4L3X
Nitrite complex of TvNiR, first middle dose data set
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005509 | molecular_function | calcium ion binding |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0019645 | biological_process | anaerobic electron transport chain |
A | 0020037 | molecular_function | heme binding |
A | 0030288 | cellular_component | outer membrane-bounded periplasmic space |
A | 0042128 | biological_process | nitrate assimilation |
A | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
A | 0042597 | cellular_component | periplasmic space |
A | 0046872 | molecular_function | metal ion binding |
A | 0097164 | biological_process | ammonium ion metabolic process |
B | 0005509 | molecular_function | calcium ion binding |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0019645 | biological_process | anaerobic electron transport chain |
B | 0020037 | molecular_function | heme binding |
B | 0030288 | cellular_component | outer membrane-bounded periplasmic space |
B | 0042128 | biological_process | nitrate assimilation |
B | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
B | 0042597 | cellular_component | periplasmic space |
B | 0046872 | molecular_function | metal ion binding |
B | 0097164 | biological_process | ammonium ion metabolic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC A 601 |
Chain | Residue |
A | HIS113 |
A | ARG242 |
A | CYS299 |
A | HIS300 |
A | TYR303 |
A | CYS305 |
A | HIS361 |
A | ASN486 |
A | HEC603 |
A | NO2609 |
A | HOH714 |
A | ALA114 |
A | HOH803 |
A | HOH804 |
A | HOH809 |
A | HOH922 |
A | HOH1211 |
A | ASP125 |
A | HIS126 |
A | VAL129 |
A | ARG131 |
A | CYS184 |
A | CYS187 |
A | LYS188 |
site_id | AC2 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE HEC A 602 |
Chain | Residue |
A | CYS66 |
A | HIS70 |
A | GLN73 |
A | LEU225 |
A | CYS227 |
A | CYS230 |
A | HIS231 |
A | ALA290 |
A | MET384 |
A | TYR395 |
A | THR396 |
A | HIS398 |
A | HEC607 |
A | HOH781 |
A | HOH866 |
A | HOH882 |
A | HOH1185 |
site_id | AC3 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC A 603 |
Chain | Residue |
A | SER84 |
A | PRO116 |
A | ARG117 |
A | HIS119 |
A | PHE121 |
A | MET122 |
A | ASP125 |
A | CYS187 |
A | LYS188 |
A | MET229 |
A | CYS296 |
A | CYS299 |
A | HIS300 |
A | HIS383 |
A | MET384 |
A | HEC601 |
A | HEC604 |
A | CA611 |
A | HOH704 |
A | HOH720 |
A | HOH800 |
site_id | AC4 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC A 604 |
Chain | Residue |
A | HIS300 |
A | PHE367 |
A | HIS372 |
A | VAL377 |
A | ALA378 |
A | CYS379 |
A | CYS382 |
A | HIS383 |
A | THR402 |
A | ARG404 |
A | LYS431 |
A | ASN486 |
A | PHE490 |
A | HIS491 |
A | HEC603 |
A | HEC605 |
A | CA611 |
A | GOL613 |
A | HOH800 |
A | HOH810 |
A | HOH912 |
A | HOH919 |
A | HOH991 |
A | HOH1035 |
site_id | AC5 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE HEC A 605 |
Chain | Residue |
A | HOH1285 |
A | ASN141 |
A | TRP142 |
A | GLN143 |
A | HIS372 |
A | PRO403 |
A | ALA410 |
A | CYS411 |
A | CYS414 |
A | HIS415 |
A | TRP418 |
A | ILE427 |
A | HEC604 |
A | HOH944 |
site_id | AC6 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE HEC A 606 |
Chain | Residue |
A | CYS14 |
A | PHE15 |
A | HIS18 |
A | VAL33 |
A | ASN34 |
A | CYS35 |
A | CYS38 |
A | HIS39 |
A | THR59 |
A | LEU194 |
A | PHE228 |
A | PRO233 |
A | HIS234 |
A | ARG239 |
A | PHE274 |
A | ARG276 |
A | ARG282 |
A | HEC607 |
A | HEC608 |
A | HOH760 |
A | HOH1213 |
A | HOH1236 |
site_id | AC7 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE HEC A 607 |
Chain | Residue |
A | LYS29 |
A | HIS30 |
A | HIS37 |
A | ALA65 |
A | CYS66 |
A | CYS69 |
A | HIS70 |
A | CYS227 |
A | HIS231 |
A | ALA236 |
A | HEC602 |
A | HEC606 |
A | HOH1058 |
A | HOH1207 |
A | HOH1244 |
A | HOH1312 |
A | HOH1328 |
A | HOH1331 |
B | THR68 |
site_id | AC8 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC A 608 |
Chain | Residue |
A | GLN13 |
A | CYS14 |
A | CYS17 |
A | HIS18 |
A | HIS39 |
A | HIS44 |
A | VAL45 |
A | ALA48 |
A | SER49 |
A | SER50 |
A | ARG52 |
A | MET53 |
A | ARG56 |
A | PRO57 |
A | THR59 |
A | LEU194 |
A | ARG276 |
A | GLY277 |
A | HEC606 |
A | HOH762 |
A | HOH779 |
A | HOH1005 |
A | HOH1233 |
A | HOH1238 |
site_id | AC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE NO2 A 609 |
Chain | Residue |
A | ARG131 |
A | TYR303 |
A | HIS361 |
A | HEC601 |
A | HOH920 |
A | HOH922 |
A | HOH1211 |
site_id | BC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA A 610 |
Chain | Residue |
A | GLU302 |
A | TYR303 |
A | LYS358 |
A | GLN360 |
A | HOH869 |
A | HOH966 |
site_id | BC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA A 611 |
Chain | Residue |
A | PRO116 |
A | HEC603 |
A | HEC604 |
A | GOL613 |
A | HOH912 |
A | HOH929 |
A | HOH1035 |
site_id | BC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE MPD A 612 |
Chain | Residue |
A | ARG87 |
A | VAL128 |
A | GLN138 |
A | PHE139 |
A | TRP142 |
A | ARG497 |
A | HOH1115 |
site_id | BC4 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL A 613 |
Chain | Residue |
A | ARG96 |
A | GLU115 |
A | PRO116 |
A | ASN486 |
A | HEC604 |
A | CA611 |
A | HOH806 |
A | HOH810 |
A | HOH1035 |
A | HOH1039 |
site_id | BC5 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL A 614 |
Chain | Residue |
A | ASP101 |
A | ALA110 |
A | PHE111 |
A | GLN175 |
A | TRP444 |
A | ILE504 |
A | LYS508 |
A | HOH717 |
A | HOH939 |
site_id | BC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL A 615 |
Chain | Residue |
A | ASP251 |
A | LYS271 |
A | ARG322 |
A | HOH845 |
site_id | BC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 A 616 |
Chain | Residue |
A | THR351 |
A | LYS447 |
A | ASN515 |
A | HOH745 |
A | HOH1072 |
A | HOH1202 |
site_id | BC8 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE NO2 A 617 |
Chain | Residue |
A | GLN169 |
A | SER212 |
A | GLU213 |
A | VAL214 |
A | NO2618 |
A | HOH906 |
A | HOH1125 |
site_id | BC9 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE NO2 A 618 |
Chain | Residue |
A | SER212 |
A | GLU213 |
A | VAL214 |
A | NO2617 |
A | HOH822 |
A | HOH963 |
A | HOH1055 |
A | HOH1125 |
site_id | CC1 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC B 601 |
Chain | Residue |
B | HIS113 |
B | ALA114 |
B | ASP125 |
B | HIS126 |
B | VAL129 |
B | ARG131 |
B | CYS184 |
B | CYS187 |
B | LYS188 |
B | ARG242 |
B | CYS299 |
B | HIS300 |
B | TYR303 |
B | CYS305 |
B | HIS361 |
B | ASN486 |
B | HEC603 |
B | NO2609 |
B | HOH741 |
B | HOH828 |
B | HOH829 |
B | HOH834 |
B | HOH948 |
B | HOH1238 |
site_id | CC2 |
Number of Residues | 18 |
Details | BINDING SITE FOR RESIDUE HEC B 602 |
Chain | Residue |
B | CYS66 |
B | HIS70 |
B | GLN73 |
B | LEU225 |
B | CYS227 |
B | CYS230 |
B | HIS231 |
B | ALA290 |
B | MET384 |
B | TYR395 |
B | THR396 |
B | HIS398 |
B | HEC607 |
B | HOH807 |
B | HOH891 |
B | HOH907 |
B | HOH1212 |
B | HOH1271 |
site_id | CC3 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC B 603 |
Chain | Residue |
B | SER84 |
B | PRO116 |
B | ARG117 |
B | HIS119 |
B | PHE121 |
B | MET122 |
B | ASP125 |
B | CYS187 |
B | MET229 |
B | CYS296 |
B | CYS299 |
B | HIS300 |
B | HIS383 |
B | MET384 |
B | HEC601 |
B | HEC604 |
B | CA611 |
B | HOH731 |
B | HOH746 |
B | HOH825 |
B | HOH1061 |
site_id | CC4 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC B 604 |
Chain | Residue |
B | PHE367 |
B | HIS372 |
B | VAL377 |
B | ALA378 |
B | CYS379 |
B | CYS382 |
B | HIS383 |
B | THR402 |
B | PRO403 |
B | ARG404 |
B | LYS431 |
B | ASN486 |
B | PHE490 |
B | HIS491 |
B | HEC603 |
B | HEC605 |
B | CA611 |
B | GOL613 |
B | HOH825 |
B | HOH835 |
B | HOH938 |
B | HOH945 |
B | HOH1017 |
B | HOH1061 |
site_id | CC5 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE HEC B 605 |
Chain | Residue |
B | ASN141 |
B | TRP142 |
B | GLN143 |
B | VAL371 |
B | HIS372 |
B | ASN375 |
B | PRO403 |
B | ALA410 |
B | CYS411 |
B | CYS414 |
B | HIS415 |
B | TRP418 |
B | ILE427 |
B | HEC604 |
site_id | CC6 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC B 606 |
Chain | Residue |
B | CYS14 |
B | PHE15 |
B | HIS18 |
B | HIS25 |
B | VAL33 |
B | ASN34 |
B | CYS35 |
B | CYS38 |
B | HIS39 |
B | LEU194 |
B | PHE228 |
B | PRO233 |
B | HIS234 |
B | ARG239 |
B | PHE274 |
B | ARG276 |
B | ARG282 |
B | HEC607 |
B | HEC608 |
B | HOH786 |
B | HOH1236 |
site_id | CC7 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE HEC B 607 |
Chain | Residue |
A | THR68 |
B | LYS29 |
B | HIS30 |
B | HIS37 |
B | ALA65 |
B | CYS66 |
B | THR68 |
B | CYS69 |
B | HIS70 |
B | CYS227 |
B | HIS231 |
B | ALA236 |
B | HEC602 |
B | HEC606 |
B | HOH707 |
B | HOH724 |
B | HOH1084 |
B | HOH1234 |
B | HOH1264 |
B | HOH1280 |
site_id | CC8 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE HEC B 608 |
Chain | Residue |
B | GLN13 |
B | CYS14 |
B | CYS17 |
B | HIS18 |
B | HIS39 |
B | HIS44 |
B | VAL45 |
B | ALA48 |
B | SER49 |
B | ARG51 |
B | ARG51 |
B | ARG52 |
B | MET53 |
B | ARG56 |
B | PRO57 |
B | THR59 |
B | LEU194 |
B | GLN275 |
B | ARG276 |
B | HEC606 |
B | HOH788 |
B | HOH805 |
B | HOH1031 |
B | HOH1236 |
B | HOH1262 |
B | HOH1291 |
site_id | CC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE NO2 B 609 |
Chain | Residue |
B | ARG131 |
B | TYR303 |
B | HIS361 |
B | HEC601 |
B | HOH946 |
B | HOH948 |
B | HOH1238 |
site_id | DC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA B 610 |
Chain | Residue |
B | GLU302 |
B | TYR303 |
B | LYS358 |
B | GLN360 |
B | HOH894 |
B | HOH992 |
site_id | DC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA B 611 |
Chain | Residue |
B | PRO116 |
B | HEC603 |
B | HEC604 |
B | GOL613 |
B | HOH938 |
B | HOH955 |
B | HOH1061 |
site_id | DC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE MPD B 612 |
Chain | Residue |
B | ARG87 |
B | VAL128 |
B | GLN138 |
B | PHE139 |
B | TRP142 |
B | ARG497 |
B | HOH1142 |
site_id | DC4 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL B 613 |
Chain | Residue |
B | ARG96 |
B | GLU115 |
B | PRO116 |
B | ASN486 |
B | HEC604 |
B | CA611 |
B | HOH831 |
B | HOH835 |
B | HOH1061 |
B | HOH1065 |
site_id | DC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL B 614 |
Chain | Residue |
B | ASP101 |
B | ALA110 |
B | GLN175 |
B | TRP444 |
B | ILE504 |
B | LYS508 |
B | HOH743 |
B | HOH965 |
site_id | DC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 B 615 |
Chain | Residue |
B | THR351 |
B | LYS447 |
B | ASN515 |
B | HOH1098 |
B | HOH1229 |
B | HOH1298 |
B | HOH1304 |
site_id | DC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NO2 B 616 |
Chain | Residue |
B | GLN169 |
B | GLU213 |
B | VAL214 |
B | NO2617 |
B | HOH1152 |
site_id | DC8 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE NO2 B 617 |
Chain | Residue |
B | SER212 |
B | GLU213 |
B | VAL214 |
B | NO2616 |
B | HOH847 |
B | HOH989 |
B | HOH1081 |
B | HOH1152 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 32 |
Details | BINDING: covalent => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y |
Chain | Residue | Details |
A | CYS14 | |
A | CYS230 | |
A | CYS296 | |
A | CYS299 | |
A | CYS379 | |
A | CYS382 | |
A | CYS411 | |
A | CYS414 | |
B | CYS14 | |
B | CYS17 | |
B | CYS35 | |
A | CYS17 | |
B | CYS38 | |
B | CYS66 | |
B | CYS69 | |
B | CYS184 | |
B | CYS187 | |
B | CYS227 | |
B | CYS230 | |
B | CYS296 | |
B | CYS299 | |
B | CYS379 | |
A | CYS35 | |
B | CYS382 | |
B | CYS411 | |
B | CYS414 | |
A | CYS38 | |
A | CYS66 | |
A | CYS69 | |
A | CYS184 | |
A | CYS187 | |
A | CYS227 |
site_id | SWS_FT_FI2 |
Number of Residues | 28 |
Details | BINDING: axial binding residue => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y |
Chain | Residue | Details |
A | HIS18 | |
A | HIS372 | |
A | HIS383 | |
A | HIS398 | |
A | HIS415 | |
A | HIS491 | |
B | HIS18 | |
B | HIS30 | |
B | HIS39 | |
B | HIS44 | |
B | HIS70 | |
A | HIS30 | |
B | HIS119 | |
B | LYS188 | |
B | HIS234 | |
B | HIS300 | |
B | HIS372 | |
B | HIS383 | |
B | HIS398 | |
B | HIS415 | |
B | HIS491 | |
A | HIS39 | |
A | HIS44 | |
A | HIS70 | |
A | HIS119 | |
A | LYS188 | |
A | HIS234 | |
A | HIS300 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | BINDING: axial binding residue => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743 |
Chain | Residue | Details |
A | HIS231 | |
B | HIS231 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y |
Chain | Residue | Details |
A | GLU302 | |
A | TYR303 | |
A | LYS358 | |
A | GLN360 | |
B | GLU302 | |
B | TYR303 | |
B | LYS358 | |
B | GLN360 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | CROSSLNK: 3'-(S-cysteinyl)-tyrosine (Tyr-Cys) => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:22281743 |
Chain | Residue | Details |
A | TYR303 | |
A | CYS305 | |
B | TYR303 | |
B | CYS305 |