Structure of PDB 5eax Chain B Binding Site BS01

Receptor Information

>5eax Chain B (length=1046) Species: 10090 (Mus musculus)

MEPLDELDLLLLEAVPRVELLRKKADALFPETVLSRGVDNRYLVLAVETS
QNERGAEEKRLHVTASQDREHEVLCILRNGWSSVPVEPGDIVHLEGDCTS
EPWIIDDDFGYFILYPDMMISGTSVASSIRCLRRAVLSETFRGSDPATRQ
MLIGTILHEVFQKAISESFAPERLQELALQTLREVRHLKEMYRLNLSQDE
ILCEVEEYLPSFSKWAEDFMRKGPSSEFPQMQLSLPSDGRSSPCNIEVVK
SLDIEESIWSPRFGLKGKIAVTVGVKIHRDCKMKYKVMPLELKTGKESNS
IEHRSQVVLYTLLSQERREDPEAGWLLYLKTGQMYPVPANHLDKRELLKL
RNWLAASLLHRVSRAAPGEEARLSALPQIIEEEKTCKYCSQIGNCALYSR
AVEEDDASIPEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDNRK
THQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPA
TNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTV
FRLDREERHGDISTPLGNLSKLMESTDPSKRLRELIIDFREPQFIAYLSS
VLPHDAKDTVANILKGLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTIC
ALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKVHPDI
QKFTEEEICRSRSIASLAHLEELYNSHPIVATTCMGINHPIFSRKTFDFC
IVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPPLVVNREARALGMSESL
FKRLERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLECGSDRVANAVLA
LPNLKDARLSLQLYADYSDSPWLAGVLEPDNPVCFLNTDKVPAPEQVENG
GVSNVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRIISDLLARSSV
GMVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGELLKDWRRLNVALTRAK
HKLILLGSVSSLKRFPPLGTLFDHLNAEQLILDLPSREHESLSHIL

Ligand information

>5eax Chain H (length=17)

ttttttttttttttttt

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5eax Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.
• Resolution: 3.05 Å
• Binding residue (original residue number in PDB): S127 T129 R148 Q156 M157 G160 T161 K274 G275 K276 E299 K301 T302 G303 Y396 G495 Q496 R518 K533 E566 R568 Y678 T679 H680 K705 M745 G746 L795 R799 G910 Y944 R945 T967 K970 G993 E994 R1001
• Binding residue (residue number reindexed from 1): S121 T123 R142 Q150 M151 G154 T155 K266 G267 K268 E291 K293 T294 G295 Y388 G485 Q486 R508 K523 E556 R558 Y668 T669 H670 K695 M735 G736 L785 R789 G900 Y934 R935 T957 K960 G983 E984 R991

Enzymatic activity

• Enzyme Commision number: 3.1.-.-
  3.6.4.12: DNA helicase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003678 DNA helicase activity
• GO:0004386 helicase activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0016890 site-specific endodeoxyribonuclease activity, specific for altered base
• GO:0017108 5'-flap endonuclease activity
• GO:0017116 single-stranded DNA helicase activity
• GO:0043139 5'-3' DNA helicase activity
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0000076 DNA replication checkpoint signaling
• GO:0000723 telomere maintenance
• GO:0000729 DNA double-strand break processing
• GO:0006259 DNA metabolic process
• GO:0006260 DNA replication
• GO:0006264 mitochondrial DNA replication
• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0032508 DNA duplex unwinding
• GO:0033567 DNA replication, Okazaki fragment processing
• GO:0043137 DNA replication, removal of RNA primer
• GO:0043504 mitochondrial DNA repair
• GO:0045740 positive regulation of DNA replication
• GO:0090304 nucleic acid metabolic process
• GO:1902990 mitotic telomere maintenance via semi-conservative replication

Cellular Component

• GO:0000781 chromosome, telomeric region
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005739 mitochondrion
• GO:0005760 gamma DNA polymerase complex
• GO:0042645 mitochondrial nucleoid

External links

• PDB: RCSB:5eax, PDBe:5eax, PDBj:5eax
• PDBsum: 5eax
• PubMed: 26491943
• UniProt: Q6ZQJ5|DNA2_MOUSE DNA replication ATP-dependent helicase/nuclease DNA2 (Gene Name=Dna2)