Structure of PDB 7c4c Chain A

Receptor sequence

>7c4cA (length=332) Species: 185431 (Trypanosoma brucei brucei TREU927)

SSMILKYPYRVVDTHEKLKEAVTSLQGARSIALDIEAFCTTDQAKQLGRI
SLVQACSDAKPVVFLFDVLTLTPDVFVKDMQSLLSDREIRKLFFDCRRDV
EALSCQLGVKPEGVLDLQVFFTAIQWKLRSVNRRSGMGYVLKSVAGLTRQ
EGDSAVQTAMTLGNRPVWDIRPLPDHFLEYAAGDVRHILLLSNYLVGNKD
VPVDVVAVERLTAQYVEHYAVGKPVITEADATPAEVNRAWLERYIGPGGG
CHFCGAKGHTEAECFKKQNGKAKCSFCGEVGHTARNCFKKHPQLLTCEKC
GQLGHTGTSCFRTNPCKHCGGPHSSANCHKVI

3D structure

• PDB: 7c4c Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei.
• Chain: A
• Resolution: 2.265 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	A	C320 C323 H328 C333	C274 C277 H282 C287
BS02	ZN	A	C297 C300 H305 C310	C251 C254 H259 C264
BS03	ZN	A	H61 K65 D125	H15 K19 D79
BS04	ZN	A	E197 H233	E151 H187
BS05	ZN	A	C362 H369 C374	C316 H323 C328
BS06	ZN	A	C346 H351 C356	C300 H305 C310
BS07	MN	A	D80 E82 D230	D34 E36 D184
BS08	MN	A	D80 D145	D34 D99
BS09	MN	A	A330 R331 K336 H337	A284 R285 K290 H291
BS10	5GP	A	D80 E82 A83 L93 M206 W214	D34 E36 A37 L47 M160 W168
BS11	5GP	A	E325 H328 N332 C333 F334	E279 H282 N286 C287 F288
BS12	5GP	A	D141 Q164	D95 Q118
BS13	5GP	A	H305 E309 F311	H259 E263 F265

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0003676 nucleic acid binding
• GO:0008270 zinc ion binding
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process

Cellular Component

• GO:0005739 mitochondrion
• GO:1990923 PET complex

External links

• PDB: RCSB:7c4c, PDBe:7c4c, PDBj:7c4c
• PDBsum: 7c4c
• PubMed: 33332555
• UniProt: Q38DE2