Structure of PDB 5byr Chain B

Receptor sequence

>5byrB (length=572) Species: 1501 (Clostridium pasteurianum) [Search protein sequence]

KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTV
EVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPC
NRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCG
RCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACP
VAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTG
KIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCP
GWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVT
VMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDS
EADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGL
NGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHG
GCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKM
YQNYFGKPGEGRAHEILHFKYK

3D structure

PDB

5byr A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.

Chain

Resolution

1.82 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	E279 E282 C299 S319 K358 E361 Q366 C503
Catalytic site (residue number reindexed from 1)	E278 E281 C298 S318 K357 E360 Q365 C502
Enzyme Commision number	1.12.7.2: ferredoxin hydrogenase.

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)
BS01	SF4	B	C300 C355 M497 C499 C503	C299 C354 M496 C498 C502
BS02	SF4	B	C157 T161 T163 M166 C190 L191 L192 C193 G194 C196	C156 T160 T162 M165 C189 L190 L191 C192 G193 C195
BS03	SF4	B	C147 L148 L149 C150 G151 C153 I177 C200 P201 A204 L205	C146 L147 L148 C149 G150 C152 I176 C199 P200 A203 L204
BS04	SF4	B	H94 F96 K97 C98 C101 R104 C107 K146	H93 F95 K96 C97 C100 R103 C106 K145
BS05	FES	B	A32 C34 F35 C46 E47 C49 C62	A31 C33 F34 C45 E46 C48 C61
BS06	4WW	B	A230 P231 S232 I268 C299 P324 Q325 M353 P354 K358 F417 M497 C503	A229 P230 S231 I267 C298 P323 Q324 M352 P353 K357 F416 M496 C502
BS07	MG	B	N40 D42	N39 D41

Gene Ontology

	Molecular Function
GO:0005506	iron ion binding
GO:0008901	ferredoxin hydrogenase activity
GO:0016491	oxidoreductase activity
GO:0046872	metal ion binding
GO:0051536	iron-sulfur cluster binding
GO:0051539	4 iron, 4 sulfur cluster binding

View graph for
Molecular Function

External links

PDB	RCSB:5byr, PDBe:5byr, PDBj:5byr
PDBsum	5byr
PubMed	29896366
UniProt	P29166\|PHF1_CLOPA Iron hydrogenase 1

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