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
**[[1tfz]], [[1tg5]], [[6j63]], [[5ywh]], [[5ywg]] - AtHPPD + Fe+3 + inhibitor <br />
-
**[[6jx9]] – AtHPPD + Co+2 + inhibitor <br />
+
**[[6jx9]], [[6lgt]], [[6m6d]] – AtHPPD + Co+2 + inhibitor <br />
**[[5xgk]] – AtHPPD + Fe+3 + hydroxyphenylpyruvate <br />
**[[5xgk]] – AtHPPD + Fe+3 + hydroxyphenylpyruvate <br />
-
**[[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
+
**[[5dhw]], [[6isd]] – AtHPPD + Fe+3 + sulcotrione <br />
**[[5yy7]], [[5yy6]], [[5ywk]] – AtHPPD + Co+2 + benquitrione <br />
**[[5yy7]], [[5yy6]], [[5ywk]] – AtHPPD + Co+2 + benquitrione <br />
**[[5ywi]] – AtHPPD (mutant) + Co+2 + NTBC <br />
**[[5ywi]] – AtHPPD (mutant) + Co+2 + NTBC <br />
Line 370: Line 385:
**[[3fe5]] – HAD + Fe+3 - bovine<br />
**[[3fe5]] – HAD + Fe+3 - bovine<br />
**[[1zvf]] – HAD + Ni+2 - yeast<br />
**[[1zvf]] – HAD + Ni+2 - yeast<br />
-
**[[5v28]], [[4r52]] – CmHAD + Fe+2 – ''Cupriavidus metallidurans''<br />
+
**[[5v28]], [[4r52]], [[6vi5]] – CmHAD + Fe+2 – ''Cupriavidus metallidurans''<br />
**[[5v27]], [[5v26]], [[6d60]], [[6bvr]], [[6bvp]] – CmHAD (mutant) + Fe+2 <br />
**[[5v27]], [[5v26]], [[6d60]], [[6bvr]], [[6bvp]] – CmHAD (mutant) + Fe+2 <br />
**[[1yfu]], [[4hvq]], [[4hvr]], [[4i3p]], [[4l2n]] – CmHAD + Fe+3<br />
**[[1yfu]], [[4hvq]], [[4hvr]], [[4i3p]], [[4l2n]] – CmHAD + Fe+3<br />
Line 379: Line 394:
**[[1yfy]] – CmHAD + Fe+3 + hydroxyanthranilate<br />
**[[1yfy]] – CmHAD + Fe+3 + hydroxyanthranilate<br />
**[[6d62]], [[6d61]], [[6cd3]], [[6bvs]], [[6bvq]] – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative<br />
**[[6d62]], [[6d61]], [[6cd3]], [[6bvs]], [[6bvq]] – CmHAD (mutant) + Fe+2 + hydroxyanthranilate derivative<br />
 +
**[[6vi6]], [[6vi8]], [[6vi9]], [[6vib]], [[6x11]] – CmHAD + Fe+2 + inhibitor<br />
 +
**[[6via]] – CmHAD + Fe+2 + Fe+3 + OH + dihydroxepine derivative<br />
**[[4wzc]] – HAD + Fe+2 + enedioate derivative – ''Ralstonia metallidurans''<br />
**[[4wzc]] – HAD + Fe+2 + enedioate derivative – ''Ralstonia metallidurans''<br />
Line 451: Line 468:
* 1,2-dihydroxy-3-keto-methylthiopentene dioxygenase (KMTPD) or acereductone dioxygenase
* 1,2-dihydroxy-3-keto-methylthiopentene dioxygenase (KMTPD) or acereductone dioxygenase
 +
**[[7jxg]] – hKMTPD + Fe+2<br />
 +
**[[4qgn]] – hKMTPD + Fe+3<br />
**[[5i8s]] – mKMTPD + Ni+2 + pentanoate + valerate<br />
**[[5i8s]] – mKMTPD + Ni+2 + pentanoate + valerate<br />
**[[5i8t]] – mKMTPD + Ni+2 + lactate <br />
**[[5i8t]] – mKMTPD + Ni+2 + lactate <br />
Line 456: Line 475:
**[[5i91]] – mKMTPD + Ni+2 + keto-methylthio-butyrate<br />
**[[5i91]] – mKMTPD + Ni+2 + keto-methylthio-butyrate<br />
**[[5i93]] – mKMTPD + Ni+2 + keto-pentanoate<br />
**[[5i93]] – mKMTPD + Ni+2 + keto-pentanoate<br />
-
**[[4qgn]] – hKMTPD + Fe+3<br />
 
**[[4qgl]], [[4qgm]] – BaKMTPD + Cd+2<br />
**[[4qgl]], [[4qgm]] – BaKMTPD + Cd+2<br />
* Indoleamine 2,3-dioxygenase 1 (IAD)
* Indoleamine 2,3-dioxygenase 1 (IAD)
-
**[[6azu]] – hIAD + heme <br />
+
**[[6azu]], [[7a62]] – hIAD + heme <br />
**[[6e45]], [[6e44]], [[7a62]] – hIAD 1 (mutant) + heme <br />
**[[6e45]], [[6e44]], [[7a62]] – hIAD 1 (mutant) + heme <br />
-
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]] – hIAD + heme + imidazole derivative<br />
+
**[[5ek2]], [[5ek3]], [[5ek4]], [[4pk5]], [[5xe1]], [[5wn8]], [[7ah4]], [[7ah5]], [[7ah6]] – hIAD + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
**[[4u72]], [[4u74]], [[6e42]], [[6e41]], [[6e40]] – hIAD (mutant) + heme + imidazole derivative<br />
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
**[[6f0a]] – hIAD + heme + imidazole derivative + Ala<br />
-
**[[6azw]], [[6azv]], [[6v52]] – hIAD + inhibitor<br />
+
**[[6azw]], [[6azv]], [[6v52]], [[6wjy]], [[6wpe]], [[6x5y]] – hIAD + inhibitor<br />
 +
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]], [[6kof]], [[6kps]], [[6kw7]], [[6o3i]], [[6pu7]], [[6pz1]], [[6r63]] – hIAD + heme + inhibitor<br />
**[[5etw]], [[6mq6]], [[6dpr]], [[6dpq]], [[6kof]], [[6kps]], [[6kw7]], [[6o3i]], [[6pu7]], [[6pz1]], [[6r63]] – hIAD + heme + inhibitor<br />
 +
**[[6ubp]] – hIAD 1 + heme + CO + Trp<br />
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
**[[5wmu]], [[6e35]] – hIAD + heme + CN + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
**[[5wmw]], [[6cxv]], [[6cxu]] – hIAD (mutant) + heme + CN + Trp<br />
Line 474: Line 494:
**[[5whr]] – hIAD + heme + pyrrolydine derivative <br />
**[[5whr]] – hIAD + heme + pyrrolydine derivative <br />
**[[6e46]] – hIAD 1 + heme + Trp<br />
**[[6e46]] – hIAD 1 + heme + Trp<br />
-
**[[6e43]] – hIAD 1 (mutant) + inhibitor<br />
 
* Thymine dioxygenase (TD)
* Thymine dioxygenase (TD)
Line 512: Line 531:
**[[6s0r]], [[6s0t]] – SkKBD + Ni+2 – ''Streptomyces kanamyceticus''<br />
**[[6s0r]], [[6s0t]] – SkKBD + Ni+2 – ''Streptomyces kanamyceticus''<br />
**[[6s0v]] – SkKBD + Ni+2 + neamine<br />
**[[6s0v]] – SkKBD + Ni+2 + neamine<br />
-
**[[6s0w]] – SkKBD + Ni+2 + kanamycin<br />
+
**[[6s0w]], [[7cl3]] – SkKBD + Ni+2 + kanamycin<br />
**[[6s0u]] – SkKBD + Ni+2 + oxoglutarate<br />
**[[6s0u]] – SkKBD + Ni+2 + oxoglutarate<br />
**[[6s0s]] – SkKBD + Ni+2 + ribostamycin + oxoglutarate<br />
**[[6s0s]] – SkKBD + Ni+2 + ribostamycin + oxoglutarate<br />
 +
**[[7cl4]] – SkKBD + Ni+2 + oxalylglycine<br />
 +
**[[7cl5]] – SkKBD + Ni+2 + oxalylglycine + kanamycin<br />
 +
**[[7cl6]] – SkKBD + Ni+2 + oxalylglycine + neamine<br />
}}
}}
[[Category:Topic Page]]
[[Category:Topic Page]]

Revision as of 09:11, 30 June 2021

3D structures of dioxygenase

Updated on 30-June-2021

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman

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