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| == Structural highlights == | | == Structural highlights == |
| Jmjd2a uses <scene name='59/596434/Cv/2'>9 residues for interaction with the methylated peptide</scene> and <scene name='59/596434/Cv/3'>4 residues are involved with binding to the peptide's trimethyllysine moiety</scene>. An <scene name='59/596434/Cv/5'>O2 molecules are recruited into the catalytic center</scene><ref>PMID:17567753</ref>. Water molecules shown as red spheres. | | Jmjd2a uses <scene name='59/596434/Cv/7'>9 residues for interaction with the methylated peptide</scene> and <scene name='59/596434/Cv/8'>4 residues are involved with binding to the peptide's trimethyllysine moiety</scene>. An <scene name='59/596434/Cv/9'>O2 molecules are recruited into the catalytic center</scene><ref>PMID:17567753</ref>. Water molecules shown as red spheres. |
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| <scene name='59/596434/Cv/6'>Zn coordination site</scene>. | | <scene name='59/596434/Cv/10'>Zn coordination site</scene>. |
| </StructureSection>
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| ==3D structures of jumonji domain-containing protein == | | ==3D structures of jumonji domain-containing protein == |
| | [[Jumonji domain-containing protein 3D structures]] |
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| Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
| | </StructureSection> |
| {{#tree:id=OrganizedByTopic|openlevels=0|
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| *Jmjd2a (Lysine-specific demethylase 4A)
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| **[[2gf7]], [[2qqr]], [[5d6w]], [[5d6x]] – hJmjd2a double TUDOR domain – human <br />
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| **[[2gp3]] – hJmjd2a catalytic domain + Fe<br />
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| **[[5fyc]], [[5tvs]] – hJmjd2a catalytic domain + Ni<br />
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| *Jmjd2a binary complex with peptide
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| **[[2gfa]], [[5d6y]] – hJmjd2a double TUDOR domain + peptide with trimethyllysine<br />
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| **[[2qqs]] – hJmjd2a double TUDOR domain + histone H4 peptide with trimethyllysine<br />
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| **[[2oq6]], [[2os2]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine <br />
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| **[[2ot7]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with methyllysine <br />
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| **[[2pxj]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with methyllysine <br />
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| **[[2ox0]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with dimethyllysine <br />
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| **[[5ly2]], [[5ly1]] – hJmjd2a catalytic domain + Ni + peptide inhibitor <br />
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| **[[5fwe]] – hJmjd2a catalytic domain + Ni + Zn + oxalylglycine + peptide <br />
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| *Jmjd2a binary complex with other molecules
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| **[[2oq7]] – hJmjd2a catalytic domain + Ni + oxalylglycine <br />
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| **[[2vd7]], [[2wwj]], [[3njy]], [[3pdq]], [[3rvh]], [[4gd4]], [[4ai9]], [[4bis]] – hJmjd2a catalytic domain + Ni + inhibitor <br />
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| **[[2gp5]] – hJmjd2a catalytic domain + Fe + α-ketoglutarate <br />
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| **[[2ybk]], [[5tvr]] – hJmjd2a catalytic domain + Ni + α-ketoglutarate derivative<br />
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| **[[4ura]], [[5fpv]] – hJmjd2a catalytic domain + Ni + inhibitor<br />
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| **[[5anq]] – hJmjd2a catalytic domain + Fe + inhibitor<br />
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| **[[5a7n]], [[5a7o]], [[5a7p]], [[5a7q]], [[5a7s]], [[5a7w]], [[5a80]] – hJmjd2a catalytic domain + Mn + inhibitor<br />
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| **[[5f2s]], [[5f2w]], [[5f32]], [[5f37]], [[5f39]], [[5f3c]], [[5f3e]], [[5f3g]], [[5f3i]], [[6cg1]], [[6cg2]], [[5vmp]], [[5vgi]], [[5var]] – hJmjd2a catalytic domain + Zn + inhibitor<br />
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| **[[5fy8]] – hJmjd2a catalytic domain + Ni + threo-isocitrate<br />
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| **[[5fyi]] – hJmjd2a catalytic domain + Ni + pyruvate<br />
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| **[[5fyh]] – hJmjd2a catalytic domain + Mn + fumarate<br />
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| *Jmjd2a ternary complex
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| **[[2q8c]], [[2ybp]], [[2ybs]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + α-ketoglutarate derivative<br />
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| **[[2q8d]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + succinate <br />
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| **[[2q8e]], [[2p5b]] – hJmjd2a catalytic domain + Fe + histone H3 peptide with trimethyllysine + oxalylglycine <br />
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| **[[4v2v]], [[4v2w]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylglycine <br />
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| **[[3u4s]] – hJmjd2a catalytic domain + Ni + histone H3 peptide with trimethyllysine + oxalylcysteine <br />
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| *Jmjd1a (Lysine-specific demethylase 5A; KDM5A)
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| **[[5v9p]], [[5v9t]], [[5iwf]], [[5iw0]], [[5ivy]], [[5ivv]], [[5ivj]], [[5ivf]], [[5ive]], [[5ivc]], [[5ivb]], [[5isl]], [[6bh5]], [[6bh4]], [[6bh3]], [[6bh2]], [[6bh1]], [[6bh0]], [[6bgz]], [[6bgy]], [[6bgx]], [[6bgw]], [[6bgv]], [[6bgu]] – hJmj1a + inhibitor <br />
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| **[[5k4l]], [[5ceh]] – hJmj1a + inhibitor + peptide<br />
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| **[[5c11]] – hJmj1a PHD finger domain + H3 peptide<br />
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| **[[5e6h]] – hJmj1a residues 1-87, 348-588 + Mn + oxoglutarate<br />
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| **[[4tn7]] – mJmj1a residues 36-364 + NO + Fe + H3 peptide - mouse <br />
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| **[[4qxh]], [[4qxb]] – mJmj1a residues 36-364 + Ni + oxalylglycine <br />
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| **[[4qxc]] – mJmj1a residues 36-364 + Ni + oxalylglycine + H3 peptide <br />
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| **[[4qx8]], [[4qx7]], [[4qwn]] – mJmj1a residues 36-364 + Ni + oxoglutarate + H3 peptide <br />
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| * Lysine-specific demethylase 5C; KDM5C; JARID1C
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| **[[5fwj]] – hLSD5C Jmj domain + inhibitor<br />
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| **[[2jrz]] – hLSD5C Bright/ARID domain - NMR<br />
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| *lysine-specific demethylase 5D or JARID1D
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| **[[2yqe]] – hLSD5D ARID domain - NMR<br />
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| *Jmjd1b (Lysine-specific demethylase 2B; KDM2B)
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| **[[4o64]] – hJmj1b zinc finger domain + Zn <br />
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| **[[4c8d]], [[5fv3]] – hJmj1b catalytic domain + Mn + oxalylglycine <br />
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| **[[5fup]] – hJmj1b catalytic domain + Mn + Zn + oxoglutatate <br />
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| **[[5lwb]], [[5lw9]], [[5fzm]], [[5fzl]], [[5fzk]], [[5fzi]], [[5fzh]], [[5fzg]], [[5fzf]], [[5fze]], [[5fzd]], [[5fzc]], [[5fzb]], [[5fza]], [[5fz9]], [[5fz8]], [[5fz7]], [[5fz6]], [[5fz4]], [[5fz3]], [[5fz1]], [[5fz0]], [[5fyz]], [[5fyy]], [[5fyv]], [[5fyu]], [[5fyt]], [[5fyb]], [[5fy9]], [[5fy5]], [[5fy4]], [[5fun]], [[5fpu]], [[5fpl]], [[5a3w]], [[5a3t]], [[5a3p]], [[5a3n]] – hJmj1b catalytic domain + Mn + Zn + inhibitor <br />
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| **[[5jh5]] – hJmj1b + S-phase kinase-associated protein + polycomb protein + BCOR-like protein <br />
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| *Jmjd2b (Lysine-specific demethylase 4B)
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| **[[4lxl]] – hJmjd2b catalytic domain + Ni + histone H3 peptide with trimethyllysine <br />
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| **[[4uc4]] – hJmjd2b tudor domain <br />
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| *Jmjd2c (Lysine-specific demethylase 4C)
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| **[[2xdp]] – hJmjd2c tudor domain <br />
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| **[[2xml]], [[4xdo]] – hJmjd2c catalytic domain + Ni + oxalylglycine <br />
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| **[[4xdp]] – hJmjd2c catalytic domain + Fe <br />
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| **[[5fjh]], [[5fjk]] – hJmjd2c catalytic domain + Ni + inhibitor<br />
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| **[[5kr7]] – hJmjd2c catalytic domain + Fe + Zn + inhibitor<br />
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| *Jmjd2d (Lysine-specific demethylase 4D)
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| **[[3dxu]] – hJmjd2d catalytic domain + Fe + oxalylglycine <br />
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| **[[3dxt]], [[5pnw]], [[5pnv]], [[5pnu]], [[5pns]], [[5pnr]], [[5pnq]], [[5pnp]], [[5pno]], [[5pnn]], [[5pnm]], [[5pnl]], [[5pnk]], [[5pnj]], [[5pni]], [[5pnh]], [[5png]], [[5pnf]], [[5pne]], [[5pnd]], [[5pnc]], [[5pnb]], [[5pna]], [[5pn9]], [[5pn8]], [[5pn7]], [[5pn6]], [[5pn5]], [[5pn4]], [[5pn3]], [[5pn2]], [[5pn1]], [[5pn0]], [[5pmz]], [[5pmy]], [[5pmx]], [[5pmw]], [[5pmv]], [[5pmu]], [[5pmt]], [[5pms]], [[5pmr]], [[5pmq]], [[5pmp]], [[5pmo]], [[5pmn]], [[5pmm]], [[5pml]], [[5pmk]], [[5pmj]], [[5pmi]], [[5pmh]], [[5pmj]], [[5pmi]], [[5pmh]], [[5pmg]], [[5pmf]], [[5pme]], [[5pmd]], [[5pmc]], [[5pmb]], [[5pma]], [[5pm9]], [[5pm8]], [[5pm7]], [[5pm6]], [[5pm5]], [[5pm4]], [[5pm3]], [[5pm2]], [[5pm1]], [[5pm0]], [[5plz]], [[5ply]], [[5plx]], [[5plw]], [[5plv]], [[5plu]], [[5plt]], [[5pls]], [[5plr]], [[5plq]], [[5plp]], [[5plo]], [[5pln]], [[5plm]], [[5pll]], [[5plk]], [[5plj]], [[5pli]], [[5plh]], [[5plg]], [[5plf]], [[5ple]], [[5pld]], [[5plc]], [[5plb]], [[5pla]], [[5pl9]], [[5pl8]], [[5pl7]], [[5pl6]], [[5pl5]], [[5pl4]], [[5pl3]], [[5pl2]], [[5pl1]], [[5pl0]], [[5pkz]], [[5pky]], [[5pkx]], [[5pkw]], [[5pkv]], [[5pku]], [[5pkt]], [[5pks]], [[5pkr]], [[5pkq]], [[5pkp]], [[5pko]], [[5pkn]], [[5pkm]], [[5pkl]], [[5pkk]], [[5pkj]], [[5pki]], [[5pkh]], [[5pkg]], [[5pkf]], [[5pke]], [[5pkd]], [[5pkc]],
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| [[5pkb]], [[5pka]], [[5pk9]], [[5pk8]], [[5pk7]], [[5pk6]], [[5pk5]], [[5pk4]], [[5pk3]], [[5pk2]], [[5pk1]], [[5pk0]],
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| [[5pjz]], [[5pjy]], [[5pjx]], [[5pjw]], [[5pjv]], [[5pju]], [[5pjt]], [[5pjs]], [[5pjr]], [[5pjq]], [[5pjp]], [[5pjo]], [[5pjn]], [[5pjm]], [[5pjl]], [[5pjk]], [[5pjj]], [[5pji]], [[5pjh]], [[5pjg]], [[5pjf]], [[5pje]], [[5pjd]], [[5pjc]], [[5pjb]], [[5pja]], [[5pj9]], [[5pj8]], [[5pj7]], [[5pj6]], [[5pj5]], [[5pj4]], [[5pj3]], [[5pj2]], [[5pj1]], [[5pj0]], [[5piz]], [[5piy]], [[5pix]], [[5piw]], [[5piv]], [[5piu]], [[5pit]], [[5pis]], [[5pir]], [[5piq]], [[5pip]], [[5pio]], [[5pin]], [[5pim]], [[5pil]], [[5pik]], [[5pij]], [[5pii]], [[5pih]], [[5pig]], [[5pif]], [[5pie]], [[5pid]], [[5pic]], [[5pib]], [[5pia]], [[5pi9]], [[5pi8]], [[5pi7]], [[5pi6]], [[5pi5]], [[5pi4]], [[5pi3]], [[5pi2]], [[5pi1]], [[5pi0]], [[5phz]], [[5phy]], [[5phx]], [[5phw]], [[5phv]], [[5phu]], [[5pht]], [[5phs]], [[5phr]], [[5phq]], [[5php]], [[5pho]], [[5phn]], [[5phm]], [[5phl]], [[5phk]], [[5phj]], [[5phi]], [[5phh]], [[5phg]], [[5phf]], [[5phe]], [[5phd]], [[5phc]], [[5phb]], [[5pha]], [[5ph9]], [[5ph8]], [[5ph7]], [[5ph6]], [[5ph5]], [[5ph4]], [[5ph3]], [[5ph2]], [[5ph1]], [[5ph0]],
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| [[5pka]], [[5pk9]], [[5pk8]], [[5pk7]], [[5pk6]], [[5pk5]], [[5pk4]], [[5pk3]], [[5pk2]], [[5pk1]], [[5pk0]], [[5plj]], [[5pli]], [[5plh]], [[5plg]] – hJmjd2d catalytic domain + Zn<br />
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| **[[4hoo]] – hJmjd2d catalytic domain (mutant) + Ni<br />
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| **[[4d6q]], [[5f5a]], [[5f5c]], [[5f5i]] – hJmjd2d catalytic domain + Ni + inhibitor<br />
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| **[[5fp4]], [[5fp8]], [[5fp9]], [[5fpa]], [[5fpb]], [[5fp7]] – hJmjd2d catalytic domain + Fe + inhibitor<br />
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| **[[4d6r]], [[4d6s]] – hJmjd2d catalytic domain + Ni + inhibitor + oxalylglycine <br />
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| **[[4hon]] – hJmjd2d catalytic domain + Ni + histone H3 peptide with trimethyllysine + α-ketoglutarate <br />
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| *Jmjd3 (Lysine-specific demethylase 6B)
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| **[[2xxz]] – hJmjd3 catalytic domain + Ni <br />
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| **[[2xue]] – hJmjd3 catalytic domain + Fe + α-ketoglutarate <br />
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| **[[4ask]] – hJmjd3 catalytic and Zinc finger domains + Co + inhibitor <br />
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| **[[4eyu]], [[4ez4]] – mJmjd3 C terminal + Ni + oxalylglycine - mouse <br />
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| **[[4ezh]] – mJmjd3 C terminal + Ni + histone H3 peptide with trimethyllysine + oxalylglycine <br />
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| **[[5fp3]] – hJmjd3 catalytic domain + inhibitor<br />
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| *Jmjd5 (Lysine-specific demethylase 8)
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| **[[6f4m]] – hJmjd5 catalytic domain <br />
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| **[[3uyj]], [[4qu1]] – hJmjd5 catalytic domain + Ni + α-ketoglutarate <br />
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| **[[4gjz]] – hJmjd5 catalytic domain + Co + α-ketoglutarate <br />
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| **[[6f4n]] – hJmjd5 catalytic domain + Mn + α-ketoglutarate <br />
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| **[[6f4o]] – hJmjd5 catalytic domain + Mn + succinate <br />
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| **[[4aap]] – hJmjd5 catalytic domain + Zn + oxalylglycine <br/ >
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| **[[6avs]] – hJmjd5 catalytic domain + Zn + NMMA <br/ >
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| **[[5fbj]], [[6ax3]] – hJmjd5 catalytic domain + Zn + oxoglutarate <br/ >
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| **[[4gjy]] – hJmjd5 catalytic domain + Co + oxalylglycine <br />
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| **[[4gaz]] – hJmjd5 catalytic domain + Ni + oxalylglycine <br />
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| **[[6f4p]] – hJmjd5 catalytic domain + Mn + oxalylglycine + RPS6<br />
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| **[[6f4q]] – hJmjd5 catalytic domain (mutant) + Mn + oxalylglycine + RPS6<br />
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| **[[6f4r]], [[6f4s]], [[6f4t]] – hJmjd5 catalytic domain (mutant) + Mn + oxalylglycine + RCCD1<br />
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| *Jmjd6
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| **[[3ld8]] – hJmjd6 catalytic domain + antibody + Fe <br />
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| **[[3ldb]] – hJmjd6 catalytic domain + antibody + Fe + α-ketoglutarate <br />
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| **[[6fqc]] – hJmjd6 catalytic domain + polypeptide + Mn <br />
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| *Jmjd7
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| **[[4qu2]] – hJmjd7 catalytic domain + Ni + α-ketoglutarate <br />
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| **[[5nfn]] – hJmjd7 catalytic domain + Mn + oxoglutarate <br/ >
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| **[[5nfo]] – hJmjd7 catalytic domain (mutant) + Mn + oxoglutarate <br/ >
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| }}
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| == References == | | == References == |
| <references/> | | <references/> |
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| [[Category:Topic Page]] | | [[Category:Topic Page]] |