Structure of PDB 3tor Chain B Binding Site BS03
Receptor Information
>3tor Chain B (length=441) Species:
562
(Escherichia coli) [
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TVEAKNETFAPQHPDQYLSWKATSEQSERVDALAEDPRLVILWAGYPFSR
DYNKPRGHAFAVTDVRETLRTGAPKNAEDGPLPMACWSCKSPDVARLIQK
DGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTLSRPYAA
RAMEAIGKPFEKAGRFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVE
NMEQYYDKIAFSDWTNSLSKTPMLKAQHPEYETWTAGIHGKNNVTCIDCH
MPKVQNAEGKLYTDHKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSI
NDLKIKVEDQLVHAHFEAKAALDAGATEAEMKPIQDDIRHAQWRWDLAIA
SHGIHMHAPEEGLRMLGTAMDKAADARTKLARLLATKGITHEIQIPDIST
KEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARKNGLLS
Ligand information
Ligand ID
HEC
InChI
InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
InChIKey
HXQIYSLZKNYNMH-LJNAALQVSA-N
SMILES
Software
SMILES
ACDLabs 10.04
O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
OpenEye OEToolkits 1.5.0
CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
CACTVS 3.341
C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
CACTVS 3.341
CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
Formula
C34 H34 Fe N4 O4
Name
HEME C
ChEMBL
DrugBank
ZINC
PDB chain
3tor Chain B Residue 4 [
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Receptor-Ligand Complex Structure
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PDB
3tor
Characterization of the active site and calcium binding in cytochrome c nitrite reductases.
Resolution
2.0 Å
Binding residue
(original residue number in PDB)
H49 Q52 Y53 W56 G159 C160 C163 H164 F171 G174 P176 R201 Q205 I283 M287 K289 Y298 T299 H301
Binding residue
(residue number reindexed from 1)
H13 Q16 Y17 W20 G123 C124 C127 H128 F135 G138 P140 R165 Q169 I247 M251 K253 Y262 T263 H265
Annotation score
1
Enzymatic activity
Enzyme Commision number
1.7.2.2
: nitrite reductase (cytochrome; ammonia-forming).
Gene Ontology
Molecular Function
GO:0005506
iron ion binding
GO:0005509
calcium ion binding
GO:0016491
oxidoreductase activity
GO:0016966
nitric oxide reductase activity
GO:0020037
heme binding
GO:0042279
nitrite reductase (cytochrome, ammonia-forming) activity
GO:0046872
metal ion binding
Biological Process
GO:0009061
anaerobic respiration
GO:0019645
anaerobic electron transport chain
GO:0042128
nitrate assimilation
Cellular Component
GO:0030288
outer membrane-bounded periplasmic space
GO:0042597
periplasmic space
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:3tor
,
PDBe:3tor
,
PDBj:3tor
PDBsum
3tor
PubMed
22103542
UniProt
P0ABK9
|NRFA_ECOLI Cytochrome c-552 (Gene Name=nrfA)
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