Nitrite reductase: Difference between revisions
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The Ca<sup>2+</sup> ion within <scene name='Journal:JBIC:16/Cv/14'> the conserved site</scene> is coordinated in bidentate fashion by <scene name='Journal:JBIC:16/Cv/15'>Glu205</scene>, and in monodentate fashion by the <scene name='Journal:JBIC:16/Cv/16'>Tyr206 and Lys254</scene> backbone carbonyls, and the <scene name='Journal:JBIC:16/Cv/17'>Gln256</scene> side-chain carbonyl. In the ''S. oneidensis'' structure only <scene name='Journal:JBIC:16/Cv/18'>one water molecule</scene> is assigned to the Ca<sup>2+</sup> ion in subunit B. In subunit A the difference electron density that represents this water molecule is very close to the noise level, and it is difficult to identify even one water molecule there. The <scene name='Journal:JBIC:16/Cv/14'>carbonyl side chain of Asp242 and the hydroxyl of Tyr235</scene> come near to the open calcium coordination sites, but are not within bonding distance. Instead they interact with the water molecule that is weakly coordinated to the Ca<sup>2+</sup> ion. The ccNiR calcium ions appear to play a vital role in organizing the <scene name='Journal:JBIC:16/Cv/13'>active site</scene> (as was mentioned above <font color='magenta'><b>hemes-1</b></font> are the active sites). | The Ca<sup>2+</sup> ion within <scene name='Journal:JBIC:16/Cv/14'> the conserved site</scene> is coordinated in bidentate fashion by <scene name='Journal:JBIC:16/Cv/15'>Glu205</scene>, and in monodentate fashion by the <scene name='Journal:JBIC:16/Cv/16'>Tyr206 and Lys254</scene> backbone carbonyls, and the <scene name='Journal:JBIC:16/Cv/17'>Gln256</scene> side-chain carbonyl. In the ''S. oneidensis'' structure only <scene name='Journal:JBIC:16/Cv/18'>one water molecule</scene> is assigned to the Ca<sup>2+</sup> ion in subunit B. In subunit A the difference electron density that represents this water molecule is very close to the noise level, and it is difficult to identify even one water molecule there. The <scene name='Journal:JBIC:16/Cv/14'>carbonyl side chain of Asp242 and the hydroxyl of Tyr235</scene> come near to the open calcium coordination sites, but are not within bonding distance. Instead they interact with the water molecule that is weakly coordinated to the Ca<sup>2+</sup> ion. The ccNiR calcium ions appear to play a vital role in organizing the <scene name='Journal:JBIC:16/Cv/13'>active site</scene> (as was mentioned above <font color='magenta'><b>hemes-1</b></font> are the active sites). | ||
==3D structures of nitrite reductase== | |||
[[Nitrite reductase 3D structures]] | |||
</StructureSection> | </StructureSection> | ||
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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]] | **[[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 /> | ||
**[[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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**[[2dv6]] - NIR + Cu – ''Hyphomicrobium denitrificans''<br /> | **[[2dv6]] - NIR + 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]] - 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]] - GtNIR (mutant) + Cu <br /> | ||
**[[5tb7]], [[5ue6]] - NIR + Cu – ''Neisseria gonorrhoeae''<br /> | **[[5tb7]], [[5ue6]] - NIR + Cu – ''Neisseria gonorrhoeae''<br /> | ||
**[[6hbe]] - NIR + Cu – ''Thermus scotoductus''<br /> | |||
**[[6qpu]] – RpNIR + Cu – ''Ralstonia pickettii''<br /> | |||
*Cu-containing nitrite reductase with variety of metals | *Cu-containing nitrite reductase with variety of metals | ||
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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]] - 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]] - AcNIR + NO2 + Cu<br /> | ||
**[[4csz]] - AcNIR (mutant) + NO2 + Cu <br /> | **[[4csz]] - AcNIR (mutant) + NO2 + Cu <br /> | ||
**[[4csp]] - AcNIR (mutant) + Zn + Cu <br /> | **[[4csp]] - AcNIR (mutant) + Zn + Cu <br /> | ||
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**[[3wkp]], [[3x1n]] - GtNIR (mutant) + NO2 + Cu <br /> | **[[3wkp]], [[3x1n]] - GtNIR (mutant) + NO2 + Cu <br /> | ||
**[[3wni]], [[3wnj]] - GtNIR + O2 + Cu <br /> | **[[3wni]], [[3wnj]] - GtNIR + O2 + Cu <br /> | ||
**[[5ytn]] - GtNIR (mutant) + H2O2 + Cu <br /> | |||
**[[6qpt]] – RpNIR + Cu + NO2 <br /> | |||
**[[6qpv]], [[6qpz]], [[6qq1]] – RpNIR (mutant) + Cu + heme <br /> | |||
**[[6qpx]], [[6qq0]], [[6qq2]] – RpNIR (mutant) + Cu + heme + NO2<br /> | |||
*'''Heme-containing nitrite reductase - (Cytochrome C-552)''' | *'''Heme-containing nitrite reductase - (Cytochrome C-552)''' | ||