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Dioxygenase 3D structures

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Line 75: Line 75:
**[[5m26]] – SpHQD + Fe+3 + hydroquinone derivative<br />
**[[5m26]] – SpHQD + Fe+3 + hydroquinone derivative<br />
**[[5m21]] – SpHQD + Fe+3 + hydroxybenzoate<br />
**[[5m21]] – SpHQD + Fe+3 + hydroxybenzoate<br />
 +
**[[3n9t]] – PpHQD + Fe+3 <br />
*Nitrobenzene dioxygenase (NBDO)
*Nitrobenzene dioxygenase (NBDO)
Line 90: Line 91:
**[[3t4h]], [[3t4v]], [[3t3y]] – EcAlkb + Fe+3 + inhibitor – ''Escherichia coli''<br />
**[[3t4h]], [[3t4v]], [[3t3y]] – EcAlkb + Fe+3 + inhibitor – ''Escherichia coli''<br />
**[[2fdj]], [[2fdg]] – EcAlkb + Mn+2 + succinate <br />
**[[2fdj]], [[2fdg]] – EcAlkb + Mn+2 + succinate <br />
-
**[[4jht]] – EcAlkb + Mn+2 + quinoline derivative <br />
+
**[[4jht]], [[7nro]] – EcAlkb + Mn+2 + inhibitor<br />
**[[4rfr]] – EcAlkb + Mn+2 + rhein<br />
**[[4rfr]] – EcAlkb + Mn+2 + rhein<br />
**[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
**[[2fdf]] – EcAlkb (mutant) + Co+2 + oxoglutarate <br />
Line 129: Line 130:
**[[6ie3]] – hAlkbh1 + Mn <br />
**[[6ie3]] – hAlkbh1 + Mn <br />
**[[6ie2]] – hAlkbh1 + Mn + oxoglutarate <br />
**[[6ie2]] – hAlkbh1 + Mn + oxoglutarate <br />
-
**[[6ksf]] – mAlkbh1 catalytic domain + succinate + DNA<br />
+
**[[6imc]] – hAlkbh1 catalytic domain + Mn + oxalylglycine <br />
 +
**[[6ksf]] – mAlkbh1 catalytic domain 4-384 + succinate + DNA<br />
 +
**[[6l94]] – mAlkbh1 catalytic domain + Fe+2<br />
**[[4nj4]], [[4o7x]] – hAlkbh5 residues 66-292 + Mn<br />
**[[4nj4]], [[4o7x]] – hAlkbh5 residues 66-292 + Mn<br />
**[[4o61]] – hAlkbh5 residues 74-294 + citrate<br />
**[[4o61]] – hAlkbh5 residues 74-294 + citrate<br />
Line 135: Line 138:
**[[4nro]] – hAlkbh5 residues 66-292 + Mn + ketoglutarate <br />
**[[4nro]] – hAlkbh5 residues 66-292 + Mn + ketoglutarate <br />
**[[4oct]] – hAlkbh5 residues 66-292 + Mn + oxoglutarate <br />
**[[4oct]] – hAlkbh5 residues 66-292 + Mn + oxoglutarate <br />
 +
**[[7v4g]] – hAlkbh5 residues 66-292 + Mn + RNA<br />
 +
**[[7wkv]] – hAlkbh5 residues 66-292 + Mn + oxoglutarate + RNA<br />
 +
**[[7wl0]] – hAlkbh5 residues 66-292 + Mn + oxalylglycine + RNA<br />
**[[4nrp]] – hAlkbh5 residues 66-292 + Mn + oxalylglycine <br />
**[[4nrp]] – hAlkbh5 residues 66-292 + Mn + oxalylglycine <br />
**[[4nrq]] – hAlkbh5 residues 66-292 + Mn + pyridine dicarboxylate <br />
**[[4nrq]] – hAlkbh5 residues 66-292 + Mn + pyridine dicarboxylate <br />
**[[4npl]] – zfAlkbh5 residues 38-287 + Mn + ketoglutarate – zebra fish<br />
**[[4npl]] – zfAlkbh5 residues 38-287 + Mn + ketoglutarate – zebra fish<br />
**[[4npm]] – zfAlkbh5 residues 38-287 + Mn + succinate <br />
**[[4npm]] – zfAlkbh5 residues 38-287 + Mn + succinate <br />
 +
**[[7vjs]] – hAlkbh6 + Ni <br />
 +
**[[7vjv]] – hAlkbh6 + Mn + ketoglutarate <br />
**[[4qkb]], [[4qkd]] – hAlkbh7 residues 17-215 (mutant) + Mn + ketoglutarate <br />
**[[4qkb]], [[4qkd]] – hAlkbh7 residues 17-215 (mutant) + Mn + ketoglutarate <br />
**[[4qkf]] – hAlkbh7 residues 17-215 (mutant) + Mn + oxalylglycine <br />
**[[4qkf]] – hAlkbh7 residues 17-215 (mutant) + Mn + oxalylglycine <br />
Line 145: Line 153:
**[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
**[[4idz]] – hFto + Ni+2 + oxalylglycine<br />
 +
**[[7ckk]] – hFto + inhibitor + oxalylglycine<br />
**[[4ie0]], [[4ie5]], [[4qho]] – hFto + Zn+2 + pyrimidine derivative<br />
**[[4ie0]], [[4ie5]], [[4qho]] – hFto + Zn+2 + pyrimidine derivative<br />
**[[4ie4]], [[4ie6]] – hFto + Zn+2 + quinoline derivative<br />
**[[4ie4]], [[4ie6]] – hFto + Zn+2 + quinoline derivative<br />
Line 150: Line 159:
**[[4qkn]] – hFto + Mn+2 + meclofenamic acid<br />
**[[4qkn]] – hFto + Mn+2 + meclofenamic acid<br />
**[[4cxw]], [[4cxx]], [[4cxy]] – hFto + Ni+2 + inhibitor<br />
**[[4cxw]], [[4cxx]], [[4cxy]] – hFto + Ni+2 + inhibitor<br />
-
**[[6aej]] – hFto + Zn+2 + inhibitor<br />
+
**[[6aej]], [[7e8z]] – hFto + Zn+2 + inhibitor<br />
**[[6ak4]] – hFto (mutant) + Zn+2 + inhibitor<br />
**[[6ak4]] – hFto (mutant) + Zn+2 + inhibitor<br />
**[[6akw]] – hFto + oxoglutarate + inhibitor<br />
**[[6akw]] – hFto + oxoglutarate + inhibitor<br />
**[[5f8p]], [[5dab]] – hFto + Fe+2 + oxoglutarate + inhibitor<br />
**[[5f8p]], [[5dab]] – hFto + Fe+2 + oxoglutarate + inhibitor<br />
**[[4zs2]], [[4zs3]] – hFto + Mn+2 + oxoglutarate + fluorescin<br />
**[[4zs2]], [[4zs3]] – hFto + Mn+2 + oxoglutarate + fluorescin<br />
 +
**[[7wcv]] – hFto + Mn+2 + oxoglutarate <br />
**[[5zmd]] – hFto (mutant) + Mn+2 + AMP derivative + DNA + oxalylglycine<br />
**[[5zmd]] – hFto (mutant) + Mn+2 + AMP derivative + DNA + oxalylglycine<br />
-
**[[6eoz]] – EnFto + Ni+2 + cyclopeptin – Emericela nidulans<br />
+
**[[6eoz]] – EnFto + Ni+2 + cyclopeptin – ''Emericela nidulans''<br />
-
**[[5ybl]] – EnFto + Mn+2 + oxoglutarate <br />
+
**[[5y7t]], [[5y7r]] – EnFto + Fe+3 + oxoglutarate + cyclopeptin<br />
**[[5y7t]], [[5y7r]] – EnFto + Fe+3 + oxoglutarate + cyclopeptin<br />
**[[5oa8]], [[5oa7]], [[5oa4]] – EnFto (mutant) + Ni+2 + oxoglutarate + cyclopeptin<br />
**[[5oa8]], [[5oa7]], [[5oa4]] – EnFto (mutant) + Ni+2 + oxoglutarate + cyclopeptin<br />
Line 179: Line 188:
**[[6k0f]] – AnAsqJ + Fe+3 + H2O2 + cyclopeptin + oxoglutarate<br />
**[[6k0f]] – AnAsqJ + Fe+3 + H2O2 + cyclopeptin + oxoglutarate<br />
**[[6jzm]], [[6k30]], [[6kd9]] – AnAsqJ + Fe+3 + cyclopeptin + succinate<br />
**[[6jzm]], [[6k30]], [[6kd9]] – AnAsqJ + Fe+3 + cyclopeptin + succinate<br />
 +
**[[7eyt]], [[7eyu]], [[7eyw]] – AnAsqJ (mutant) + Fe+2 + terpenoid<br />
 +
**[[7olk]] – EnAsqJ + Ni+2 + inhibitor<br />
 +
**[[7oll]], [[7olm]], [[7olo]], [[7olq]] – EnAsqJ (mutant) + Ni+2 + inhibitor<br />
 +
**[[7olt]] – EnAsqJ + Ni+2 + cyclopeptin<br />
 +
**[[7olr]] – EnAsqJ + Ni+2 + oxoglutarate + cyclopeptin<br />
 +
 +
* Fe(II)/(alpha)-ketoglutarate-dependent dioxygenase (PrhA)
 +
 +
**[[5ybm]] – PbPrhA – ''Penicillium brasilianum''<br />
 +
**[[5ybn]], [[7olp]] – PbPrhA + Fe+3 + oxoglutarate + cyclopeptin <br />
 +
**[[5ybs]], [[5ybt]] – PbPrhA (mutant) + Fe+3 + oxoglutarate + berkeleyone <br />
 +
**[[5ybo]], [[5ybp]], [[5ybq]], [[5ybr]] – PbPrhA (mutant) + Fe+3 + oxoglutarate + preaustinoid <br />
 +
**[[7qtf]] – StPlaO1 + succinate - Streptomyces<br />
 +
**[[7qtg]] – StPlaO1 + Fe+2<br />
 +
**[[7qtd]] – StPlaO1 + Fe+2 + oxoglutarate <br />
 +
**[[7qte]] – StPlaO1 + Co + succinate <br />
 +
**[[5ybl]] – EnAusE + Mn+2 + oxoglutarate <br />
 +
 +
* Gamma-butyrobetaine dioxygenase
 +
 +
**[[4bhf]] – hGBBD + inhibitor <br />
 +
**[[3n6w]] – hGBBD + Zn <br />
 +
**[[3o2g]] – hGBBD + Zn + oxalylglycine <br />
 +
**[[3ms5]] – hGBBD + Ni + Zn + oxalylglycine <br />
 +
**[[4bg1]], [[4bgk]], [[4bgm]], [[4bhf]], [[4bhi]] – hGBBD + Zn + inhibitor<br />
 +
**[[4c8r]] – hGBBD + Ni + Zn + inhibitor<br />
 +
**[[4bhg]], [[4c5w]] – hGBBD + Zn + oxalylglycine + inhibitor<br />
 +
**[[4cwd]] – hGBBD + Ni + Zn + oxalylglycine + inhibitor<br />
*Leucoanthocyanidin dioxygenase (LACD)
*Leucoanthocyanidin dioxygenase (LACD)
Line 188: Line 225:
**[[6asd]] – hTET1 + DNA <br />
**[[6asd]] – hTET1 + DNA <br />
-
**[[5d9y]], [[5deu]], [[4nm6]] – hTET2 + DNA <br />
+
**[[5d9y]], [[5deu]], [[4nm6]], [[7ne6]] – hTET2 + DNA <br />
 +
**[[7ne3]] – hTET2 (mutant) + DNA <br />
**[[4z3c]] – hTET3 + DNA <br />
**[[4z3c]] – hTET3 + DNA <br />
**[[5exh]] – mTET3 + DNA – mouse <br />
**[[5exh]] – mTET3 + DNA – mouse <br />
 +
**[[7w5p]] – CcTET + DNA – ''Coprinopsis cinerea''<br />
 +
**[[7vpn]] – CcTET + oxalylglycine + Mn<br />
*'''Dioxygenase extradiol family'''
*'''Dioxygenase extradiol family'''

Revision as of 10:57, 29 January 2023

3D structures of dioxygenase

Updated on 29-January-2023

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman

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