Nitrite reductase 3D structures: Difference between revisions

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New page: ==3D structures of nitrite reductase== Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| *'''Cu-containing nitrite re...
 
Michal Harel (talk | contribs)
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*'''Cu-containing nitrite reductase with copper only'''
*'''Cu-containing nitrite reductase with copper only'''


**[[1nia]], [[1nib]], [[1nic]], [[1nid]], [[1nie]], [[1nif]], [[2nrd]], [[1kcb]], [[1rzp]], [[1rzq]], [[2bw4]], [[2bw5]], [[2avf]], [[5l6k]], [[5i6l]], [[5l6m]], [[5i6n]], [[5l6o]], [[5i6p]], [[5n8f]], [[5n8g]], [[5n8h]], [[5n8i]],  [[6gsq]], [[6gt2]], [[6gtj]] – AcNIR + Cu – ''Achromobacter cycloclastes''<br />
**[[1nia]], [[1nib]], [[1nic]], [[1nid]], [[1nie]], [[1nif]], [[2nrd]], [[1kcb]], [[1rzp]], [[1rzq]], [[2bw4]], [[2bw5]], [[2avf]], [[5l6k]], [[5i6l]], [[5l6m]], [[5i6n]], [[5l6o]], [[5i6p]], [[5n8f]], [[5n8g]], [[5n8h]], [[5n8i]],  [[6gsq]], [[6gt2]], [[6gtj]], [[9rll]], [[9t6o]], [[9t6p]] – AcNIR + Cu – ''Achromobacter cycloclastes''<br />
**[[6knf]], [[6kng]], [[9t6q]], [[9t6u]] – AcNIR + Cu – Cryo EM<br />
**[[2afn]], [[1aq8]], [[1as7]], [[2fjs]], [[2pp7]], [[2pp8]], [[3h4h]], [[3h56]], [[4ysc]], [[4yse]], [[5d4h]], [[5d4i]], [[5d4j]], [[5f7a]], [[5f7b]]  - AfNIR + Cu – ''Alcaligenes faecalis''<br />
**[[2afn]], [[1aq8]], [[1as7]], [[2fjs]], [[2pp7]], [[2pp8]], [[3h4h]], [[3h56]], [[4ysc]], [[4yse]], [[5d4h]], [[5d4i]], [[5d4j]], [[5f7a]], [[5f7b]]  - AfNIR + Cu – ''Alcaligenes faecalis''<br />
**[[1ntd]], [[1npj]], [[1npn]], [[1zdq]], [[3h4f]] - AfNIR (mutant) + Cu<br />
**[[1ntd]], [[1npj]], [[1npn]], [[1zdq]], [[3h4f]] - AfNIR (mutant) + Cu<br />
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**[[1oe2]], [[2jfc]] - AxNIR (mutant) + Cu<br />
**[[1oe2]], [[2jfc]] - AxNIR (mutant) + Cu<br />
**[[1mzz]], [[2dy2]] - RsNIR + Cu – ''Rhodobacter sphaeroides''<br />
**[[1mzz]], [[2dy2]] - RsNIR + Cu – ''Rhodobacter sphaeroides''<br />
**[[2dv6]] - NIR + Cu – ''Hyphomicrobium denitrificans''<br />
**[[2dv6]], [[6tfo]] - HdNIR + Cu – ''Hyphomicrobium denitrificans''<br />
**[[3wia]] - GkNIR + Cu – ''Geobacillus kaustophilus''<br />
**[[3wia]] - GkNIR + Cu – ''Geobacillus kaustophilus''<br />
**[[3wkq]], [[3x1e]], [[4ysa]], [[4ysd]], [[4yso]], [[4ysp]], [[4ysq]], [[4ysr]], [[4yss]], [[4yst]], [[4ysu]], [[4zk8]], [[5ytl]] - GtNIR + Cu - ''Geobacillus thermodentntrificans''<br />
**[[3wkq]], [[3x1e]], [[4ysa]], [[4ysd]], [[4yso]], [[4ysp]], [[4ysq]], [[4ysr]], [[4yss]], [[4yst]], [[4ysu]], [[4zk8]], [[5ytl]] - GtNIR + Cu - ''Geobacillus thermodentntrificans''<br />
**[[3x1f]], [[3x1g]] - GtNIR (mutant) + Cu <br />
**[[3x1f]], [[3x1g]], [[5ytm]], [[9kws]], [[9kwt]] - GtNIR (mutant) + Cu <br />
**[[5tb7]], [[5ue6]] - NIR + Cu – ''Neisseria gonorrhoeae''<br />
**[[5tb7]], [[5ue6]] - NIR + Cu – ''Neisseria gonorrhoeae''<br />
**[[6hbe]] - NIR + Cu – ''Thermus scotoductus''<br />
**[[6hbe]] - NIR + Cu – ''Thermus scotoductus''<br />
**[[6qpu]] – RpNIR + Cu – ''Ralstonia pickettii''<br />
**[[6qpu]] – RpNIR + Cu – ''Ralstonia pickettii''<br />
**[[6thf]], [[6zar]], [[6zas]], [[7qyc]], [[8r8s]], [[8rfo]], [[8rfp]], [[8rfq]], [[8rfr]], [[8rfs]], [[8rft]], [[8rfu]], [[8rfv]], [[8rfw]], [[8rfx]], [[8rfy]], [[8ru9]], [[8s2q]], [[8ryv]], [[8s0w]], [[8s5x]], [[8s5y]], [[8s63]], [[8s64]], [[8s68]], [[8s69]], [[9hs0]], [[9roc]], [[9ros]] – BrNIR + Cu – ''Bradyrhizobium''<br />
**[[7p2f]] – NIR + Cu – ''Sinorhizobium meliloti''<br />
**[[4knt]] – NIR + Cu – ''Nitrosomonas europaea''<br />
**[[9cck]] – NIR + Cu – ''Nitrosopumilus maritimus''<br />


*Cu-containing nitrite reductase with variety of metals
*Cu-containing nitrite reductase with variety of metals
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**[[3wi9]] - GkNIR + Zn + Cu <br />
**[[3wi9]] - GkNIR + Zn + Cu <br />
**[[5onx]], [[5ony]] - NIR + Zn + Cu – ''Alcaligenes xylosoxydans''<br />
**[[5onx]], [[5ony]] - NIR + Zn + Cu – ''Alcaligenes xylosoxydans''<br />
**[[6the]] – BrNIR + Cu + Yb + Er + Tb <br />
**[[4csp]] - AcNIR (mutant) + Zn + Cu <br />


*Cu-containing nitrite reductase binary complex
*Cu-containing nitrite reductase binary complex
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**[[1wa2]] - AxNIR (mutant) + NO2 + Zn + Cu<br />
**[[1wa2]] - AxNIR (mutant) + NO2 + Zn + Cu<br />
**[[5b1j]] - AxNIR + pseudoazurin + Cu <br />
**[[5b1j]] - AxNIR + pseudoazurin + Cu <br />
**[[2bwd]], [[2bwi]], [[5og2]], [[5og3]], [[5og4]], [[5og5]], [[5og6]], [[5ogf]], [[5ogg]], [[5of5]], [[5of6]], [[5of7]], [[5of8]], [[5ofc]], [[5ofd]], [[5ofe]], [[5off]], [[5ofg]], [[5ofh]], [[5i6k]], [[5i6m]], [[5i6o]], [[5akr]], [[6gb8]], [[6gbb]], [[6gby]], [[6gcg]], [[6gt0]], [[6gti]], [[6gtk]], [[6gtl]], [[6gtn]] - AcNIR + NO2 + Cu<br />
**[[2bwd]], [[2bwi]], [[5og2]], [[5og3]], [[5og4]], [[5og5]], [[5og6]], [[5ogf]], [[5ogg]], [[5of5]], [[5of6]], [[5of7]], [[5of8]], [[5ofc]], [[5ofd]], [[5ofe]], [[5off]], [[5ofg]], [[5ofh]], [[5i6k]], [[5i6m]], [[5i6o]], [[5akr]], [[6gb8]], [[6gbb]], [[6gby]], [[6gcg]], [[6gt0]], [[6gti]], [[6gtk]], [[6gtl]], [[6gtn]], [[9rn0]] - AcNIR + NO2 + Cu<br />
**[[4csz]] - AcNIR (mutant) + NO2 + Cu <br />
**[[4csz]] - AcNIR (mutant) + NO2 + Cu <br />
**[[4csp]] - AcNIR (mutant) + Zn + Cu <br />
**[[2y1a]], [[6zu6]], [[6zua]], [[6zub]], [[6zud]], [[6zut]] - AcNIR + NO + Cu<br />
**[[2y1a]] - AcNIR + NO + Cu<br />
**[[2dws]], [[2dwt]] - RsNIR + NO2 + Cu<br />
**[[2dws]], [[2dwt]] - RsNIR + NO2 + Cu<br />
**[[3wkp]], [[3x1n]] - GtNIR (mutant) + NO2 + Cu <br />
**[[3wkp]], [[3x1n]], [[9kvl]], [[9kwu]], [[9kwv]] - GtNIR (mutant) + NO2 + Cu <br />
**[[3wni]], [[3wnj]] - GtNIR + O2 + Cu <br />
**[[3wni]], [[3wnj]] - GtNIR + O2 + Cu <br />
**[[5ytn]] - GtNIR (mutant) + H2O2 + Cu <br />
**[[5ytn]] - GtNIR (mutant) + H2O2 + Cu <br />
**[[9kvm]] - GtNIR (mutant) + formate + Cu <br />
**[[6qpt]] – RpNIR + Cu + NO2 <br />
**[[6qpt]] – RpNIR + Cu + NO2 <br />
**[[6zat]], [[6zax]], [[7zcn]], [[7zcr]], [[7zcs]], [[8rg8]], [[8rg9]], [[8rgb]], [[8rgc]], [[8rgd]], [[8rur]], [[8ryj]], [[8ryr]], [[9evm]], [[8ryu]] – BrNIR + Cu + NO2 <br />
**[[7zco]], [[7zcp]], [[7zcq]] – BrNIR + Cu + NO + NO2 <br />
**[[6zaw]] – BrNIR + Cu + NO <br />
**[[6zau]] – BrNIR + Cu + NO2 + NO<br />
**[[6qpv]], [[6qpz]], [[6qq1]] – RpNIR (mutant) + Cu + heme <br />
**[[6qpv]], [[6qpz]], [[6qq1]] – RpNIR (mutant) + Cu + heme <br />
**[[6qpx]], [[6qq0]], [[6qq2]] – RpNIR (mutant) + Cu + heme + NO2<br />
**[[6qpx]], [[6qq0]], [[6qq2]] – RpNIR (mutant) + Cu + heme + NO2<br />


*'''Heme-containing nitrite reductase - (Cytochrome C-552)'''
*'''Heme-containing nitrite reductase - (Cytochrome C-552)''' see [[Cytochrome c nitrite reductase]]
 
**[[1aof]], [[1qks]], [[1hj4]], [[1hj5]], [[1h9x]], [[1hcm]] - PpNIR – ''Paracoccus pantotrophus''<br />
**[[1gq1]] - PpNIR (mutant)<br />
**[[1nir]], [[1bl9]], [[1n15]], [[1n50]], [[1n90]] – PaNIR – ''Pseudomonas aeruginosa''<br />
**[[1hzu]] - PaNIR (mutant)<br />
**[[1qdb]] - NIR – ''Sulfurospirillum deleyianum''<br />
**[[1fs7]], [[1fs8]] - WsNIR – ''Wolinella succinogenes''<br />
**[[3bng]] - WsNIR (mutant) <br />
**[[1gu6]], [[2rdz]], [[3tor]] – EcNIR – ''Escherichia coli''<br />
**[[2rf7]], [[4wjy]] - EcNIR (mutant) <br />
**[[2jo6]] – EcNIR small subunit – NMR<BR />
**[[2jza]] - NIR small subunit – ''Pectobacterium atrosepticum'' - NMR<BR />
**[[1oah]] – NIR – ''Desulfovibrio desulfuricans''<br />
**[[2j7a]] - DvNIR – ''Desulfovibrio vulgaris''<br />
**[[2ot4]], [[3gm6]], [[3fo3]], [[3sce]], [[3uu9]], [[4q0t]], [[4q17]], [[4q1o]], [[4q4u]], [[4q5b]], [[4q5c]] - TnNIR – ''Thioalkalivibrio nitratireducens''<br />
**[[3m97]] – PdNIR soluble domain – ''Paracoccus denitrificans''<br />
**[[2ai5]] – HtNIR – ''Hydrogenophilus thermophilus'' – NMR<BR />
**[[2d0s]], [[1ynr]], [[3vym]] – HtNIR<BR />
**[[1ayg]] – NIR - ''Hydrogenobacter thermoluteolus'' – NMR<BR />
**[[1i6d]], [[1i6e]], [[1c7m]] – PdNIR functional domain – NMR<BR />
**[[1ql3]], [[1ql4]] - PdNIR functional domain<BR />
**[[1dt1]], [[1qyz]], [[1r0q]], [[1c52]], [[3vnw]] – TtNIR – ''Thermus thermophilus''<BR />
**[[2fwl]] – TtNIR + NIR oxidase subunit II <BR />
**[[1cno]] – NIR – ''Pseudomonas nautica''<br />
**[[3ubr]] – SoNIR – ''Shewanella oneidensis''<br />
**[[3sqx]] – TpNIR – ''Thioalkalivibrio paradoxus''<br />
 
*Heme-containing nitrite reductase binary complex
 
**[[1dy7]] - PpNIR + CO<br />
**[[1hj3]] - PpNIR + O2<br />
**[[2e81]] - WsNIR + NH2OH<br />
**[[3bnf]] - WsNIR  + sulfite <BR />
**[[2vr0]] - DvNIR + HQNO inhibitor<br />
**[[3ziy]], [[4ax3]], [[6fja]], [[6f1q]] – RpNIR + Cu – ''Ralstonia pickettii''<br />
**[[3ayf]] – NIR + Zn – ''Geobacillus stearothermophilus''<br />
**[[2yqb]], [[3zbm]] – RpNIR (mutant) + Cu <br />
**[[3o0r]] – PaNIR + antibody<br />
**[[5guw]] – PaNIR + nitric oxide reductase<br />
**[[3sxq]] – TpNIR + Co<br />
 
*Heme-containing nitrite reductase binary complex with cyanide
 
**[[1h9y]] - PpNIR + CN<br />
**[[1gjq]] - PaNIR + CN<br />
**[[1e2r]] - PdNIR+ CN <br />
 
*Heme-containing nitrite reductase binary complex with nitric oxide
 
**[[1nno]] - PaNIR + NO<br />
**[[1hzv]] - PaNIR (mutant) + NO<br />
**[[1aom]], [[1aoq]], [[5ocb]], [[5ocf]] - PpNIR + NO + NO2<br />
** [[5obo]] - PpNIR (mutant) + Cu + NO2<br />
 
*Heme-containing nitrite reductase binary complex with nitrite
 
**[[2e80]] - WsNIR + NO2<br />
**[[3bnh]] - WsNIR (mutant) + NO<br />
**[[3d1i]], [[3rkh]], [[3owm]], [[4l38]], [[4l3x]], [[4l3y]], [[4l3z]] - TnNIR + NO2
 
*Heme-containing nitrite reductase binary complex with azide
 
**[[2zo5]] - TnNIR + N3<br />
**[[3s7w]] - TnNIR + NO2 + N3<br />
**[[1fs9]] - WsNIR + N3
 
*Heme-containing nitrite reductase binary complex with sulfite
 
**[[3mmo]] - WsNIR + SO3<BR />
**[[3bnj]] - WsNIR (mutant) + SO3<BR />
**[[3lg1]], [[3lgq]], [[3f29]], [[3ttb]] - TnNIR + SO3<BR />
**[[3l1t]] - EcNIR + SO3<BR />


*'''Siroheme-containing assimilatory nitrite reductase'''  
*'''Siroheme-containing assimilatory nitrite reductase'''  
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