5D0A
Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005737 | cellular_component | cytoplasm |
A | 0006400 | biological_process | tRNA modification |
A | 0008033 | biological_process | tRNA processing |
A | 0008616 | biological_process | queuosine biosynthetic process |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0046872 | molecular_function | metal ion binding |
A | 0051536 | molecular_function | iron-sulfur cluster binding |
A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
A | 0052693 | molecular_function | epoxyqueuosine reductase activity |
B | 0005737 | cellular_component | cytoplasm |
B | 0006400 | biological_process | tRNA modification |
B | 0008033 | biological_process | tRNA processing |
B | 0008616 | biological_process | queuosine biosynthetic process |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0046872 | molecular_function | metal ion binding |
B | 0051536 | molecular_function | iron-sulfur cluster binding |
B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
B | 0052693 | molecular_function | epoxyqueuosine reductase activity |
C | 0005737 | cellular_component | cytoplasm |
C | 0006400 | biological_process | tRNA modification |
C | 0008033 | biological_process | tRNA processing |
C | 0008616 | biological_process | queuosine biosynthetic process |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0046872 | molecular_function | metal ion binding |
C | 0051536 | molecular_function | iron-sulfur cluster binding |
C | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
C | 0052693 | molecular_function | epoxyqueuosine reductase activity |
D | 0005737 | cellular_component | cytoplasm |
D | 0006400 | biological_process | tRNA modification |
D | 0008033 | biological_process | tRNA processing |
D | 0008616 | biological_process | queuosine biosynthetic process |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0046872 | molecular_function | metal ion binding |
D | 0051536 | molecular_function | iron-sulfur cluster binding |
D | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
D | 0052693 | molecular_function | epoxyqueuosine reductase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 8 |
Details | binding site for residue SF4 A 501 |
Chain | Residue |
A | ALA153 |
A | LYS154 |
A | ASN155 |
A | CYS188 |
A | CYS191 |
A | CYS194 |
A | CYS247 |
A | LEU249 |
site_id | AC2 |
Number of Residues | 8 |
Details | binding site for residue SF4 A 502 |
Chain | Residue |
A | PRO199 |
A | LEU209 |
A | CYS214 |
A | ILE215 |
A | CYS240 |
A | THR242 |
A | CYS243 |
A | CYS198 |
site_id | AC3 |
Number of Residues | 38 |
Details | binding site for residue B12 A 503 |
Chain | Residue |
A | SER32 |
A | LEU33 |
A | ARG36 |
A | SER47 |
A | PHE49 |
A | GLU50 |
A | ARG57 |
A | CYS97 |
A | ASP134 |
A | LEU138 |
A | SER139 |
A | ASP140 |
A | ARG141 |
A | ALA142 |
A | SER152 |
A | ASN155 |
A | CYS156 |
A | MET157 |
A | ILE158 |
A | SER165 |
A | VAL167 |
A | LEU169 |
A | PRO206 |
A | LEU209 |
A | SER216 |
A | PHE217 |
A | GLY239 |
A | CYS240 |
A | ASP241 |
A | CYS243 |
A | GLN244 |
A | HOH630 |
A | HOH632 |
A | HOH635 |
A | HOH652 |
A | HOH683 |
A | HOH692 |
A | HOH747 |
site_id | AC4 |
Number of Residues | 7 |
Details | binding site for residue GOL A 504 |
Chain | Residue |
A | PHE49 |
A | ASP134 |
A | GLN220 |
A | TYR238 |
A | TRP294 |
A | HOH652 |
A | HOH653 |
site_id | AC5 |
Number of Residues | 6 |
Details | binding site for residue PO4 A 505 |
Chain | Residue |
A | LYS112 |
A | HIS258 |
A | PRO259 |
A | GLU260 |
A | HOH639 |
A | HOH682 |
site_id | AC6 |
Number of Residues | 7 |
Details | binding site for residue SF4 B 501 |
Chain | Residue |
B | ALA153 |
B | LYS154 |
B | ASN155 |
B | CYS188 |
B | CYS191 |
B | CYS194 |
B | CYS247 |
site_id | AC7 |
Number of Residues | 8 |
Details | binding site for residue SF4 B 502 |
Chain | Residue |
B | CYS198 |
B | LEU203 |
B | LEU209 |
B | CYS214 |
B | ILE215 |
B | CYS240 |
B | THR242 |
B | CYS243 |
site_id | AC8 |
Number of Residues | 35 |
Details | binding site for residue B12 B 503 |
Chain | Residue |
B | SER165 |
B | VAL167 |
B | LEU169 |
B | PRO206 |
B | GLY207 |
B | LEU209 |
B | SER216 |
B | GLY239 |
B | CYS240 |
B | ASP241 |
B | CYS243 |
B | GLN244 |
B | HOH616 |
B | HOH628 |
B | HOH640 |
B | HOH643 |
B | HOH668 |
B | HOH677 |
B | SER32 |
B | LEU33 |
B | ARG36 |
B | SER47 |
B | GLU50 |
B | ARG57 |
B | CYS97 |
B | ASP134 |
B | LEU138 |
B | SER139 |
B | ASP140 |
B | ARG141 |
B | SER152 |
B | ASN155 |
B | CYS156 |
B | MET157 |
B | ILE158 |
site_id | AC9 |
Number of Residues | 6 |
Details | binding site for residue GOL B 504 |
Chain | Residue |
B | ASP134 |
B | GLN220 |
B | TYR238 |
B | TRP294 |
B | HOH657 |
B | HOH677 |
site_id | AD1 |
Number of Residues | 4 |
Details | binding site for residue PO4 B 505 |
Chain | Residue |
B | LYS112 |
B | HIS258 |
B | PRO259 |
B | GLU260 |
site_id | AD2 |
Number of Residues | 7 |
Details | binding site for residue SF4 C 501 |
Chain | Residue |
C | ALA153 |
C | LYS154 |
C | ASN155 |
C | CYS188 |
C | CYS191 |
C | CYS194 |
C | CYS247 |
site_id | AD3 |
Number of Residues | 7 |
Details | binding site for residue SF4 C 502 |
Chain | Residue |
C | CYS198 |
C | LEU209 |
C | CYS214 |
C | ILE215 |
C | CYS240 |
C | THR242 |
C | CYS243 |
site_id | AD4 |
Number of Residues | 38 |
Details | binding site for residue B12 C 503 |
Chain | Residue |
C | SER32 |
C | LEU33 |
C | ARG36 |
C | SER47 |
C | PHE49 |
C | GLU50 |
C | ARG57 |
C | CYS97 |
C | ASP134 |
C | LEU138 |
C | SER139 |
C | ASP140 |
C | ARG141 |
C | GLU145 |
C | SER152 |
C | ASN155 |
C | CYS156 |
C | MET157 |
C | ILE158 |
C | SER165 |
C | VAL167 |
C | LEU169 |
C | PRO206 |
C | GLY207 |
C | LEU209 |
C | SER216 |
C | PHE217 |
C | GLY239 |
C | CYS240 |
C | ASP241 |
C | CYS243 |
C | GLN244 |
C | HOH642 |
C | HOH648 |
C | HOH657 |
C | HOH673 |
C | HOH678 |
C | HOH692 |
site_id | AD5 |
Number of Residues | 7 |
Details | binding site for residue GOL C 504 |
Chain | Residue |
C | PHE49 |
C | ASP134 |
C | GLN220 |
C | TYR238 |
C | TRP294 |
C | HOH653 |
C | HOH678 |
site_id | AD6 |
Number of Residues | 4 |
Details | binding site for residue PO4 C 505 |
Chain | Residue |
C | LYS112 |
C | HIS258 |
C | PRO259 |
C | GLU260 |
site_id | AD7 |
Number of Residues | 8 |
Details | binding site for residue SF4 D 501 |
Chain | Residue |
D | ALA153 |
D | LYS154 |
D | ASN155 |
D | CYS188 |
D | CYS191 |
D | CYS194 |
D | CYS247 |
D | LEU249 |
site_id | AD8 |
Number of Residues | 6 |
Details | binding site for residue SF4 D 502 |
Chain | Residue |
D | CYS198 |
D | LEU209 |
D | CYS214 |
D | ILE215 |
D | CYS240 |
D | CYS243 |
site_id | AD9 |
Number of Residues | 36 |
Details | binding site for residue B12 D 503 |
Chain | Residue |
D | SER32 |
D | LEU33 |
D | ARG36 |
D | SER47 |
D | GLU50 |
D | ARG57 |
D | CYS97 |
D | ASP134 |
D | LEU138 |
D | SER139 |
D | ASP140 |
D | ARG141 |
D | ALA142 |
D | SER152 |
D | ASN155 |
D | CYS156 |
D | ILE158 |
D | SER165 |
D | VAL167 |
D | LEU169 |
D | PRO206 |
D | GLY207 |
D | LEU209 |
D | SER216 |
D | GLY239 |
D | CYS240 |
D | ASP241 |
D | CYS243 |
D | GLN244 |
D | HOH614 |
D | HOH648 |
D | HOH655 |
D | HOH666 |
D | HOH678 |
D | HOH693 |
D | HOH744 |
site_id | AE1 |
Number of Residues | 7 |
Details | binding site for residue GOL D 504 |
Chain | Residue |
D | PHE49 |
D | ASP134 |
D | GLN220 |
D | TYR238 |
D | TRP294 |
D | HOH628 |
D | HOH693 |
site_id | AE2 |
Number of Residues | 5 |
Details | binding site for residue PO4 D 505 |
Chain | Residue |
D | LYS112 |
D | HIS258 |
D | PRO259 |
D | GLU260 |
D | HOH659 |
Functional Information from PROSITE/UniProt
site_id | PS00198 |
Number of Residues | 12 |
Details | 4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CgSCTkCLdACP |
Chain | Residue | Details |
A | CYS188-PRO199 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 4 |
Details | ACT_SITE: Proton donor => ECO:0000305|PubMed:27638883 |
Chain | Residue | Details |
A | ASP134 | |
B | ASP134 | |
C | ASP134 | |
D | ASP134 |
site_id | SWS_FT_FI2 |
Number of Residues | 68 |
Details | BINDING: BINDING => ECO:0000269|PubMed:27638883, ECO:0007744|PDB:5D0B |
Chain | Residue | Details |
A | ARG57 | |
A | CYS191 | |
A | CYS194 | |
A | CYS198 | |
A | CYS214 | |
A | SER216 | |
A | CYS240 | |
A | CYS243 | |
A | CYS247 | |
B | ARG57 | |
B | CYS97 | |
A | CYS97 | |
B | ASP134 | |
B | SER139 | |
B | SER152 | |
B | ASN155 | |
B | ILE158 | |
B | LEU169 | |
B | CYS188 | |
B | CYS191 | |
B | CYS194 | |
B | CYS198 | |
A | ASP134 | |
B | CYS214 | |
B | SER216 | |
B | CYS240 | |
B | CYS243 | |
B | CYS247 | |
C | ARG57 | |
C | CYS97 | |
C | ASP134 | |
C | SER139 | |
C | SER152 | |
A | SER139 | |
C | ASN155 | |
C | ILE158 | |
C | LEU169 | |
C | CYS188 | |
C | CYS191 | |
C | CYS194 | |
C | CYS198 | |
C | CYS214 | |
C | SER216 | |
C | CYS240 | |
A | SER152 | |
C | CYS243 | |
C | CYS247 | |
D | ARG57 | |
D | CYS97 | |
D | ASP134 | |
D | SER139 | |
D | SER152 | |
D | ASN155 | |
D | ILE158 | |
D | LEU169 | |
A | ASN155 | |
D | CYS188 | |
D | CYS191 | |
D | CYS194 | |
D | CYS198 | |
D | CYS214 | |
D | SER216 | |
D | CYS240 | |
D | CYS243 | |
D | CYS247 | |
A | ILE158 | |
A | LEU169 | |
A | CYS188 |
site_id | SWS_FT_FI3 |
Number of Residues | 28 |
Details | BINDING: BINDING => ECO:0000269|PubMed:27638883 |
Chain | Residue | Details |
A | GLN220 | |
B | ASN280 | |
B | ARG281 | |
B | ARG295 | |
B | LYS297 | |
B | LYS298 | |
C | GLN220 | |
C | LYS222 | |
C | ASN280 | |
C | ARG281 | |
C | ARG295 | |
A | LYS222 | |
C | LYS297 | |
C | LYS298 | |
D | GLN220 | |
D | LYS222 | |
D | ASN280 | |
D | ARG281 | |
D | ARG295 | |
D | LYS297 | |
D | LYS298 | |
A | ASN280 | |
A | ARG281 | |
A | ARG295 | |
A | LYS297 | |
A | LYS298 | |
B | GLN220 | |
B | LYS222 |