Structure of PDB 7lxd Chain A Binding Site BS01

Receptor Information
>7lxd Chain A (length=1190) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYFRIQLNNQDYYMSKPTFLDPSHESLPLNQFSQVPNIRVFGALPTGHQV
LCHVHGILPYMFIKYDGQITDTSTLRHQRCAQVHKTLEVKIRASFKKLGN
LNFVADVSVVKGIPFYGYHVGWNLFYKISLLNPSCLSRISELIRDGKIFG
KKFEIYESHIPYLLQWTADFNLFGCSWINVDRCYFRSPVLNSILDIDKLT
INDDLQLLLDRFCDFKCNVLSRRDFPRVGNGLIEIDILPQFIKNREKLQH
RDIHHDFLEKREELSLKEYKETKRHVSGHQWQSSGEFEAFYKKAQHKTST
FDGQIPNFENFIDKNQKFSAINTPYEALPQLWPRLPQIEINNGKRAFVYG
EPPFGYQDILNKLEDEGFPKIDYKDPFFSNPVDLENKPYAYAGKRFEISS
THVSTRIPVQFGGETVSVYNKPTFDMFSSWKYALKPPTYDAVQKWYNKVP
SSSVHDSLTHLTLEIHANTRSDKIPDPAIDEVSMIIWCLEEETFPLDLDI
AYEGIMIVHKASEDSTFPTKIQHCINEIPVMFYESEFEMFEALTDLVLLL
DPDILSGFEIHNFSWGYIIERCQKIHQFDIVRELARVKCQISGIMITGRH
MINIWRALRSDVNLTQYTIESAAFNILHKRLPHFSFESLTNMWNAKKSTT
ELKTVLNYWLSRAQINIQLLRKQDYIARNIEQARLIGIDFHSVYYRGSQF
KVESFLIRICKSESFILLSPGKKDVRKQKALECVPLVMEPESAFYKSPLI
VLDFQSLYPSIMIGYNYCYSTMIGRVREINLTENNLGVSKFSLPRNILAL
LKNDVTIAPNGVVYAKTSVRKSTLSKMLTDILDVRVMIKKTMNEIGDDNT
TLKRLLNNKQLALKLLANVTYGYTSASFSGRMPCSDLADSIVQTGRETLE
KAIDIIEKDETWNAKVVYGDTDSLFVYLPGKTAIEAFSIGHAMAERVTQN
NPKPIFLKFEKVYHPSILISKKRYVGFSYESPSQTLPIFDAKGIETRDGI
PAQQKIIEKCIRLLFQTKDLSKIKKYLQNEFFKIQIGKVSAQDFCFAKEV
KPQYKERIPYLVVKGKQGQLLRERCVSPEEFLEGENLELDSEYYINKILI
PPLDRLFNLIGINVGNWAQEIVKSTTTLSFLIKKLKRQKEYQTLKTVCRT
CSYRYTSDAGIENDHIASKCNSYDCPVFYSRVKAERYLRD
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain7lxd Chain A Residue 1601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7lxd Cryo-EM reveals conformational flexibility in apo DNA polymerase zeta.
Resolution4.11 Å
Binding residue
(original residue number in PDB)		R852 P854 V1445 C1446 C1449 C1468 C1473 V1475 F1476
Binding residue
(residue number reindexed from 1)		R630 P632 V1147 C1148 C1151 C1170 C1175 V1177 F1178
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0000724 double-strand break repair via homologous recombination
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006974 DNA damage response
GO:0019985 translesion synthesis
GO:0042276 error-prone translesion synthesis
GO:0070987 error-free translesion synthesis
Cellular Component
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0016035 zeta DNA polymerase complex
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7lxd, PDBe:7lxd, PDBj:7lxd
PDBsum7lxd
PubMed34174285
UniProtP14284|DPOZ_YEAST DNA polymerase zeta catalytic subunit (Gene Name=REV3)

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