Structure of PDB 6v93 Chain A Binding Site BS05

Receptor Information
>6v93 Chain A (length=1259) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDYFRIQLNNQDYYMSKPTFLDPSHGESLPLNQFSQVPNIRVFGALPTGH
QVLCHVHGILPYMFIKYDGQITDTSTLRHQRCAQVHKTLEVKIRASFKKL
GNLNFVADVSVVKGIPFYGYHVGWNLFYKISLLNPSCLSRISELIRDGKI
FGKKFEIYESHIPYLLQWTADFNLFGCSWINVDRCYFRSPVLNSILDIDK
LTINDDLQLLLDRFCDFKCNVLSRRDFPRVGNGLIEIDILPQFIKNREKL
QHRDIHHDFLEKLVKPYVSSARDMINELTMQREELSLKEYKEPPETKRHV
SGHQWQSSGEFEAFYKKAQHKTSTGQIPNFENFIDKNQKFSAINTPYEAL
PQLWPRLPQIAGLRYGKRAFVYGEPPFGYQDILNKLEDEGFPKIDYKDPF
FSNPVDLENKPYAYAGKRFEISSTHVSTRIPVQFGGETVSVYNKPTFDMF
SSWKYALKPPTYDAVQKWYNKVPSVHDSLTHLTLEIHANTRSDKIPDPAI
DEVSMIIWCLEEETFPLDLDIAYEGIMIVHKADSTFPTKIQHCINEIPVM
FYESEFEMFEALTDLVLLLDPDILSGFEIHNFSWGYIIERCQKIHQFDIV
RELARVKCSDTWGYAHSSGIMITGRHMINIWRALRSDVNLTQYTIESAAF
NILHKRLPHFSFESLTNMWNAKKSTTELKTVLNYWLSRAQINIQLLRKQD
YIARNIEQARLIGIDFHSVYYRGSQFKVESFLIRICKSESFILLSPGKKD
VRKQKALECVPLVMEPESAFYKSPLIVLDFQSLYPSIMIGYNYCYSTMIG
RVREINLTENNLGVSKFSLPRNILALLKNDVTIAPNGVVYAKTSVRKSTL
SKMLTDILDVRVMIKKTMNEIGDDNTTLKRLLNNKQLALKLLANVTYGYT
SASFSGRMPCSDLADSIVQTGRETLEKAIDIIEKDETWNAKVVYGDTDSL
FVYLPGKTAIEAFSIGHAMAERVTQNNPKPIFLKFEKVYHPSILISKKRY
VGFSYESPSQTLPIFDAKGIETVRRDGIPAQQKIIEKCIRLLFQTKDLSK
IKKYLQNEFFKIQIGKVSAQDFCFAKEVKLGAYKSEKTAPAGAVVVKRRI
NEDHRAEPQYKERIPYLVVKGKQGQLLRERCVSPEEFLEGENLELDSEYY
INKILIPPLDRLFNLIGINVGNWAQEEKRSTTTLSFLIKKLKRQKEYQTL
KTVCRTCSYRYTSDAGIENDHIASKCNSYDCPVFYSRVKAERYLRDNQSV
QREEALISL
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain6v93 Chain A Residue 1603 [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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PDB6v93 Structure and mechanism of B-family DNA polymerase zeta specialized for translesion DNA synthesis.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D975 D1144
Binding residue
(residue number reindexed from 1)		D779 D948
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6v93, PDBe:6v93, PDBj:6v93
PDBsum6v93
PubMed32807989
UniProtP14284|DPOZ_YEAST DNA polymerase zeta catalytic subunit (Gene Name=REV3)

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