Structure of PDB 6qii Chain B

Receptor sequence

>6qiiB (length=291) Species: 1434108 (Methanosarcina barkeri MS)

MIEDPYLGKYVTCVSARSTDKEILKKAQDGGIATALMVYALEEGFIDGTI
VAGEGDKPWQPKPVVAMTREDILKARGTRYNISPQISWLKEATRSFGLDK
VGVTGVCCQMQAVRKAQLYPINMRDVPGKVAFTVGLFCMENFSYKSLQSI
VEDHANQSLGSVKKMEITKGKFWVYTERGNVATVPLKATHKYEQPGCHVC
LDYVSNLADISTGSVGSPDGWSTVFIRTKVGNEIWSKAVADGMFETKPIE
EVKPGLDLLRKLAKEKIDKNQKTVEERKTFGINKGLRNPYA

3D structure

• PDB: 6qii X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases.
• Chain: B
• Resolution: 2.28 Å

Enzymatic activity

• Enzyme Commision number: 1.12.98.1: coenzyme F420 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)	Binding affinity
BS01	BU3	B	W88 E91	W88 E91
BS02	BU3	B	Q117 P127	Q117 P127
BS03	FAD	B	A27 Q28 D29 G31 I32 A33 T34 A52 A75 G77 T78 R79 Y80 L136 F137 C138 M139 N141 Y203 G213 S214 V215	A27 Q28 D29 G31 I32 A33 T34 A52 A75 G77 T78 R79 Y80 L136 F137 C138 M139 N141 Y203 G213 S214 V215
BS04	SF4	B	V106 C107 C108 C138 M139 E140 C197 C200 K266	V106 C107 C108 C138 M139 E140 C197 C200 K266
BS05	BU3	B	E54 W59 R79	E54 W59 R79

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016151 nickel cation binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0050454 coenzyme F420 hydrogenase activity
• GO:0050660 flavin adenine dinucleotide binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0052592 oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor

External links

• PDB: RCSB:6qii, PDBe:6qii, PDBj:6qii
• PDBsum: 6qii
• PubMed: 31591784
• UniProt: A0A0E3QWH3